Plant Functional Genomics and Crop Genetic Improvement

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agronomy agronomy	3.4	6.7	2011	17.6 Days	CHF 2600
Crops crops	1.9	2.4	2021	22.1 Days	CHF 1000
International Journal of Molecular Sciences ijms	4.9	9.0	2000	16.8 Days	CHF 2900
Life life	3.4	6.0	2011	17.8 Days	CHF 2600
Plants plants	4.1	7.6	2012	18.9 Days	CHF 2700

8 pages, 253 KiB

Open AccessEditorial

Harnessing Knowledge from Plant Functional Genomics and Multi-Omics for Genetic Improvement

by Yaqiong Wang, Jian Zeng, Guangxiao Yang, Yongfang Wan and Yin Li

Int. J. Mol. Sci. 2023, 24(12), 10347; https://doi.org/10.3390/ijms241210347 - 19 Jun 2023

Cited by 2 | Viewed by 1984

Plant biology research has currently entered the post-genomics era with the advances in genomic technologies [...] Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

24 pages, 1992 KiB

Open AccessReview

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

by Huan Li, Muhammad Tahir ul Qamar, Li Yang, Junchao Liang, Jun You and Linhai Wang

Int. J. Mol. Sci. 2023, 24(4), 3105; https://doi.org/10.3390/ijms24043105 - 4 Feb 2023

Cited by 15 | Viewed by 4254

Abstract

Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame [...] Read more.

Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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16 pages, 6774 KiB

Open AccessArticle

Genome-Wide Identification of MADS-Box Family Genes in Safflower (Carthamus tinctorius L.) and Functional Analysis of CtMADS24 during Flowering

by Yifei Wang, Hengshuo Ge, Naveed Ahmad, Jia Li, Yijin Wang, Xinyi Liu, Weican Liu, Xiaowei Li, Nan Wang, Fawei Wang and Yuanyuan Dong

Int. J. Mol. Sci. 2023, 24(2), 1026; https://doi.org/10.3390/ijms24021026 - 5 Jan 2023

Cited by 10 | Viewed by 3209

Abstract

Safflower is an important economic crop with a plethora of industrial and medicinal applications around the world. The bioactive components of safflower petals are known to have pharmacological activity that promotes blood circulation and reduces blood stasis. However, fine-tuning the genetic mechanism of [...] Read more.

Safflower is an important economic crop with a plethora of industrial and medicinal applications around the world. The bioactive components of safflower petals are known to have pharmacological activity that promotes blood circulation and reduces blood stasis. However, fine-tuning the genetic mechanism of flower development in safflower is still required. In this study, we report the genome-wide identification of MADS-box transcription factors in safflower and the functional characterization of a putative CtMADS24 during vegetative and reproductive growth. In total, 77 members of MADS-box-encoding genes were identified from the safflower genome. The phylogenetic analysis divided CtMADS genes into two types and 15 subfamilies. Similarly, bioinformatic analysis, such as of conserved protein motifs, gene structures, and cis-regulatory elements, also revealed structural conservation of MADS-box genes in safflower. Furthermore, the differential expression pattern of CtMADS genes by RNA-seq data indicated that type II genes might play important regulatory roles in floral development. Similarly, the qRT-PCR analysis also revealed the transcript abundance of 12 CtMADS genes exhibiting tissue-specific expression in different flower organs. The nucleus-localized CtMADS24 of the AP1 subfamily was validated by transient transformation in tobacco using GFP translational fusion. Moreover, CtMADS24-overexpressed transgenic Arabidopsis exhibited early flowering and an abnormal phenotype, suggesting that CtMADS24 mediated the expression of genes involved in floral organ development. Taken together, these findings provide valuable information on the regulatory role of CtMADS24 during flower development in safflower and for the selection of important genes for future molecular breeding programs. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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12 pages, 4197 KiB

Open AccessArticle

Agronomic Trait Analysis and Genetic Mapping of a New Wheat Semidwarf Gene Rht-SN33d

by Chaojie Wang, Lili Zhang, Yongdun Xie, Ahsan Irshad, Huijun Guo, Jiayu Gu, Linshu Zhao, Hongchun Xiong, Shirong Zhao, Chengshe Wang and Luxiang Liu

Int. J. Mol. Sci. 2023, 24(1), 583; https://doi.org/10.3390/ijms24010583 - 29 Dec 2022

Cited by 5 | Viewed by 2616

Abstract

Plant height is a key agronomic trait that is closely to the plant morphology and lodging resistance in wheat. However, at present, the few dwarf genes widely used in wheat breeding have narrowed wheat genetic diversity. In this study, we selected a semi-dwarf [...] Read more.

Plant height is a key agronomic trait that is closely to the plant morphology and lodging resistance in wheat. However, at present, the few dwarf genes widely used in wheat breeding have narrowed wheat genetic diversity. In this study, we selected a semi-dwarf wheat mutant dwarf33 that exhibits decreased plant height with little serious negative impact on other agronomic traits. Genetic analysis and mutant gene mapping indicated that dwarf33 contains a new recessive semi-dwarf gene Rht-SN33d, which was mapped into ~1.3 Mb interval on the 3DL chromosome. The gibberellin metabolism-related gene TraesCS3D02G542800, which encodes gibberellin 2-beta-dioxygenase, is considered a potential candidate gene of Rht-SN33d. Rht-SN33d reduced plant height by approximately 22.4% in mutant dwarf33. Further study revealed that shorter stem cell length may be the main factor causing plant height decrease. In addition, the coleoptile length of dwarf33 was just 9.3% shorter than that of wild-type Shaannong33. These results will help to expand our understanding of new mechanisms of wheat height regulation, and obtain new germplasm for wheat improvement. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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18 pages, 3223 KiB

Open AccessArticle

Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng

by Yue Jiang, Sizhang Liu, Li Li, Kaiyou Zang, Yanfang Wang, Mingzhu Zhao, Kangyu Wang, Lei Zhu, Ping Chen, Jun Lei, Yi Wang and Meiping Zhang

Int. J. Mol. Sci. 2022, 23(22), 14016; https://doi.org/10.3390/ijms232214016 - 13 Nov 2022

Cited by 11 | Viewed by 2375

Abstract

Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few [...] Read more.

Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involved in ginsenoside biosynthesis have been cloned through orthologue analysis. Here, we report the identification of 21 genes controlling Rb1 biosynthesis by stepwise ginseng transcriptome and Rb1 content integrated analysis. We first identified the candidate genes for Rb1 biosynthesis by integrated analysis of genes with the trait from four aspects, including gene transcript differential expression between highest- and lowest-Rb1 content cultivars, gene transcript expression–Rb1 content correlation, and biological impacts of gene mutations on Rb1 content, followed by the gene transcript co-expression network. Twenty-two candidate genes were identified, of which 21 were functionally validated for Rb1 biosynthesis by gene regulation, genetic transformation, and mutation analysis. These genes were strongly correlated in expression with the previously cloned genes encoding key enzymes for Rb1 biosynthesis. Based on the correlations, a pathway for Rb1 biosynthesis was deduced to indicate the roles of the genes in Rb1 biosynthesis. Moreover, the genes formed a strong co-expression network with the previously cloned Rb1 biosynthesis genes, and the variation in the network was associated with the variation in the Rb1 content. These results indicate that Rb1 biosynthesis is a process of correlative interactions among Rb1 biosynthesis genes. Therefore, this study provides new knowledge, 21 new genes, and 96 biomarkers for Rb1 biosynthesis useful for enhanced research and breeding in ginseng. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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17 pages, 31120 KiB

Open AccessArticle

Cloning of Maize TED Transposon into Escherichia coli Reveals the Polychromatic Sequence Landscape of Refractorily Propagated Plasmids

by Chunsheng Cong, Jingsheng Tan, Chuxi Li, Fangyuan Liu, Qian Yu, Li Zhu and Yubin Li

Int. J. Mol. Sci. 2022, 23(19), 11993; https://doi.org/10.3390/ijms231911993 - 9 Oct 2022

Cited by 2 | Viewed by 2809

Abstract

MuDR, the founder member of the Mutator superfamily and its MURA transcripts, has been identified as toxic sequences to Escherichia coli (E. coli), which heavily hindered the elucidation of the biochemical features of MURA transposase and confined the broader application [...] Read more.

MuDR, the founder member of the Mutator superfamily and its MURA transcripts, has been identified as toxic sequences to Escherichia coli (E. coli), which heavily hindered the elucidation of the biochemical features of MURA transposase and confined the broader application of the Mutator system in other organisms. To harness less constrained systems as alternatives, we attempted to clone TED and Jittery, two recently isolated autonomous Mutator-like elements (MULEs) from maize, respectively. Their full-length transcripts and genomic copies are successfully cloned when the incubation time for bacteria to recover from heat shock is extended appropriately prior to plating. However, during their proliferation in E. coli, TED transformed plasmids are unstable, as evidenced by derivatives from which frameshift, deletion mutations, or IS transposon insertions are readily detected. Our results suggest that neither leaky expression of the transposase nor the presence of terminal inverse repeats (TIRs) are responsible for the cloning barriers, which were once ascribed to the presence of the Shine–Dalgarno-like sequence. Instead, the internal sequence of TED (from 1250 to 2845 bp), especially the exons in this region, was the most likely causer. The findings provide novel insights into the property and function of the Mutator superfamily and shed light on the dissection of toxic effects on cloning from MULEs. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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14 pages, 3066 KiB

Open AccessArticle

LjAMT2;2 Promotes Ammonium Nitrogen Transport during Arbuscular Mycorrhizal Fungi Symbiosis in Lotus japonicus

by Yanping Wang, Wenqing Zhou, Jiandong Wu, Kailing Xie and Xiaoyu Li

Int. J. Mol. Sci. 2022, 23(17), 9522; https://doi.org/10.3390/ijms23179522 - 23 Aug 2022

Cited by 24 | Viewed by 2725

Abstract

Arbuscular mycorrhizal fungi (AMF) are important symbiotic microorganisms in soil that engage in symbiotic relationships with legumes, resulting in mycorrhizal symbiosis. Establishment of strong symbiotic relationships between AMF and legumes promotes the absorption of nitrogen by plants. Ammonium nitrogen can be directly utilised [...] Read more.

Arbuscular mycorrhizal fungi (AMF) are important symbiotic microorganisms in soil that engage in symbiotic relationships with legumes, resulting in mycorrhizal symbiosis. Establishment of strong symbiotic relationships between AMF and legumes promotes the absorption of nitrogen by plants. Ammonium nitrogen can be directly utilised by plants following ammonium transport, but there are few reports on ammonium transporters (AMTs) promoting ammonium nitrogen transport during AM symbiosis. Lotus japonicus is a typical legume model plant that hosts AMF. In this study, we analysed the characteristics of the Lotus japonicus ammonium transporter LjAMT2;2, and found that it is a typical ammonium transporter with mycorrhizal-induced and ammonium nitrogen transport-related cis-acting elements in its promoter region. LjAMT2;2 facilitated ammonium transfer in yeast mutant supplement experiments. In the presence of different nitrogen concentrations, the LjAMT2;2 gene was significantly upregulated following inoculation with AMF, and induced by low nitrogen. Overexpression of LjAMT2;2 increased the absorption of ammonium nitrogen, resulting in doubling of nitrogen content in leaves and roots, thus alleviating nitrogen stress and promoting plant growth. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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19 pages, 10446 KiB

Open AccessArticle

Isolation and Characterization of an LBD Transcription Factor CsLBD39 from Tea Plant (Camellia sinensis) and Its Roles in Modulating Nitrate Content by Regulating Nitrate-Metabolism-Related Genes

by Rui-Min Teng, Ni Yang, Jing-Wen Li, Chun-Fang Liu, Yi Chen, Tong Li, Ya-Hui Wang, Ai-Sheng Xiong and Jing Zhuang

Int. J. Mol. Sci. 2022, 23(16), 9294; https://doi.org/10.3390/ijms23169294 - 18 Aug 2022

Cited by 8 | Viewed by 2551

Abstract

Nitrate nitrogen is an important nitrogen source for tea plants’ growth and development. LBD transcription factors play important roles in response to the presence of nitrate in plants. The functional study of LBD transcription factors in tea plants remains limited. In this study, [...] Read more.

Nitrate nitrogen is an important nitrogen source for tea plants’ growth and development. LBD transcription factors play important roles in response to the presence of nitrate in plants. The functional study of LBD transcription factors in tea plants remains limited. In this study, the LBD family gene CsLBD39 was isolated and characterized from tea plants. Sequence analysis indicated that CsLBD39 contained a highly conserved CX₂CX₆CX₃CX domain. The phylogenetic tree assay showed that CsLBD39 belonged to class II subfamily of the LBD family. CsLBD39 was highly expressed in flowers and root; we determined that its expression could be induced by nitrate treatment. The CsLBD39 protein was located in the nucleus and has transcriptional activation activity in yeast. Compared with the wild type, overexpression of CsLBD39 gene in Arabidopsis resulted in smaller rosettes, shorter main roots, reduced lateral roots and lower plant weights. The nitrate content and the expression levels of genes related to nitrate transport and regulation were decreased in transgenic Arabidopsis hosting CsLBD39 gene. Compared with the wild type, CsLBD39 overexpression in transgenic Arabidopsis had smaller cell structure of leaves, shorter diameter of stem cross section, and slender and compact cell of stem longitudinal section. Under KNO₃ treatment, the contents of nitrate, anthocyanins, and chlorophyll in leaves, and the content of nitrate in roots of Arabidopsis overexpressing CsLBD39 were reduced, the expression levels of nitrate transport and regulation related genes were decreased. The results revealed that CsLBD39 may be involved in nitrate signal transduction in tea plants as a negative regulator and laid the groundwork for future studies into the mechanism of nitrate response. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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13 pages, 3012 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica

by Hengzhao Liu, Hang Ye, Jiangtao Wang, Shenqun Chen, Mengdi Li, Gang Wang, Na Hou and Peng Zhao

Agronomy 2022, 12(8), 1914; https://doi.org/10.3390/agronomy12081914 - 14 Aug 2022

Cited by 6 | Viewed by 2865

Abstract

The YABBY gene family is a plant transcription factor that exists in all seed plants. YABBY family members have been studied extensively in various plants and were to play significant roles in plant growth and development. Juglans, especially walnuts, are important economic [...] Read more.

The YABBY gene family is a plant transcription factor that exists in all seed plants. YABBY family members have been studied extensively in various plants and were to play significant roles in plant growth and development. Juglans, especially walnuts, are important economic tree species that are widely distributed worldwide. However, the identification and related research of YABBY in Juglans have not been reported to date. In this study, we identified 19 YABBY genes from two Juglans species, namely, J. regia and J. mandshurica. Ten JrYABBY genes and nine JmYABBY genes were divided into five subfamilies (YAB1/3, YAB2, INO, CRC, and YAB5). Sequence analysis revealed that all encoded YABBY protein sequences had a highly conserved YABBY and C2C2 zinc-finger domains. An analysis of the assumed cis-acting elements revealed that JrYABBY and JmYABBY genes were deeply involved in phytohormone and light responses. Further, gene expression pattern analysis suggested that most walnut YABBY genes were likely involved in peel and flower development and responses to biotic stress. This study not only suppled novel insights into the evolutionary basis of YABBY gene families in Juglans, but also provided clues for the further functional verification and investigation of YABBY genes in other tree species. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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12 pages, 2044 KiB

Open AccessArticle

Identification and Fine Mapping of the Candidate Gene Controlling Multi-Inflorescence in Brassica napus

by Hongchen Lu, Hanfei Wu, Guangfeng Zhu, Caijun Yin, Lun Zhao, Jing Wen, Bin Yi, Chaozhi Ma, Jinxing Tu, Tingdong Fu and Jinxiong Shen

Int. J. Mol. Sci. 2022, 23(13), 7244; https://doi.org/10.3390/ijms23137244 - 29 Jun 2022

Cited by 5 | Viewed by 2453

Abstract

As a desirable agricultural trait, multi-inflorescence (MI) fulfills the requirement of mechanized harvesting and yield increase in rapeseed (Brassica napus L.). However, the genetic mechanism underlying the multi-inflorescence trait remain poorly understood. We previously identified a difference of one pair of dominant [...] Read more.

As a desirable agricultural trait, multi-inflorescence (MI) fulfills the requirement of mechanized harvesting and yield increase in rapeseed (Brassica napus L.). However, the genetic mechanism underlying the multi-inflorescence trait remain poorly understood. We previously identified a difference of one pair of dominant genes between the two mapping parental materials. In this study, phenotype and expression analysis indicated that the imbalance of the CLAVATA (CLV)-WUSCHEL (WUS) feedback loop may contribute to the abnormal development of the shoot apical meristem (SAM). BnaMI was fine-mapped to a 55 kb genomic region combining with genotype and phenotype of 5768 BCF₁ individuals using a traditional mapping approach. Through comparative and expression analyses, combined with the annotation in Arabidopsis, five genes in this interval were identified as candidate genes. The present findings may provide assistance in functional analysis of the mechanism associated with multi-inflorescence and yield increase in rapeseed. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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13 pages, 3863 KiB

Open AccessArticle

A Maize CBM Domain Containing the Protein ZmCBM48-1 Positively Regulates Starch Synthesis in the Rice Endosperm

by Xiaojian Peng, Wei Yu, Yirong Chen, Yingli Jiang, Yaru Ji, Long Chen, Beijiu Cheng and Jiandong Wu

Int. J. Mol. Sci. 2022, 23(12), 6598; https://doi.org/10.3390/ijms23126598 - 13 Jun 2022

Cited by 5 | Viewed by 2770

Abstract

Starch directly determines the grain yield and quality. The key enzymes participating in the process of starch synthesis have been cloned and characterized. Nevertheless, the regulatory mechanisms of starch synthesis remain unclear. In this study, we identified a novel starch regulatory gene, ZmCBM48-1 [...] Read more.

Starch directly determines the grain yield and quality. The key enzymes participating in the process of starch synthesis have been cloned and characterized. Nevertheless, the regulatory mechanisms of starch synthesis remain unclear. In this study, we identified a novel starch regulatory gene, ZmCBM48-1, which contained a carbohydrate-binding module 48 (CBM48) domain. ZmCBM48-1 was highly expressed in the maize endosperm and was localized in the plastids. Compared with the wild type lines, the overexpression of ZmCBM48-1 in rice altered the grain size and 1000-grain weight, increased the starch content, and decreased the soluble sugar content. Additionally, the transgenic rice seeds exhibited an alterant endosperm cell shape and starch structure. Meanwhile, the physicochemical characteristics (gelatinization properties) of starch were influenced in the transgenic lines of the endosperm compared with the wild type seeds. Furthermore, ZmCBM48-1 played a positive regulatory role in the starch synthesis pathway by up-regulating several starch synthesis-related genes. Collectively, the results presented here suggest that ZmCBM48-1 acts as a key regulatory factor in starch synthesis, and could be helpful for devising strategies for modulating starch production for a high yield and good quality in maize endosperm. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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27 pages, 9722 KiB

Open AccessArticle

JAZ1-3 and MYC2-1 Synergistically Regulate the Transformation from Completely Mixed Flower Buds to Female Flower Buds in Castanea mollisima

by Hua Cheng, Sanxing Zha, Yanyan Luo, Li Li, Shiyan Wang, Shuai Wu, Shuiyuan Cheng and Linling Li

Int. J. Mol. Sci. 2022, 23(12), 6452; https://doi.org/10.3390/ijms23126452 - 9 Jun 2022

Cited by 22 | Viewed by 2876

Abstract

Chestnut (Castanea mollisima) is an important woody food crop, but its yield has been low in cultivation, mainly due to the problems of fewer female flowers and more male flowers. Therefore, regulating the transition of chestnut flowers and effectively balancing the [...] Read more.

Chestnut (Castanea mollisima) is an important woody food crop, but its yield has been low in cultivation, mainly due to the problems of fewer female flowers and more male flowers. Therefore, regulating the transition of chestnut flowers and effectively balancing the proportion of male and female to improve the yield are key factor to be solved in production. In this study, the chestnut floral buds in pre- and post-winter were used as materials. The data of metabolites, hormones, and gene expression during flower bud differentiation of chestnut were analyzed by transcriptomics and metabolomics to preliminarily reveal the possible reason of male and female flower bud transformation in pre- and post-winter. The analysis of Differentially Expressed Genes (DEGs) showed that there were 6323 DEGs in the Complete mixed flower bud (CMF) group in pre- and post-winter, of which 3448 genes were up-regulated and 2875 genes were down-regulated. There were 8037 DEGs in the Incomplete mixed flower bud (IMF) in pre- and post-winter, of which 4546 genes were up-regulated and 3491 genes were down-regulated. A total of 726 genes from the two flower buds were enriched into 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in post winter, of which plant hormone signal transduction accounted for 4.13%. The analysis results of differential metabolites showed that the differential metabolites of the two flower buds were mainly concentrated in the secondary metabolic synthesis pathway. The difference of hormone content showed that the content of Gibberellin 9 (GA9) and GA19 in CMF was higher than that in IMF in pre-winter, but the opposite in post-winter. Methyl jasmonate (MeJA) content was only very high in CMF in pre-winter, while Jasmonoyl-(l)-Isoleucine (JA-ILE) showed high content in CMF in post-winter. In post-winter, higher concentration of JA-ILE was positively correlated with the expression of Flowering Locus T (CmFT), and CmFT gene was significantly positively correlated with the expression levels of MYC2-1, MYC2-2 and LFY 3 (LEAFY 3). The higher concentration of JA-ILE was negatively correlated with the transcription level of JAZ1-3. In vitro experiments further verified that Jasmonate-Zim 1–3 (JAZ 1–3) combined with MYC2-1 inhibited the transcription of CmFT gene, while MYC2-1 alone promoted the expression of FT. The results suggested that a higher concentration of GA is conducive to breaking the dormancy of flower buds and promoting the development of male flower buds, while a lower concentration of GA and a higher concentration of JA-ILE are conducive to the differentiation and formation of female flower buds in post-winter, in which JAZ1-3 and MYC2-1 play a key role in the differentiation of female flower buds of chestnut. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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19 pages, 6486 KiB

Open AccessArticle

The Formation of Hollow Trait in Cucumber (Cucumis sativus L.) Fruit Is Controlled by CsALMT2

by Geng Zhou, Chen Chen, Xiaohong Liu, Kankan Yang, Chong Wang, Xiangyang Lu, Yun Tian and Huiming Chen

Int. J. Mol. Sci. 2022, 23(11), 6173; https://doi.org/10.3390/ijms23116173 - 31 May 2022

Cited by 10 | Viewed by 3138

Abstract

The hollow trait is crucial for commercial quality of cucumber (Cucumis sativus L.) fruit, and its molecular regulatory mechanism is poorly understood due to its environmental sensitivity. In the previous research, we obtained the hollow and the non-hollow materials of ecotype cucumbers [...] Read more.

The hollow trait is crucial for commercial quality of cucumber (Cucumis sativus L.) fruit, and its molecular regulatory mechanism is poorly understood due to its environmental sensitivity. In the previous research, we obtained the hollow and the non-hollow materials of ecotype cucumbers of South China, which were not easily affected by the external environment through a systematic breeding method. In this study, first, we proposed to use the percentage of the hollow area as the criterion to compare the hollow characteristics between two materials, and to analyze the formation mechanism of early hollow trait from the perspective of cytology. The results showed that the hollow trait occurred in the early stage of fruit development, and formed with the opening of carpel ventral zipped bi-cell layer, which formed rapidly from 2 to 4 days, and then slowed to a constant rate from 14 to 16 days. Meanwhile, the different genetic populations were constructed using these materials, and fine mapping was performed by bulked segregant analysis (BSA) and kompetitive allele specific PCR (KASP) method. The Csa1G630860 (CsALMT2), encoding protein ALMT2, was determined as a candidate gene for regulating the hollow trait in fruit. Furthermore, the expression profile of CsALMT2 was analyzed by qRT-PCR and fluorescence in situ hybridization. The expression of CsALMT2 had obvious tissue specificity, and it was abundantly expressed in the ovule development zone inside the fruit. In the hollow material of cucumber fruit, the expression of CsALMT2 was significantly downregulated. The subcellular localization in tobacco leaves indicated that CsALMT2 was distributed on the plasma membrane. In conclusion, in this study, for the first time, we found the regulatory gene of hollow trait in cucumber fruit, which laid the foundation for subsequent research on the molecular mechanism of hollow trait formation in cucumber fruit, and made it possible to apply this gene in cucumber breeding. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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14 pages, 9906 KiB

Open AccessArticle

Serine Hydroxymethyltransferase (SHMT) Gene Family in Wheat (Triticum aestivum L.): Identification, Evolution, and Expression Analysis

by Hao Liu, Na Li, Yuan Zhao, Guo-Zhang Kang, Yan-Hong Zhao and Hua-Wei Xu

Agronomy 2022, 12(6), 1346; https://doi.org/10.3390/agronomy12061346 - 31 May 2022

Cited by 5 | Viewed by 2952

Abstract

Serine hydroxymethyltransferase (SHMT) plays a vital role in one-carbon metabolic, photorespiration, and various stress responses. However, the genome-wide analysis has not been performed in wheat. In this study, a total of 12 TaSHMT genes were identified in wheat and classified into groups Ⅰa, [...] Read more.

Serine hydroxymethyltransferase (SHMT) plays a vital role in one-carbon metabolic, photorespiration, and various stress responses. However, the genome-wide analysis has not been performed in wheat. In this study, a total of 12 TaSHMT genes were identified in wheat and classified into groups Ⅰa, Ⅰb, and Ⅱb. TaSHMT genes in each group shared similar conserved domain distributions. Chromosomal location, synteny, and cis-elements analysis of TaSHMTs were also analyzed. Real-time PCR results indicated that most TaSHMT genes were mainly expressed in leaves and stems during the wheat seedling stage. Most TaSHMT genes could respond to various abiotic stress. The growth of yeast cells expressing TaSHMT2.1 was inhibited under salt and dehydration stress. Moreover, the gene ontology (GO) annotation and protein interaction of TaSHMT genes were analyzed. These results increase our understanding of SHMT genes and provide robust candidate genes for further functional investigations aimed at crop improvement. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 2694 KiB

Open AccessArticle

Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean

by Mengshi Liu, Jiacan Jiang, Yapeng Han, Mengying Shi, Xianli Li, Yingxiang Wang, Zhicheng Dong and Cunyi Yang

Plants 2022, 11(11), 1398; https://doi.org/10.3390/plants11111398 - 25 May 2022

Cited by 9 | Viewed by 2407

Abstract

Histone modifications, such as methylation and demethylation, have crucial roles in regulating chromatin structure and gene expression. Lysine-specific histone demethylases (LSDs) belong to the amine oxidase family, which is an important family of histone lysine demethylases (KDMs), and functions in maintaining homeostasis of [...] Read more.

Histone modifications, such as methylation and demethylation, have crucial roles in regulating chromatin structure and gene expression. Lysine-specific histone demethylases (LSDs) belong to the amine oxidase family, which is an important family of histone lysine demethylases (KDMs), and functions in maintaining homeostasis of histone methylation. Here, we identified six LSD-like (LDL) genes from the important leguminous soybean. Phylogenetic analyses divided the six GmLDLs into four clusters with two highly conserved SWRIM and amine oxidase domains. Indeed, demethylase activity assay using recombinant GmLDL proteins in vitro demonstrated that GmLDLs have demethylase activity toward mono- and dimethylated Lys4 but not trimethylated histone 3, similar to their orthologs previously reported in animals. Using real-time PCR experiments in combination with public transcriptome data, we found that these six GmLDL genes exhibit comparable expressions in multiple tissues or in response to different abiotic stresses. Moreover, our genetic variation investigation of GmLDL genes among 761 resequenced soybean accessions indicates that GmLDLs are well conserved during soybean domestication and improvement. Taken together, these findings demonstrate that GmFLD, GmLDL1a, and GmLDL1b are bona fide H3K4 demethylases towards H4K4me1/2 and GmLDLs exist in various members with likely conserved and divergent roles in soybeans. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 3695 KiB

Open AccessArticle

Sequence Analysis and Functional Verification of the Effects of Three Key Structural Genes, PdTHC2’GT, PdCHS and PdCHI, on the Isosalipurposide Synthesis Pathway in Paeonia delavayi var. lutea

by Hongzhu Zou, Lulu Han, Meng Yuan, Mengjie Zhang, Lin Zhou and Yan Wang

Int. J. Mol. Sci. 2022, 23(10), 5696; https://doi.org/10.3390/ijms23105696 - 19 May 2022

Cited by 9 | Viewed by 2262

Abstract

Isosalipurposide (ISP) is the most important yellow pigment in tree peony. In ISP biosynthesis, CHS catalyzes 1-molecule coumaroyl-CoA and 3-molecule malonyl-CoA to form 2′,4′,6′,4-tetrahyroxychalcone (THC), and THC generates a stable ISP in the vacuole under the action of chalcone2′-glucosyltransferases (THC2′GT). In [...] Read more.

Isosalipurposide (ISP) is the most important yellow pigment in tree peony. In ISP biosynthesis, CHS catalyzes 1-molecule coumaroyl-CoA and 3-molecule malonyl-CoA to form 2′,4′,6′,4-tetrahyroxychalcone (THC), and THC generates a stable ISP in the vacuole under the action of chalcone2′-glucosyltransferases (THC2′GT). In tree peony, the details of the THC2’GT gene have not yet been reported. In this study, the candidate THC2’GT gene (PdTHC2’GT) in Paeonia delavayi var. lutea was screened. At the same time, we selected the upstream CHS gene (PdCHS) and the competitive CHI gene (PdCHI) to study the biosynthesis pathway of ISP. We successfully cloned three genes and sequenced them; subcellular localization showed that the three genes were located in the nucleus and cytoplasm. The overexpression of PdTHC2’GT in tobacco caused the accumulation of ISP in tobacco petals, which indicated that PdTHC2’GT was the key structural gene in the synthesis of ISP. After the overexpression of PdCHS and PdCHI in tobacco, the accumulation of anthocyanins in tobacco petals increased to different degrees, showing the role of PdCHS and PdCHI in anthocyanin accumulation. The analysis of NtCHS and NtCHI of transgenic tobacco lines by qRT-PCR showed that the THC2’GT gene could increase the expression of CHS. THC2’GT and CHI were found to be competitive; hence, the overexpression of THC2’GT could lead to a decrease in CHI expression. The CHS gene and CHI gene could increase the expression of each other. In conclusion, we verified the key structural gene PdTHC2’GT and studied the operation of the genes in its upstream and competitive pathway, providing a new perspective for the biosynthesis of ISP and new candidate genes for the directional breeding of tree peony. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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17 pages, 4851 KiB

Open AccessArticle

Genome-Wide Identification of Expansin Genes in Wild Soybean (Glycine soja) and Functional Characterization of Expansin B1 (GsEXPB1) in Soybean Hair Root

by Xu Feng, Cuiting Li, Fumeng He, Yongqing Xu, Li Li, Xue Wang, Qingshan Chen and Fenglan Li

Int. J. Mol. Sci. 2022, 23(10), 5407; https://doi.org/10.3390/ijms23105407 - 12 May 2022

Cited by 18 | Viewed by 2962

Abstract

Wild soybean, the progenitor and close relative of cultivated soybean, has an excellent environmental adaptation ability and abundant resistance genes. Expansins, as a class of cell wall relaxation proteins, have important functions in regulating plant growth and stress resistance. In the present study, [...] Read more.

Wild soybean, the progenitor and close relative of cultivated soybean, has an excellent environmental adaptation ability and abundant resistance genes. Expansins, as a class of cell wall relaxation proteins, have important functions in regulating plant growth and stress resistance. In the present study, we identified a total of 75 members of the expansin family on the basis of recent genomic data published for wild soybean. The predicted results of promoter elements structure showed that wild soybean expansin may be associated with plant hormones, stress responses, and growth. Basal transcriptome data of vegetative organs suggest that the transcription of expansin members has some organ specificity. Meanwhile, the transcripts of some members had strong responses to salt, low temperature and drought stress. We screened and obtained an expansin gene, GsEXPB1, which is transcribed specifically in roots and actively responds to salt stress. The results of A. tumefaciens transient transfection showed that this protein was localized in the cell wall of onion epidermal cells. We initially analyzed the function of GsEXPB1 by a soybean hairy root transformation assay and found that overexpression of GsEXPB1 significantly increased the number of hairy roots, root length, root weight, and the tolerance to salt stress. This research provides a foundation for subsequent studies of expansins in wild soybean. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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18 pages, 3231 KiB

Open AccessArticle

BRITTLE CULM17, a Novel Allele of TAC4, Affects the Mechanical Properties of Rice Plants

by Guangzheng Li, Xiaofang Zeng, Yan Li, Jianrong Li, Xiaozhen Huang and Degang Zhao

Int. J. Mol. Sci. 2022, 23(10), 5305; https://doi.org/10.3390/ijms23105305 - 10 May 2022

Cited by 5 | Viewed by 2559

Abstract

Lodging resistance of rice (Oryza sativa L.) has always been a hot issue in agricultural production. A brittle stem mutant, osbc17, was identified by screening an EMS (Ethylmethane sulfonate) mutant library established in our laboratory. The stem segments and leaves of [...] Read more.

Lodging resistance of rice (Oryza sativa L.) has always been a hot issue in agricultural production. A brittle stem mutant, osbc17, was identified by screening an EMS (Ethylmethane sulfonate) mutant library established in our laboratory. The stem segments and leaves of the mutant were obviously brittle and fragile, with low mechanical strength. Examination of paraffin sections of flag leaf and internode samples indicated that the number of cell layers in mechanical tissue of the mutant was decreased compared with the wild type, Pingtangheinuo, and scanning electron microscopy revealed that the mechanical tissue cell walls of the mutant were thinner. Lignin contents of the internodes of mature-stage rice were significantly lower in the mutant than in the wild type. By the MutMap method, we found candidate gene OsBC17, which was located on rice chromosome 2 and had a 2433 bp long coding sequence encoding a protein sequence of 810 amino acid residues with unknown function. According to LC-MS/MS analysis of intermediate products of the lignin synthesis pathway, the accumulation of caffeyl alcohol in the osbc17 mutant was significantly higher than in Pingtangheinuo. Caffeyl alcohol can be polymerized to the catechyl lignin monomer by laccase ChLAC8; however, ChLAC8 and OsBC17 are not homologous proteins, which suggests that the osbc17 gene is involved in this process by regulating laccase expression. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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13 pages, 2210 KiB

Open AccessArticle

Cloning and Functional Analysis of TaWRI1Ls, the Key Genes for Grain Fatty Acid Synthesis in Bread Wheat

by Fengping Yang, Guoyu Liu, Ziyan Wu, Dongxue Zhang, Yufeng Zhang, Mingshan You, Baoyun Li, Xiuhai Zhang and Rongqi Liang

Int. J. Mol. Sci. 2022, 23(10), 5293; https://doi.org/10.3390/ijms23105293 - 10 May 2022

Cited by 9 | Viewed by 2233

Abstract

WRINKLED1 (WRI1), an APETALA2 (AP2) transcription factor (TF), critically regulates the processes related to fatty acid synthesis, storage oil accumulation, and seed development in plants. However, the WRI1 genes remain unknown in allohexaploid bread wheat (Triticum aestivum L.). In this study, based [...] Read more.

WRINKLED1 (WRI1), an APETALA2 (AP2) transcription factor (TF), critically regulates the processes related to fatty acid synthesis, storage oil accumulation, and seed development in plants. However, the WRI1 genes remain unknown in allohexaploid bread wheat (Triticum aestivum L.). In this study, based on the sequence of Arabidopsis AtWRI1, two TaWRI1Ls genes of bread wheat, TaWRI1L1 and TaWRI1L2, were cloned. TaWRI1L2 was closely related to monocotyledons and clustered in one subgroup with AtWRI1, while TaWRI1L1 was clustered in another subgroup with AtWRI3 and AtWRI4. Both were expressed highly in the developmental grain, subcellular localized in the nucleus, and showed transcriptional activation activity. TaWRI1L2, rather than TaWRI1L1, promoted oil body accumulation and significantly increased triglyceride (TAG) content in tobacco leaves. Overexpression of TaWRI1L2 compensated for the functional loss of AtWRI1 in an Arabidopsis mutant and restored the wild-type phenotypes of seed shape, generation, and fatty acid synthesis and accumulation. Knockout of TaWRI1L2 reduced grain size, 1000 grain weight, and grain fatty acid synthesis in bread wheat. Conclusively, TaWRI1L2, rather than TaWRI1L1, was the key transcriptional factor in the regulation of grain fatty acid synthesis in bread wheat. This study lays a foundation for gene regulation and genetic manipulation of fatty acid synthesis in wheat genetic breeding programs. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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22 pages, 6433 KiB

Open AccessArticle

Comparative Transcriptome Analysis Provides Insights into the Resistance in Pueraria [Pueraria lobata (Willd.) Ohwi] in Response to Pseudo-Rust Disease

by Xinlu Huang, Xiaoxi Huang, Lijun Guo, Longfei He, Dong Xiao, Jie Zhan, Aiqin Wang and Renfan Liang

Int. J. Mol. Sci. 2022, 23(9), 5223; https://doi.org/10.3390/ijms23095223 - 7 May 2022

Cited by 5 | Viewed by 3054

Abstract

Pueraria lobata is an important medicinal and edible homologous plant that is widely cultivated in Asian countries. However, its production and quality are seriously threatened by its susceptibility to pseudo-rust disease. The underlying molecular mechanisms are poorly known, particularly from a transcriptional perspective. [...] Read more.

Pueraria lobata is an important medicinal and edible homologous plant that is widely cultivated in Asian countries. However, its production and quality are seriously threatened by its susceptibility to pseudo-rust disease. The underlying molecular mechanisms are poorly known, particularly from a transcriptional perspective. Pseudo-rust disease is a major disease in pueraria, primarily caused by Synchytrium puerariae Miy (SpM). In this study, transcriptomic profiles were analyzed and compared between two pueraria varieties: the disease-resistant variety (GUIGE18) and the susceptible variety (GUIGE8). The results suggest that the number of DEGs in GUIGE18 is always more than in GUIGE8 at each of the three time points after SpM infection, indicating that their responses to SpM infection may be different, and that the active response of GUIGE18 to SpM infection may occur earlier than that of GUIGE8. A total of 7044 differentially expressed genes (DEGs) were identified, and 406 co-expressed DEGs were screened out. Transcription factor analysis among the DEGs revealed that the bHLH, WRKY, ERF, and MYB families may play an important role in the interaction between pueraria and pathogens. A GO and KEGG enrichment analysis of these DEGs showed that they were mainly involved in the following pathways: metabolic, defense response, plant hormone signal transduction, MAPK signaling pathway-plant, plant pathogen interaction, flavonoid biosynthesis, phenylpropanoid biosynthesis, and secondary metabolite biosynthesis. The CPK, CESA, PME, and CYP gene families may play important roles in the early stages after SpM infection. The DEGs that encode antioxidase (CAT, XDH, and SOD) were much more up-regulated. Defense enzyme activity, endogenous hormones, and flavonoid content changed significantly in the two varieties at the three infection stages. Finally, we speculated on the regulatory pathways of pueraria pseudo-rust and found that an oxidation-reduction process, flavonoid biosynthesis, and ABA signaling genes may be associated with the response to SpM infection in pueraria. These results expand the understanding of pueraria resistance and physiological regulations by multiple pathways. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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17 pages, 4081 KiB

Open AccessArticle

Mutant lpa1 Analysis of ZmLPA1 Gene Regulates Maize Leaf-Angle Development through the Auxin Pathway

by Xiangzhuo Ji, Qiaohong Gao, Fenqi Chen, Mingxing Bai, Zelong Zhuang and Yunling Peng

Int. J. Mol. Sci. 2022, 23(9), 4886; https://doi.org/10.3390/ijms23094886 - 28 Apr 2022

Cited by 12 | Viewed by 2980

Abstract

Maize plant type is one of the main factors determining maize yield, and leaf angle is an important aspect of plant type. The rice Loose Plant Architecture1 (LPA1) gene and Arabidopsis AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene are related to their [...] Read more.

Maize plant type is one of the main factors determining maize yield, and leaf angle is an important aspect of plant type. The rice Loose Plant Architecture1 (LPA1) gene and Arabidopsis AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene are related to their leaf angle. However, the homologous ZmLPA1 in maize has not been studied. In this study, the changing of leaf angle, as well as gene expression in leaves in maize mutant lpa1 and wild-type ‘B73’ under different IAA concentrations were investigated. The regulation effect of IAA on the leaf angle of lpa1 was significantly stronger than that of the wild type. Transcriptome analysis showed that different exogenous IAA treatments had a common enrichment pathway—the indole alkaloid biosynthesis pathway—and among the differentially expressed genes, four genes—AUX1, AUX/IAA, ARF and SAUR—were significantly upregulated. This study revealed the regulation mechanism of ZmLPA1 gene on maize leaf angle and provided a promising gene resource for maize breeding. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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21 pages, 2928 KiB

Open AccessArticle

Identification of Zinc Efficiency-Associated Loci (ZEALs) and Candidate Genes for Zn Deficiency Tolerance of Two Recombination Inbred Line Populations in Maize

by Jianqin Xu, Xiaoxin Qin, Zhongfu Ni, Fanjun Chen, Xiuyi Fu and Futong Yu

Int. J. Mol. Sci. 2022, 23(9), 4852; https://doi.org/10.3390/ijms23094852 - 27 Apr 2022

Cited by 10 | Viewed by 2574

Abstract

Zinc (Zn) deficiency is one of the most common micronutrient disorders in cereal plants, greatly impairing crop productivity and nutritional quality. Identifying the genes associated with Zn deficiency tolerance is the basis for understanding the genetic mechanism conferring tolerance. In this study, the [...] Read more.

Zinc (Zn) deficiency is one of the most common micronutrient disorders in cereal plants, greatly impairing crop productivity and nutritional quality. Identifying the genes associated with Zn deficiency tolerance is the basis for understanding the genetic mechanism conferring tolerance. In this study, the K22×BY815 and DAN340×K22 recombination inbred line (RIL) populations, which were derived from Zn-inefficient and Zn-efficient inbred lines, were utilized to detect the quantitative trait loci (QTLs) associated with Zn deficiency tolerance and to further identify candidate genes within these loci. The BLUP (Best Linear Unbiased Prediction) values under Zn-deficient condition (-Zn) and the ratios of the BLUP values under Zn deficient condition to the BLUP values under Zn-sufficient condition (-Zn/CK) were used to perform linkage mapping. In QTL analysis, 21 QTLs and 33 QTLs controlling the Zn score, plant height, shoot and root dry weight, and root-to-shoot ratio were detected in the K22×BY815 population and the DAN340×K22 population, explaining 5.5–16.6% and 4.2–23.3% of phenotypic variation, respectively. In addition, seventeen candidate genes associated with the mechanisms underlying Zn deficiency tolerance were identified in QTL colocalizations or the single loci, including the genes involved in the uptake, transport, and redistribution of Zn (ZmIRT1, ZmHMAs, ZmNRAMP6, ZmVIT, ZmNAS3, ZmDMAS1, ZmTOM3), and the genes participating in the auxin and ethylene signal pathways (ZmAFBs, ZmIAA17, ZmETR, ZmEIN2, ZmEIN3, ZmCTR3, ZmEBF1). Our findings will broaden the understanding of the genetic structure of the tolerance to Zn deficiency in maize. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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17 pages, 3928 KiB

Open AccessArticle

Integrative Analysis of Metabolomics and Transcriptomics Reveals Molecular Mechanisms of Anthocyanin Metabolism in the Zikui Tea Plant (Camellia sinensis cv. Zikui)

by Ju Cai, Litang Lv, Xiaofang Zeng, Fen Zhang, Yulu Chen, Weili Tian, Jianrong Li, Xiangyang Li and Yan Li

Int. J. Mol. Sci. 2022, 23(9), 4780; https://doi.org/10.3390/ijms23094780 - 26 Apr 2022

Cited by 38 | Viewed by 5691

Abstract

In this study, we performed an association analysis of metabolomics and transcriptomics to reveal the anthocyanin biosynthesis mechanism in a new purple-leaf tea cultivar Zikui (Camellia sinensis cv. Zikui) (ZK). Three glycosylated anthocyanins were identified, including petunidin 3-O-glucoside, cyanidin 3- [...] Read more.

In this study, we performed an association analysis of metabolomics and transcriptomics to reveal the anthocyanin biosynthesis mechanism in a new purple-leaf tea cultivar Zikui (Camellia sinensis cv. Zikui) (ZK). Three glycosylated anthocyanins were identified, including petunidin 3-O-glucoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside, and their contents were the highest in ZK leaves at 15 days. This is the first report on petunidin 3-O-glucoside in purple-leaf tea. Integrated analysis of the transcriptome and metabolome identified eleven dependent transcription factors, among which CsMYB90 had strong correlations with petunidin 3-O-glucoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside (PCC > 0.8). Furthermore, we also identified key correlated structural genes, including two positively correlated F3’H (flavonoid-3′-hydroxylase) genes, two positively correlated ANS (anthocyanin synthase) genes, and three negatively correlated PPO (polyphenol oxidase) genes. Overexpression of CsMYB90 in tobacco resulted in dark-purple transgenic calluses. These results showed that the increased accumulation of three anthocyanins in ZK may promote purple-leaf coloration because of changes in the expression levels of genes, including CsMYB90, F3’Hs, ANSs, and PPOs. These findings reveal new insight into the molecular mechanism of anthocyanin biosynthesis in purple-leaf tea plants and provide a series of candidate genes for the breeding of anthocyanin-rich cultivars. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 2839 KiB

Open AccessArticle

Integrative Analysis of Expression Profiles of mRNA and MicroRNA Provides Insights of Cotton Response to Verticillium dahliae

by Jun Mei, Yuqing Wu, Qingqing Niu, Meng Miao, Diandian Zhang, Yanyan Zhao, Fangfang Cai, Dongliang Yu, Liping Ke, Hongjie Feng and Yuqiang Sun

Int. J. Mol. Sci. 2022, 23(9), 4702; https://doi.org/10.3390/ijms23094702 - 24 Apr 2022

Cited by 27 | Viewed by 2885

Abstract

Cotton Verticillium wilt, caused by the notorious fungal phytopathogen Verticillium dahliae (V. dahliae), is a destructive soil-borne vascular disease and severely decreases cotton yield and quality worldwide. Transcriptional and post-transcriptional regulation of genes responsive to V. dahliae are crucial [...] Read more.

Cotton Verticillium wilt, caused by the notorious fungal phytopathogen Verticillium dahliae (V. dahliae), is a destructive soil-borne vascular disease and severely decreases cotton yield and quality worldwide. Transcriptional and post-transcriptional regulation of genes responsive to V. dahliae are crucial for V. dahliae tolerance in plants. However, the specific microRNAs (miRNAs) and the miRNA/target gene crosstalk involved in cotton resistance to Verticillium wilt remain largely limited. To investigate the roles of regulatory RNAs under V. dahliae induction in upland cotton, mRNA and small RNA libraries were constructed from mocked and infected roots of two upland cotton cultivars with the V. dahliae-sensitive cultivar Jimian 11 (J11) and the V. dahliae-tolerant cultivar Zhongzhimian 2 (Z2). A comparative transcriptome analysis revealed 8330 transcripts were differentially expressed under V. dahliae stress and associated with several specific biological processes. Moreover, small RNA sequencing identified a total of 383 miRNAs, including 330 unique conserved miRNAs and 53 novel miRNAs. Analysis of the regulatory network involved in the response to V. dahliae stress revealed 31 differentially expressed miRNA–mRNA pairs, and the up-regulation of GhmiR395 and down-regulation of GhmiR165 were possibly involved in the response to V. dahliae by regulating sulfur assimilation through the GhmiR395-APS1/3 module and the establishment of the vascular pattern and secondary cell wall formation through GhmiR165-REV module, respectively. The integrative analysis of mRNA and miRNA expression profiles from upland cotton lays the foundation for further investigation of regulatory mechanisms of resistance to Verticillium wilt in cotton and other crops. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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16 pages, 5354 KiB

Open AccessArticle

TaNBR1, a Novel Wheat NBR1-like Domain Gene Negatively Regulates Drought Stress Tolerance in Transgenic Arabidopsis

by Liuping Chen, Qian Lv, Weibing Yang, Hui Yang, Qiaoyan Chen, Bingxin Wang, Yanhong Lei and Yanzhou Xie

Int. J. Mol. Sci. 2022, 23(9), 4519; https://doi.org/10.3390/ijms23094519 - 20 Apr 2022

Cited by 8 | Viewed by 2878

Abstract

Drought stress is an important factor that severely affects crop yield and quality. Autophagy has a crucial role in the responses to abiotic stresses. In this study, we explore TaNBR1 in response to drought stress. Expression of the TaNBR1 gene was strongly induced [...] Read more.

Drought stress is an important factor that severely affects crop yield and quality. Autophagy has a crucial role in the responses to abiotic stresses. In this study, we explore TaNBR1 in response to drought stress. Expression of the TaNBR1 gene was strongly induced by NaCl, PEG, and abscisic acid treatments. The TaNBR1 protein is localized in the Golgi apparatus and autophagosome. Transgenic Arabidopsis plants overexpressing TaNBR1 exhibited reduced drought tolerance. When subjected to drought stress, compared to the wild-type (WT) lines, the transgenic overexpressing TaNBR1 plants had a lower seed germination rate, relative water content, proline content, and reduced accumulation of antioxidant enzymes, i.e., superoxide dismutase, peroxidase, and catalase, as well as higher chlorophyll losses, malondialdehyde contents, and water loss. The transgenic plants overexpressing TaNBR1 produced much shorter roots in response to mannitol stress, in comparison to the WT plants, and they exhibited greater sensitivity to abscisic acid treatment. The expression levels of the genes related to stress in the transgenic plants were affected in response to drought stress. Our results indicate that TaNBR1 negatively regulates drought stress responses by affecting the expression of stress-related genes in Arabidopsis. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 3745 KiB

Open AccessArticle

The Transcriptome and Metabolome Reveal the Potential Mechanism of Lodging Resistance in Intergeneric Hybrids between Brassica napus and Capsella bursa-pastoris

by Libin Zhang, Liyun Miao, Jianjie He, Huaixin Li and Maoteng Li

Int. J. Mol. Sci. 2022, 23(9), 4481; https://doi.org/10.3390/ijms23094481 - 19 Apr 2022

Cited by 7 | Viewed by 2719

Abstract

Lodging is one of the main reasons for the reduction in seed yield and is the limitation of mechanized harvesting in B. napus. The dissection of the regulatory mechanism of lodging resistance is an important goal in B. napus. In this [...] Read more.

Lodging is one of the main reasons for the reduction in seed yield and is the limitation of mechanized harvesting in B. napus. The dissection of the regulatory mechanism of lodging resistance is an important goal in B. napus. In this study, the lodging resistant B. napus line, YG689, derived from the hybridization between B. napus cv. Zhongyou 821 (ZY821) and Capsella bursa-pastoris, was used to dissect the regulation mechanism of hard stem formation by integrating anatomical structure, transcriptome and metabolome analyses. It was shown that the lignocellulose content of YG689 is higher than that of ZY821, and some differentially expressed genes (DEGs) involved in the lignocellulose synthesis pathway were revealed by transcriptome analyses. Meanwhile, GC–TOF–MS and UPLC–QTOF–MS identified 40, 54, and 31 differential metabolites in the bolting stage, first flower stage, and the final flower stage. The differential accumulation of these metabolites might be associated with the lignocellulose biosynthesis in B. napus. Finally, some important genes that regulate the metabolic pathway of lignocellulose biosynthesis, such as BnaA02g18920D, BnaA10g15590D, BnaC05g48040D, and NewGene_216 were identified in B. napus through the combination of transcriptomics and metabolomics data. The present results explored the potential regulatory mechanism of lignocellulose biosynthesis, which provided a new clue for the breeding of B. napus with lodging resistance in the future. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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16 pages, 4901 KiB

Open AccessArticle

Physiological and Molecular Responses of Zoysia japonica to Rust Infection

by Di Zhang, Jun Tang, Kai Wei, Shangang Jia, Yiwei Jiang, Hongwei Cai, Peisheng Mao and Manli Li

Int. J. Mol. Sci. 2022, 23(8), 4185; https://doi.org/10.3390/ijms23084185 - 10 Apr 2022

Cited by 6 | Viewed by 2519

Abstract

Zoysiagrass (Zoysia japonica) is a popular turfgrass species and is widely used for sport turf and urban landscape. Zoysiagrass is often infected by Puccinia zoysiae, which causes a loss in turf quality. The physiological and molecular mechanisms of rust resistance [...] Read more.

Zoysiagrass (Zoysia japonica) is a popular turfgrass species and is widely used for sport turf and urban landscape. Zoysiagrass is often infected by Puccinia zoysiae, which causes a loss in turf quality. The physiological and molecular mechanisms of rust resistance are poorly understood in this species. In this study, the rust-resistant and susceptible lines of zoysiagrass were inoculated with P. zoysiae, and alterations of leaf cell structure, physiological indicators and transcriptomic response were investigated at the various stages of inoculation. After inoculation, the cell membranes, nucleus, mitochondria, and chloroplast were all impaired, followed by abnormal physiological metabolism. The damage occurred earlier and more severely in the susceptible line. Changes in electrolyte leakage and chlorophyll content varied with the genotype and the inoculation stages. The transcriptome analysis showed that plant hormones, MAPK signal transduction pathway, photosynthesis and energy generation pathways were significantly enriched in the early response, in both the resistant and susceptible lines. The results provided insights into the physiological and molecular mechanisms of rust disease resistance and would benefit the breeding of rust-resistant varieties in zoysiagrass and related turfgrass species. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 2207 KiB

Open AccessArticle

Expression of a Cytochrome P450 Gene from Bermuda Grass Cynodon dactylon in Soybean Confers Tolerance to Multiple Herbicides

by Ting Zheng, Xiaoxing Yu, Yongzheng Sun, Qing Zhang, Xianwen Zhang, Mengzhen Tang, Chaoyang Lin and Zhicheng Shen

Plants 2022, 11(7), 949; https://doi.org/10.3390/plants11070949 - 31 Mar 2022

Cited by 14 | Viewed by 3274

Abstract

Bermuda grass (Cynodon dactylon) is notoriously difficult to control with some commonly used herbicides. We cloned a cytochrome P450 gene from Bermuda grass, named P450-N-Z1, which was found to confer tolerance to multiple herbicides in transgenic Arabidopsis. These herbicides [...] Read more.

Bermuda grass (Cynodon dactylon) is notoriously difficult to control with some commonly used herbicides. We cloned a cytochrome P450 gene from Bermuda grass, named P450-N-Z1, which was found to confer tolerance to multiple herbicides in transgenic Arabidopsis. These herbicides include: (1) acetolactate synthase (ALS) inhibitor herbicides nicosulfuron and penoxsulam; (2) p-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicide mesotrione; (3) synthetic auxin herbicide dicamba; (4) photosynthesis inhibitor bentazon. We further generated transgenic soybean plants expressing P450-N-Z1, and found that these transgenic soybean plants gained robust tolerance to nicosulfuron, flazasulfuron, and 2,4-dichlorophenoxyacetic acid (2,4-D) in greenhouse assays. A field trial demonstrated that transgenic soybean is tolerant to flazasulfuron and 2,4-D at 4-fold and 2-fold the recommended rates, respectively. Furthermore, we also demonstrated that flazasulfuron and dicamba are much more rapidly degraded in vivo in the transgenic soybean than in non-transgenic soybean. Therefore, P450-N-Z1 may be utilized for engineering transgenic crops for herbicide tolerance. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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14 pages, 2891 KiB

Open AccessArticle

MeNINV1: An Alkaline/Neutral Invertase Gene of Manihot esculenta, Enhanced Sucrose Catabolism and Promoted Plant Vegetative Growth in Transgenic Arabidopsis

by Ya-Jie Wang, Xing-Hou Zhen, Yang-Jiao Zhou, Yun-Lin Wang, Jing-Yi Hou, Xin Wang, Rui-Mei Li, Jiao Liu, Xin-Wen Hu, Meng-Ting Geng, Yuan Yao and Jian-Chun Guo

Plants 2022, 11(7), 946; https://doi.org/10.3390/plants11070946 - 31 Mar 2022

Cited by 17 | Viewed by 3041

Abstract

Alkaline/neutral invertase (A/N-INV) is an invertase that irreversibly decomposes sucrose into fructose as well as glucose and plays a role in plant growth and development, starch synthesis, abiotic stress, and other plant-life activities. Cassava is an economically important starch crop in tropical regions. [...] Read more.

Alkaline/neutral invertase (A/N-INV) is an invertase that irreversibly decomposes sucrose into fructose as well as glucose and plays a role in plant growth and development, starch synthesis, abiotic stress, and other plant-life activities. Cassava is an economically important starch crop in tropical regions. During the development of cassava tuber roots, A/N-INV activity is relatively high, which indicates that it may participate in sucrose metabolism and starch synthesis. In this study, MeNINV1 was confirmed to function as invertase to catalyze sucrose decomposition in yeast. The optimal enzymatic properties of MeNINV1 were a pH of 6.5, a reaction temperature of 40 °C, and sucrose as its specific catalytic substrate. VB₆, Zn²⁺, and Pb²⁺ at low concentrations as well as EDTA, DTT, Tris, Mg²⁺, and fructose inhibited A/N-INV enzymic activity. In cassava, the MeNINV1 gene was mainly expressed in the fibrous roots and the tuber root phloem, and its expression decreased as the tuber root grew. MeNINV1 was confirmed to localize in chloroplasts. In Arabidopsis, MeNINV1-overexpressing Arabidopsis had higher A/N-INV activity, and the increased glucose, fructose, and starch content in the leaves promoted plant growth and delayed flowering time but did not change its resistance to abiotic stress. Our results provide new insights into the biological function of MeNINV1. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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17 pages, 5198 KiB

Open AccessArticle

Genetic Diversity and Association Analysis for Carotenoid Content among Sprouts of Cowpea (Vigna unguiculata L. Walp)

by Frejus Ariel Kpedetin Sodedji, Dahye Ryu, Jaeyoung Choi, Symphorien Agbahoungba, Achille Ephrem Assogbadjo, Simon-Pierre Assanvo N’Guetta, Je Hyeong Jung, Chu Won Nho and Ho-Youn Kim

Int. J. Mol. Sci. 2022, 23(7), 3696; https://doi.org/10.3390/ijms23073696 - 28 Mar 2022

Cited by 15 | Viewed by 3467

Abstract

The development and promotion of biofortified foods plants are a sustainable strategy for supplying essential micronutrients for human health and nutrition. We set out to identify quantitative trait loci (QTL) associated with carotenoid content in cowpea sprouts. The contents of carotenoids, including lutein, [...] Read more.

The development and promotion of biofortified foods plants are a sustainable strategy for supplying essential micronutrients for human health and nutrition. We set out to identify quantitative trait loci (QTL) associated with carotenoid content in cowpea sprouts. The contents of carotenoids, including lutein, zeaxanthin, and β-carotene in sprouts of 125 accessions were quantified via high-performance liquid chromatography. Significant variation existed in the profiles of the different carotenoids. Lutein was the most abundant (58 ± 12.8 mg/100 g), followed by zeaxanthin (14.7 ± 3.1 mg/100 g) and β-carotene (13.2 ± 2.9 mg/100 g). A strong positive correlation was observed among the carotenoid compounds (r ≥ 0.87), indicating they can be improved concurrently. The accessions were distributed into three groups, following their carotenoid profiles, with accession C044 having the highest sprout carotenoid content in a single cluster. A total of 3120 genome-wide SNPs were tested for association analysis, which revealed that carotenoid biosynthesis in cowpea sprouts is a polygenic trait controlled by genes with additive and dominance effects. Seven loci were significantly associated with the variation in carotenoid content. The evidence of variation in carotenoid content and genomic regions controlling the trait creates an avenue for breeding cowpea varieties with enhanced sprouts carotenoid content. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 2505 KiB

Open AccessArticle

Identification and Fine Mapping of a Quantitative Trait Locus Controlling the Total Flower and Pod Numbers in Soybean

by Xia Sun, Xiaohuan Sun, Xiangwen Pan, Hengyou Zhang, Yanping Wang, Haixiang Ren and Feifei Wang

Agronomy 2022, 12(4), 790; https://doi.org/10.3390/agronomy12040790 - 25 Mar 2022

Cited by 7 | Viewed by 2437

Abstract

Total flower and pod numbers (TFPN) and effective pod numbers per plant (PNPP) are among the most important agronomic traits for soybean production. However, the underlying genetic mechanism remains unclear. In this study, we constructed a recombinant inbred line population derived from a [...] Read more.

Total flower and pod numbers (TFPN) and effective pod numbers per plant (PNPP) are among the most important agronomic traits for soybean production. However, the underlying genetic mechanism remains unclear. In this study, we constructed a recombinant inbred line population derived from a cross between JY73 (high TFPN) and TJSLH (low TFPN) to map loci for the two traits. In total, six QTL for TFPN and five QTL for PNPP were identified, among which a QTL on chromosome 4, named qFPN4, explained 9.2% and 9.6% of the phenotypic variation of TFPN and PNPP, respectively. Analysis of residual heterozygous lines for qFPN4 indicated that TFPN or PNPP was controlled by a single dominant gene at this locus and delimited the QTL into a ~2.62 Mb interval which tightly linked to an Indel marker C1-5. This mapping result was further confirmed by bulked segregant analysis (BSA) of the near isogenic lines. The genome-sequencing-based BSA also identified eight candidate genes carrying nonsynonymous SNPs and/or Indels; two genes, Glyma.04G176600 and Glyma.04G178900, were nominated as the most promising genes for qFPN4 based on additional expression and function analysis. These results improve our understanding of the genetic mechanism of TFPN and PNPP and indicate the potential for soybean yield improvement. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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19 pages, 6691 KiB

Open AccessArticle

BcSOC1 Promotes Bolting and Stem Elongation in Flowering Chinese Cabbage

by Yudan Wang, Xiu Huang, Xinmin Huang, Wei Su, Yanwei Hao, Houcheng Liu, Riyuan Chen and Shiwei Song

Int. J. Mol. Sci. 2022, 23(7), 3459; https://doi.org/10.3390/ijms23073459 - 22 Mar 2022

Cited by 30 | Viewed by 3466

Abstract

Flowering Chinese cabbage is one of the most economically important stalk vegetables. However, the molecular mechanisms underlying bolting, which is directly related to stalk quality and yield, in this species remain unknown. Previously, we examined five key stem development stages in flowering Chinese [...] Read more.

Flowering Chinese cabbage is one of the most economically important stalk vegetables. However, the molecular mechanisms underlying bolting, which is directly related to stalk quality and yield, in this species remain unknown. Previously, we examined five key stem development stages in flowering Chinese cabbage. Here, we identified a gene, BcSOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1), in flowering Chinese cabbage using transcriptome analysis, whose expression was positively correlated with bolting. Exogenous gibberellin (GA₃) and low-temperature treatments significantly upregulated BcSOC1 and promoted early bolting and flowering. Additionally, BcSOC1 overexpression accelerated early flowering and stem elongation in both Arabidopsis and flowering Chinese cabbage, whereas its knockdown dramatically delayed bolting and flowering and inhibited stem elongation in the latter; the inhibition of stem elongation was more notable than delayed flowering. BcSOC1 overexpression also induced cell expansion by upregulating genes encoding cell wall structural proteins, such as BcEXPA11 (cell wall structural proteins and enzymes) and BcXTH3 (xyloglucan endotransglycosidase/hydrolase), upon exogenous GA₃ and low-temperature treatments. Moreover, the length of pith cells was correlated with stem height, and BcSOC1 interacted with BcAGL6 (AGAMOUS-LIKE 6) and BcAGL24 (AGAMOUS-LIKE 24). Thus, BcSOC1 plays a vital role in bolting and stem elongation of flowering Chinese cabbage and may play a novel role in regulating stalk development, apart from the conserved function of Arabidopsis SOC1 in flowering alone. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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16 pages, 3530 KiB

Open AccessArticle

Comparative Transcriptomics Analysis of Roots and Leaves under Cd Stress in Calotropis gigantea L.

by Jingya Yang, Lingxiong Li, Xiong Zhang, Shibo Wu, Xiaohui Han, Xiong Li and Jianchu Xu

Int. J. Mol. Sci. 2022, 23(6), 3329; https://doi.org/10.3390/ijms23063329 - 19 Mar 2022

Cited by 20 | Viewed by 3440

Abstract

Calotropis gigantea is often found in mining areas with heavy metal pollution. However, little is known about the physiological and molecular response mechanism of C. gigantea to Cd stress. In the present study, Cd tolerance characteristic of C. gigantea and the potential mechanisms [...] Read more.

Calotropis gigantea is often found in mining areas with heavy metal pollution. However, little is known about the physiological and molecular response mechanism of C. gigantea to Cd stress. In the present study, Cd tolerance characteristic of C. gigantea and the potential mechanisms were explored. Seed germination test results showed that C. gigantea had a certain Cd tolerance capacity. Biochemical and transcriptomic analysis indicated that the roots and leaves of C. gigantea had different responses to early Cd stress. A total of 176 and 1618 DEGs were identified in the roots and leaves of C. gigantea treated with Cd compared to the control samples, respectively. Results indicated that oxidative stress was mainly initiated in the roots of C. gigantea, whereas the leaves activated several Cd detoxification processes to cope with Cd, including the upregulation of genes involved in Cd transport (i.e., absorption, efflux, or compartmentalization), cell wall remodeling, antioxidant system, and chelation. This study provides preliminary information to understand how C. gigantea respond to Cd stress, which is useful for evaluating the potential of C. gigantea in the remediation of Cd-contaminated soils. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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18 pages, 4115 KiB

Open AccessArticle

GhENODL6 Isoforms from the Phytocyanin Gene Family Regulated Verticillium Wilt Resistance in Cotton

by Man Zhang, Xingfen Wang, Jun Yang, Zhicheng Wang, Bin Chen, Xinyu Zhang, Dongmei Zhang, Zhengwen Sun, Jinhua Wu, Huifeng Ke, Liqiang Wu, Guiyin Zhang, Yan Zhang and Zhiying Ma

Int. J. Mol. Sci. 2022, 23(6), 2913; https://doi.org/10.3390/ijms23062913 - 8 Mar 2022

Cited by 16 | Viewed by 3245

Abstract

Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae, currently devastates cotton fiber yield and quality seriously, yet few resistance germplasm resources have been discovered in Gossypium hirsutum. The cotton variety Nongda601 with suitable VW resistance and high yield was [...] Read more.

Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae, currently devastates cotton fiber yield and quality seriously, yet few resistance germplasm resources have been discovered in Gossypium hirsutum. The cotton variety Nongda601 with suitable VW resistance and high yield was developed in our lab, which supplied elite resources for discovering resistant genes. Early nodulin-like protein (ENODL) is mainly related to nodule formation, and its role in regulating defense response has been seldom studied. Here, 41 conserved ENODLs in G. hirsutum were identified and characterized, which could divide into four subgroups. We found that GhENODL6 was upregulated under V. dahliae stress and hormonal signal and displayed higher transcript levels in resistant cottons than the susceptible. The GhENODL6 was proved to positively regulate VW resistance via overexpression and gene silencing experiments. Overexpression of GhENODL6 significantly enhanced the expressions of salicylic acid (SA) hormone-related transcription factors and pathogenicity-related (PR) protein genes, as well as hydrogen peroxide (H₂O₂) and SA contents, resulting in improved VW resistance in transgenic Arabidopsis. Correspondingly, in the GhENODL6 silenced cotton, the expression levels of both phenylalanine ammonia lyase (PAL) and 4-coumarate-CoA ligase (4CL) genes significantly decreased, leading to the reduced SA content mediating by the phenylalanine ammonia lyase pathway. Taken together, GhENODL6 played a crucial role in VW resistance by inducing SA signaling pathway and regulating the production of reactive oxygen species (ROS). These findings broaden our understanding of the biological roles of GhENODL and the molecular mechanisms underlying cotton disease resistance. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 3407 KiB

Open AccessArticle

Identification and DNA Marker Development for a Wheat-Leymus mollis 2Ns (2D) Disomic Chromosome Substitution

by Xianbo Feng, Xin Du, Siwen Wang, Pingchuan Deng, Yongfu Wang, Lihui Shang, Zengrong Tian, Changyou Wang, Chunhuan Chen, Jixin Zhao and Wanquan Ji

Int. J. Mol. Sci. 2022, 23(5), 2676; https://doi.org/10.3390/ijms23052676 - 28 Feb 2022

Cited by 3 | Viewed by 2550

Abstract

Leymus mollis (2n = 4x = 28, NsNsXmXm), a wild relative of common wheat (Triticum aestivum L.), carries numerous loci which could potentially be used in wheat improvement. In this study, line 17DM48 was isolated from the progeny of a [...] Read more.

Leymus mollis (2n = 4x = 28, NsNsXmXm), a wild relative of common wheat (Triticum aestivum L.), carries numerous loci which could potentially be used in wheat improvement. In this study, line 17DM48 was isolated from the progeny of a wheat and L. mollis hybrid. This line has 42 chromosomes forming 21 bivalents at meiotic metaphase I. Genomic in situ hybridization (GISH) demonstrated the presence of a pair chromosomes from the Ns genome of L. mollis. This pair substituted for wheat chromosome 2D, as shown by fluorescence in situ hybridization (FISH), DNA marker analysis, and hybridization to wheat 55K SNP array. Therefore, 17DM48 is a wheat-L. mollis 2Ns (2D) disomic substitution line. It shows longer spike and a high level of stripe rust resistance. Using specific-locus amplified fragment sequencing (SLAF-seq), 13 DNA markers were developed to identify and trace chromosome 2Ns of L. mollis in wheat background. This line provides a potential bridge germplasm for genetic improvement of wheat stripe rust resistance. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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13 pages, 1298 KiB

Open AccessArticle

Genetic Variation in ZmPAT7 Contributes to Tassel Branch Number in Maize

by Honghui Guan, Xiaojing Chen, Kailiang Wang, Xuyang Liu, Dengfeng Zhang, Yongxiang Li, Yanchun Song, Yunsu Shi, Tianyu Wang, Chunhui Li and Yu Li

Int. J. Mol. Sci. 2022, 23(5), 2586; https://doi.org/10.3390/ijms23052586 - 26 Feb 2022

Cited by 8 | Viewed by 3254

Abstract

Tassel branch number (TBN) is one of the important agronomic traits that contribute to the efficiency of seed production and has been selected strongly during the modern maize breeding process. However, the genetic mechanisms of TBN in maize are not entirely clear. In [...] Read more.

Tassel branch number (TBN) is one of the important agronomic traits that contribute to the efficiency of seed production and has been selected strongly during the modern maize breeding process. However, the genetic mechanisms of TBN in maize are not entirely clear. In this study, we used a B73 × CML247 recombination inbred lines (RILs) population to detect quantitative trait loci (QTLs) for TBN. A total of four QTLs (qTBN2a, qTBN2b, qTBN4, and qTBN6) and six candidate genes were identified through expression analysis. Further, one of the candidates (GRMZM2G010011, ZmPAT7) encoding an S-acyltransferase was selected to validate its function by CRISPR-Cas9 technology, and its loss-of-function lines showed a significant increase in TBN. A key SNP(−101) variation in the promoter of ZmPAT7 was significantly associated with TBN. A total of 17 distant eQTLs associated with the expression of ZmPAT7 were identified in expression quantitative trait loci (eQTL) analysis, and ZmNAC3 may be a major factor involved in regulating ZmPAT7. These findings of the present study promote our understanding of the genetic basis of tassel architecture and provide new gene resources for maize breeding improvement. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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21 pages, 5981 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum)

by Yi Liang, Jingqiu Xia, Yunshuang Jiang, Yuzhuo Bao, Huichan Chen, Duojia Wang, Da Zhang, Jing Yu and Jing Cang

Int. J. Mol. Sci. 2022, 23(4), 2351; https://doi.org/10.3390/ijms23042351 - 21 Feb 2022

Cited by 53 | Viewed by 5356

Abstract

The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, [...] Read more.

The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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16 pages, 2771 KiB

Open AccessArticle

CRISPR-Cas9 Mediated Mutation in OsPUB43 Improves Grain Length and Weight in Rice by Promoting Cell Proliferation in Spikelet Hull

by Qi Wu, Yingfan Liu and Junli Huang

Int. J. Mol. Sci. 2022, 23(4), 2347; https://doi.org/10.3390/ijms23042347 - 21 Feb 2022

Cited by 16 | Viewed by 3686

Abstract

Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this [...] Read more.

Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this study, we identified OsPUB43, a U-box E3 ubiquitin ligase, as an important negative regulator determining the gain size and grain weight in rice. Phenotypes of large grain are observed in ospub43 mutants, whereas overexpression of OsPUB43 results in short grains. Scanning electron microscopy analysis reveals that OsPUB43 modulates the grain size mainly by inhibiting cell proliferation in the spikelet hull. The OsPUB43 protein is localized in the cytoplasm and nucleus. The ospub43 mutants display high sensitivity to exogenous BR, while OsPUB43-OE lines are hyposensitive to BR. Furthermore, the transient transcriptional activity assay shows that OsBZR1 can activate the expression of OsPUB43. Collectively, our results indicate that OsPUB43 negatively controls the gain size by modulating the expression of BR-responsive genes as well as MADS-box genes that are required for lemma/palea specification, suggesting that OsPUB43 has a potential valuable application in the enlargement of grain size in rice. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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15 pages, 5136 KiB

Open AccessArticle

Transcriptome and Coexpression Network Analyses Provide In-Sights into the Molecular Mechanisms of Hydrogen Cyanide Synthesis during Seed Development in Common Vetch (Vicia sativa L.)

by Mingyu Li, Lu Zhao, Qiang Zhou, Longfa Fang, Dong Luo, Wenxian Liu, Iain Robert Searle and Zhipeng Liu

Int. J. Mol. Sci. 2022, 23(4), 2275; https://doi.org/10.3390/ijms23042275 - 18 Feb 2022

Cited by 5 | Viewed by 2678

Abstract

The common vetch (Vicia sativa L.) seed is an ideal plant-based protein food for humans, but its edible value is mainly limited by the presence of cyanogenic glycosides that hydrolyze to produce toxic hydrogen cyanide (HCN), and the genes that regulate HCN [...] Read more.

The common vetch (Vicia sativa L.) seed is an ideal plant-based protein food for humans, but its edible value is mainly limited by the presence of cyanogenic glycosides that hydrolyze to produce toxic hydrogen cyanide (HCN), and the genes that regulate HCN synthesis in common vetch are unknown. In this study, seeds from common vetch at 5, 10, 15, 20, 25, 30, and 35 days after anthesis were sampled, and the seven stages were further divided into five developmental stages, S1, S2, S3, S4, and S5, based on morphological and transcriptome analyses. A total of 16,403 differentially expressed genes were identified in the five developmental stages. The HCN contents of seeds in these five stages were determined by alkaline titration, and weighted gene coexpression network analysis was used to explain the molecular regulatory mechanism of HCN synthesis in common vetch seeds. Eighteen key regulatory genes for HCN synthesis were identified, including the VsGT2, VsGT17 and CYP71A genes, as well as the VsGT1 gene family. VsGT1, VsGT2, VsGT17 and CYP71A jointly promoted HCN synthesis, from 5 to 25 days after anthesis, with VsGT1-1, VsGT1-4, VsGT1-11 and VsGT1-14 playing major roles. The HCN synthesis was mainly regulated by VsGT1, from 25 to 35 days after anthesis. As the expression level of VsGT1 decreased, the HCN content no longer increased. In-depth elucidation of seed HCN synthesis lays the foundations for breeding common vetch with low HCN content. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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27 pages, 48988 KiB

Open AccessArticle

Conservation and Divergence of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family between Wheat and Rice

by Li Li, Fu Shi, Guoli Wang, Yanbin Guan, Yufan Zhang, Mingjie Chen, Junli Chang, Guangxiao Yang, Guangyuan He, Yuesheng Wang and Yin Li

Int. J. Mol. Sci. 2022, 23(4), 2099; https://doi.org/10.3390/ijms23042099 - 14 Feb 2022

Cited by 21 | Viewed by 4089

Abstract

The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family affects plant architecture, panicle structure, and grain development, representing key genes for crop improvements. The objective of the present study is to utilize the well characterized SPLs’ functions in rice to facilitate the [...] Read more.

The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family affects plant architecture, panicle structure, and grain development, representing key genes for crop improvements. The objective of the present study is to utilize the well characterized SPLs’ functions in rice to facilitate the functional genomics of TaSPL genes. To achieve these goals, we combined several approaches, including genome-wide analysis of TaSPLs, comparative genomic analysis, expression profiling, and functional study of TaSPL3 in rice. We established the orthologous relationships of 56 TaSPL genes with the corresponding OsSPLs, laying a foundation for the comparison of known SPL functions between wheat and rice. Some TaSPLs exhibited different spatial–temporal expression patterns when compared to their rice orthologs, thus implicating functional divergence. TaSPL2/6/8/10 were identified to respond to different abiotic stresses through the combination of RNA-seq and qPCR expression analysis. Additionally, ectopic expression of TaSPL3 in rice promotes heading dates, affects leaf and stem development, and leads to smaller panicles and decreased yields per panicle. In conclusion, our work provides useful information toward cataloging of the functions of TaSPLs, emphasized the conservation and divergence between TaSPLs and OsSPLs, and identified the important SPL genes for wheat improvement. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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17 pages, 2018 KiB

Open AccessFeature PaperArticle

An Efficient Modular Gateway Recombinase-Based Gene Stacking System for Generating Multi-Trait Transgenic Plants

by Guannan Qin, Suting Wu, Liying Zhang, Yanyao Li, Chunmei Liu, Jianghui Yu, Lihua Deng, Guoying Xiao and Zhiguo Zhang

Plants 2022, 11(4), 488; https://doi.org/10.3390/plants11040488 - 11 Feb 2022

Cited by 10 | Viewed by 3562

Abstract

Transgenic technology can transfer favorable traits regardless of reproductive isolation and is an important method in plant synthetic biology and genetic improvement. Complex metabolic pathway modification and pyramiding breeding strategies often require the introduction of multiple genes at once, but the current vector [...] Read more.

Transgenic technology can transfer favorable traits regardless of reproductive isolation and is an important method in plant synthetic biology and genetic improvement. Complex metabolic pathway modification and pyramiding breeding strategies often require the introduction of multiple genes at once, but the current vector assembly systems for constructing multigene expression cassettes are not completely satisfactory. In this study, a new in vitro gene stacking system, GuanNan Stacking (GNS), was developed. Through the introduction of Type IIS restriction enzyme-mediated Golden Gate cloning, GNS allows the modular, standardized assembly of target gene expression cassettes. Because of the introduction of Gateway recombination, GNS facilitates the cloning of superlarge transgene expression cassettes, allows multiple expression cassettes to be efficiently assembled in a binary vector simultaneously, and is compatible with the Cre enzyme-mediated marker deletion mechanism. The linked dual positive-negative marker selection strategy ensures the efficient acquisition of target recombinant plasmids without prokaryotic selection markers in the T-DNA region. The host-independent negative selection marker combined with the TAC backbone ensures the cloning and transfer of large T-DNAs (>100 kb). Using the GNS system, we constructed a binary vector containing five foreign gene expression cassettes and obtained transgenic rice carrying the target traits, proving that the method developed in this research is a powerful tool for plant metabolic engineering and compound trait transgenic breeding. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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25 pages, 26010 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L.

by Sarfraz Sehrish, Wahid Sumbal, Meili Xie, Chuanji Zhao, Rong Zuo, Feng Gao and Shengyi Liu

Int. J. Mol. Sci. 2022, 23(4), 1936; https://doi.org/10.3390/ijms23041936 - 9 Feb 2022

Cited by 15 | Viewed by 3489

Abstract

SET domain group encoding proteins function as histone lysine methyltransferases. These proteins are involved in various biological processes, including plant development and adaption to the environment by modifying the chromatin structures. So far, the SET domain genes (SDGs) have not been [...] Read more.

SET domain group encoding proteins function as histone lysine methyltransferases. These proteins are involved in various biological processes, including plant development and adaption to the environment by modifying the chromatin structures. So far, the SET domain genes (SDGs) have not been systematically investigated in Brassica napus (B. napus). In the current study, through genome-wide analysis, a total of 122 SDGs were identified in the B. napus genome. These BnSDGs were subdivided into seven (I–VII) classes based on phylogeny analysis, domain configurations, and motif distribution. Segmental duplication was involved in the evolution of this family, and the duplicated genes were under strong purifying selection. The promoter sequence of BnSDGs consisted of various growth, hormones, and stress-related cis-acting elements along with transcription factor binding sites (TFBSs) for 20 TF families in 59 of the 122 BnSDGs. The gene ontology (GO) analysis revealed that BnSDGs were closely associated with histone and non-histone methylation and metal binding capacity localized mostly in the nucleus. The in silico expression analysis at four developmental stages in leaf, stem root, floral organ, silique, and seed tissues showed a broad range of tissue and stage-specific expression pattern. The expression analysis under four abiotic stresses (dehydration, cold, ABA, and salinity) also provided evidence for the importance of BnSDGs in stress environments. Based on expression analysis, we performed reverse transcription-quantitative PCR for 15 target BnSDGs in eight tissues (young leaf, mature leaf, root, stem, carpel, stamen, sepal, and petals). Our results were in accordance with the in silico expression data, suggesting the importance of these genes in plant development. In conclusion, this study lays a foundation for future functional studies on SDGs in B. napus. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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11 pages, 2732 KiB

Open AccessArticle

Growth Repressor GmRAV Binds to the GmGA3ox Promoter to Negatively Regulate Plant Height Development in Soybean

by Yongguo Xue, Yuntong Zhang, Jinming Shan, Yujia Ji, Xiaoming Zhang, Wenbin Li, Dongmei Li and Lin Zhao

Int. J. Mol. Sci. 2022, 23(3), 1721; https://doi.org/10.3390/ijms23031721 - 2 Feb 2022

Cited by 16 | Viewed by 2794

Abstract

Plant height is an important component of plant architecture, and significantly affects crop quality and yield. A soybean GmRAV (Related to ABI3/VP1) transcription factor containing both AP2 and B3 domains is a growth repressor. Three GmRAV-overexpressing (GmRAV-ox) transgenic lines displayed [...] Read more.

Plant height is an important component of plant architecture, and significantly affects crop quality and yield. A soybean GmRAV (Related to ABI3/VP1) transcription factor containing both AP2 and B3 domains is a growth repressor. Three GmRAV-overexpressing (GmRAV-ox) transgenic lines displayed extremely shorter height and shortened internodes compared with control plants, whereas transgenic inhibition of GmRAV expression resulted in increased plant height. GmRAV-ox soybean plants showed a low active gibberellin level and the dwarf phenotype could be rescued by treatment with exogenous GA₃ treatment. ChIP (Chromatin immunoprecipitation)-qPCR assay showed that GmRAV could directly regulate the expression of the GA4 biosynthetic genes GA3-oxidase (GmGA3ox) by binding two CAACA motifs in the GmGA3ox promoter. The GmGA3ox promoter was bound by GmRAV, whose expression levels in leaves were both elevated in GmRAV-i-3 and decreased in GmRAV-ox-7 soybean plants. Transient expression assay in N. benthamiana also showed that the proGmRAV:GmRAV-3F6H effector strongly repressed the expression of LUC reporter gene driven by GmGA3ox promoter containing two CAACA motifs. Together, our results suggested that GmRAV protein repressed the expression of GmGA3ox by directly binding to the two CAACA motifs in the promoter to limit soybean plant height. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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19 pages, 2588 KiB

Open AccessReview

Broad Specific Xyloglucan:Xyloglucosyl Transferases Are Formidable Players in the Re-Modelling of Plant Cell Wall Structures

by Maria Hrmova, Barbora Stratilová and Eva Stratilová

Int. J. Mol. Sci. 2022, 23(3), 1656; https://doi.org/10.3390/ijms23031656 - 31 Jan 2022

Cited by 28 | Viewed by 4918

Abstract

Plant xyloglucan:xyloglucosyl transferases, known as xyloglucan endo-transglycosylases (XETs) are the key players that underlie plant cell wall dynamics and mechanics. These fundamental roles are central for the assembly and modifications of cell walls during embryogenesis, vegetative and reproductive growth, and adaptations to living [...] Read more.

Plant xyloglucan:xyloglucosyl transferases, known as xyloglucan endo-transglycosylases (XETs) are the key players that underlie plant cell wall dynamics and mechanics. These fundamental roles are central for the assembly and modifications of cell walls during embryogenesis, vegetative and reproductive growth, and adaptations to living environments under biotic and abiotic (environmental) stresses. XET enzymes (EC 2.4.1.207) have the β-sandwich architecture and the β-jelly-roll topology, and are classified in the glycoside hydrolase family 16 based on their evolutionary history. XET enzymes catalyse transglycosylation reactions with xyloglucan (XG)-derived and other than XG-derived donors and acceptors, and this poly-specificity originates from the structural plasticity and evolutionary diversification that has evolved through expansion and duplication. In phyletic groups, XETs form the gene families that are differentially expressed in organs and tissues in time- and space-dependent manners, and in response to environmental conditions. Here, we examine higher plant XET enzymes and dissect how their exclusively carbohydrate-linked transglycosylation catalytic function inter-connects complex plant cell wall components. Further, we discuss progress in technologies that advance the knowledge of plant cell walls and how this knowledge defines the roles of XETs. We construe that the broad specificity of the plant XETs underscores their roles in continuous cell wall restructuring and re-modelling. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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20 pages, 2405 KiB

Open AccessReview

ICE-CBF-COR Signaling Cascade and Its Regulation in Plants Responding to Cold Stress

by Delight Hwarari, Yuanlin Guan, Baseer Ahmad, Ali Movahedi, Tian Min, Zhaodong Hao, Ye Lu, Jinhui Chen and Liming Yang

Int. J. Mol. Sci. 2022, 23(3), 1549; https://doi.org/10.3390/ijms23031549 - 28 Jan 2022

Cited by 206 | Viewed by 11205

Abstract

Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and physiological mechanisms to adapt to cold stress. These mechanisms are regulated by a series of transcription factors and proteins for efficient [...] Read more.

Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and physiological mechanisms to adapt to cold stress. These mechanisms are regulated by a series of transcription factors and proteins for efficient cold stress acclimation. It has been established that the ICE-CBF-COR signaling pathway in plants regulates how plants acclimatize to cold stress. Cold stress is perceived by receptor proteins, triggering signal transduction, and Inducer of CBF Expression (ICE) genes are activated and regulated, consequently upregulating the transcription and expression of the C-repeat Binding Factor (CBF) genes. The CBF protein binds to the C-repeat/Dehydration Responsive Element (CRT/DRE), a homeopathic element of the Cold Regulated genes (COR gene) promoter, activating their transcription. Transcriptional regulations and post-translational modifications regulate and modify these entities at different response levels by altering their expression or activities in the signaling cascade. These activities then lead to efficient cold stress tolerance. This paper contains a concise summary of the ICE-CBF-COR pathway elucidating on the cross interconnections with other repressors, inhibitors, and activators to induce cold stress acclimation in plants. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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12 pages, 2313 KiB

Open AccessArticle

Identification of a Pm4 Allele as a Powdery Mildew Resistance Gene in Wheat Line Xiaomaomai

by Danyu Yao, Waqas Ijaz, Yi Liu, Jinghuang Hu, Wentao Peng, Bowen Zhang, Xiaolan Wen, Juan Wang, Dan Qiu, Hongjie Li, Shihe Xiao and Guozhong Sun

Int. J. Mol. Sci. 2022, 23(3), 1194; https://doi.org/10.3390/ijms23031194 - 21 Jan 2022

Cited by 16 | Viewed by 3070

Abstract

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive foliar diseases of wheat. In this study, we combined the bulked segregant RNA sequencing (BSR-seq) and comparative genomics analysis to localize the powdery mildew resistance [...] Read more.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive foliar diseases of wheat. In this study, we combined the bulked segregant RNA sequencing (BSR-seq) and comparative genomics analysis to localize the powdery mildew resistance gene in Chinese landrace Xiaomaomai. Genetic analysis of F₁ plants from a crossing of Xiaomaomai × Lumai23 and the derived F₂ population suggests that a single recessive gene, designated as pmXMM, confers the resistance in this germplasm. A genetic linkage map was constructed using the newly developed SNP markers and pmXMM was mapped to the distal end of chromosome 2AL. The two flanking markers 2AL15 and 2AL34 were closely linked to pmXMM at the genetic distance of 3.9 cM and 1.4 cM, respectively. Using the diagnostic primers of Pm4, we confirmed that Xiaomaomai carries a Pm4 allele and the gene function was further validated by the virus-induced gene silencing (VIGS). In addition, we systematically analyzed pmXMM in comparison with the other Pm4 alleles. The results suggest that pmXMM is identical to Pm4d and Pm4e at sequence level. Pm4b is also not different from Pm4c according to their genome/amino acid sequences. Only a few nucleotide variances were detected between pmXMM and Pm4a/b, which indicate the haplotype variation of the Pm4 gene. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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14 pages, 2833 KiB

Open AccessArticle

Biochemical and Expression Analyses Revealed the Involvement of Proanthocyanidins and/or Their Derivatives in Fiber Pigmentation of Gossypium stocksii

by Yujie Sun, Diandian Zhang, Hongli Zheng, Yuqing Wu, Jun Mei, Liping Ke, Dongliang Yu and Yuqiang Sun

Int. J. Mol. Sci. 2022, 23(2), 1008; https://doi.org/10.3390/ijms23021008 - 17 Jan 2022

Cited by 19 | Viewed by 2295

Abstract

The wild cotton species Gossypium stocksii produces a brown fiber that provides a valuable resource for the color improvement of naturally colored cotton (NCC) fiber. However, the biochemical basis and molecular mechanism of its fiber pigmentation remain unclear. Herein, we analyzed the dynamics [...] Read more.

The wild cotton species Gossypium stocksii produces a brown fiber that provides a valuable resource for the color improvement of naturally colored cotton (NCC) fiber. However, the biochemical basis and molecular mechanism of its fiber pigmentation remain unclear. Herein, we analyzed the dynamics of proanthocyanidins (PAs) accumulation in developing the fiber of G. stocksii, which suggested a similar role of PAs and/or their derivatives in the fiber coloration of G. stocksii. In addition, comparative transcriptomics analyses revealed that the PA biosynthetic genes were expressed at higher levels and for a longer period in developing fibers of G. stocksii than G. arboreum (white fiber), and the transcription factors, such as TT8, possibly played crucial regulatory roles in regulating the PA branch genes. Moreover, we found that the anthocyanidin reductase (ANR) was expressed at a higher level than the leucoanthocyanidin reductases (LARs) and significantly upregulated during fiber elongation, suggesting a major role of ANR in PA synthesis in G. stocksii fiber. In summary, this work revealed the accumulation of PAs and the expression enhancement of PA biosynthetic genes in developing fibers of G. stocksii. We believe this work will help our understanding of the molecular mechanisms of cotton fiber coloration and further promote the future breeding of novel NCCs. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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18 pages, 3464 KiB

Open AccessArticle

Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation

by Bo Li, Xiangzhan Zhang, Ruiwei Duan, Chunhong Han, Jian Yang, Long Wang, Suke Wang, Yanli Su, Lei Wang, Yongfei Dong and Huabai Xue

Int. J. Mol. Sci. 2022, 23(2), 746; https://doi.org/10.3390/ijms23020746 - 11 Jan 2022

Cited by 24 | Viewed by 2588

Abstract

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through [...] Read more.

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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19 pages, 5963 KiB

Open AccessArticle

Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis

by Yan Zhang, Lanjie Zheng, Liu Yun, Li Ji, Guanhui Li, Manchun Ji, Yong Shi and Xu Zheng

Int. J. Mol. Sci. 2022, 23(1), 542; https://doi.org/10.3390/ijms23010542 - 4 Jan 2022

Cited by 54 | Viewed by 5645

Abstract

Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT [...] Read more.

Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT family genes in wheat have been reported. In this study, ten CAT proteins (TaCATs) were identified in wheat and classified into three groups based on their phylogenetic features and sequence analysis. The analysis of the structure and motif composition of the TaCAT proteins suggested that a segmental duplication event occurred in the TaCAT gene family. Collinearity relationship analysis among different species showed that there were three orthologous CAT genes in rice and in maize. By analyzing the cis-elements in the promoter regions, we speculated that TaCAT genes expression might be regulated by light, oxygen deficit, methyl jasmonate and abscisic acid, and by transcription factors such as MYB. A Gene Ontology (GO)-based analysis showed that TaCAT proteins may be related to the response to various stresses, are cytoplasm localized, and may function as antioxidant enzymes. RT-qPCR and transcriptome data analyses exhibited distinct expression patterns of TaCAT genes in different tissues and in response to various treatments. In this study, a comprehensive analysis of wheat CAT genes was performed, enriching our knowledge of CAT genes and providing a foundation for further functional analyses of this gene family in wheat. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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14 pages, 4192 KiB

Open AccessArticle

Genome-Wide Association Study Identifies Candidate Genes Related to the Linoleic Acid Content in Soybean Seeds

by Qin Di, Angela Piersanti, Qi Zhang, Cristina Miceli, Hui Li and Xiaoyi Liu

Int. J. Mol. Sci. 2022, 23(1), 454; https://doi.org/10.3390/ijms23010454 - 31 Dec 2021

Cited by 31 | Viewed by 3136

Abstract

Soybean (Glycine max (L.) Merrill) oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). The high content of linoleic acid (LA) contributes to the oil having poor oxidative stability. Therefore, soybean seed with a lower LA [...] Read more.

Soybean (Glycine max (L.) Merrill) oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). The high content of linoleic acid (LA) contributes to the oil having poor oxidative stability. Therefore, soybean seed with a lower LA content is desirable. To investigate the genetic architecture of LA, we performed a genome-wide association study (GWAS) using 510 soybean cultivars collected from China. The phenotypic identification results showed that the content of LA varied from 36.22% to 72.18%. The GWAS analysis showed that there were 37 genes related to oleic acid content, with a contribution rate of 7%. The candidate gene Glyma.04G116500.1 (GmWRI14) on chromosome 4 was detected in three consecutive years. The GmWRI14 showed a negative correlation with the LA content and the correlation coefficient was −0.912. To test whether GmWRI14 can lead to a lower LA content in soybean, we introduced GmWRI14 into the soybean genome. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) showed that the overexpression of GmWRI14 leads to a lower LA content in soybean seeds. Meanwhile, RNA-seq verified that GmWRI14-overexpressed soybean lines showed a lower accumulation of GmFAD2-1A and GmFAD2-1B than control lines. Our results indicate that the down-regulation of the FAD2 gene triggered by the transcription factor GmWRI14 is the underlying mechanism reducing the LA level of seed. Our results provide novel insights into the genetic architecture of LA and pinpoint potential candidate genes for further in-depth studies. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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14 pages, 2649 KiB

Open AccessArticle

A VIN3-like Protein OsVIL1 Is Involved in Grain Yield and Biomass in Rice

by Jinmi Yoon, Hee-Joong Jeong, Gibeom Baek, Jungil Yang, Xin Peng, Win Tun, Sun-Tae Kim, Gynheung An and Lae-Hyeon Cho

Plants 2022, 11(1), 83; https://doi.org/10.3390/plants11010083 - 28 Dec 2021

Cited by 7 | Viewed by 2818

Abstract

In chromatin remodeling, the post-translational modification of histone proteins is mediated by multimeric protein complexes. VERNALIZATION INSENSITIVE3 (VIN3) forms a complex with Polycomb Repressive Complex 2 (PRC2), which mediates the trimethylation of H3K27 to repress target gene expression. In rice, four genes (OsVIL1-OsVIL4) [...] Read more.

In chromatin remodeling, the post-translational modification of histone proteins is mediated by multimeric protein complexes. VERNALIZATION INSENSITIVE3 (VIN3) forms a complex with Polycomb Repressive Complex 2 (PRC2), which mediates the trimethylation of H3K27 to repress target gene expression. In rice, four genes (OsVIL1-OsVIL4) encoding the VIN3-like proteins are expressed ubiquitously in various tissues. Null mutants of osvil2 display pleiotropic phenotypes such as altered flowering time, floral organ defects, and reduced tiller size. In contrast, osvil1 mutants did not show significant phenotypes except in fertilization compared with the wild type. However, transgenic plants overexpressing OsVIL1 showed phenotypes of increased biomass and grain yield. Cross-sections of the basal region of elongating stems revealed that the increased biomass was mediated by inducing cell proliferation in the meristem. Chromatin immunoprecipitation assay indicated that OsVIL1 repressed expression of cytokinin oxidase/dehydrogenase gene (OsCKX2) by binding to the promoter and genic regions of OsCKX2. We also observed that OsVIL1 modified the levels of H3K27me3 in the OsCKX2 chromatin. Because OsCKX2 encodes an enzyme that degrades active cytokinin, we conclude that OsVIL1 functions in the regulation of endogenous active cytokinin levels, thereby increasing plant height and productivity. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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10 pages, 1492 KiB

Open AccessCommunication

Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome

by Ilya Kirov, Ekaterina Polkhovskaya, Maxim Dudnikov, Pavel Merkulov, Anastasia Vlasova, Gennady Karlov and Alexander Soloviev

Plants 2022, 11(1), 5; https://doi.org/10.3390/plants11010005 - 21 Dec 2021

Cited by 9 | Viewed by 6810

Abstract

Sequencing and epigenetic profiling of target genes in plants are important tasks with various applications ranging from marker design for plant breeding to the study of gene expression regulation. This is particularly interesting for plants with big genome size for which whole-genome sequencing [...] Read more.

Sequencing and epigenetic profiling of target genes in plants are important tasks with various applications ranging from marker design for plant breeding to the study of gene expression regulation. This is particularly interesting for plants with big genome size for which whole-genome sequencing can be time-consuming and costly. In this study, we asked whether recently proposed Cas9-targeted nanopore sequencing (nCATS) is efficient for target gene sequencing for plant species with big genome size. We applied nCATS to sequence the full-length glutenin genes (Glu-1Ax, Glu-1Bx and Glu-1By) and their promoters in hexaploid triticale (X Triticosecale, AABBRR, genome size is 24 Gb). We showed that while the target gene enrichment per se was quite high for the three glutenin genes (up to 645×), the sequencing depth that was achieved from two MinION flowcells was relatively low (5–17×). However, this sequencing depth was sufficient for various tasks including detection of InDels and single-nucleotide variations (SNPs), read phasing and methylation profiling. Using nCATS, we uncovered SNP and InDel variation of full-length glutenin genes providing useful information for marker design and deciphering of variation of individual Glu-1By alleles. Moreover, we demonstrated that glutenin genes possess a ‘gene-body’ methylation epigenetic profile with hypermethylated CDS part and hypomethylated promoter region. The obtained information raised an interesting question on the role of gene-body methylation in glutenin gene expression regulation. Taken together, our work disclosures the potential of the nCATS approach for sequencing of target genes in plants with big genome size. Full article

(This article belongs to the Topic Plant Functional Genomics and Crop Genetic Improvement)

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