International Journal of Molecular Sciences

Editorial

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4 pages, 164 KiB

Open AccessEditorial

Research on Plant Genomics and Breeding 2.0

by Long Jin, Zhiyong Li and Jian Zhang

Int. J. Mol. Sci. 2024, 25(12), 6659; https://doi.org/10.3390/ijms25126659 - 17 Jun 2024

Cited by 1 | Viewed by 975

Abstract

Plant genomics and breeding is one among the several highly regarded disciplines in today’s field of biological sciences [...] Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

Research

Jump to: Editorial

21 pages, 9699 KiB

Open AccessArticle

Genome-Wide Identification of the ARF Gene Family in Safflower (Carthamus tinctorius L.) and Their Response Patterns to Exogenous Hormone Treatments

by Shuwei Qin, Xinrong Wen, Mengyuan Ma, Jiaxing Wang, Jianhang Zhang, Meihui Huang, Kexin Sun, Ya Zhao, Meng Zhao, Asigul Ismayil, Min Liu and Aiping Cao

Int. J. Mol. Sci. 2025, 26(8), 3773; https://doi.org/10.3390/ijms26083773 - 16 Apr 2025

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Abstract

Auxin response factors (ARFs) are a class of transcription factors widely present in plants. As an important economic crop, research on the effects of safflower ARFs on endogenous auxin and effective components is relatively limited. In this study, a total of 23 ARF [...] Read more.

Auxin response factors (ARFs) are a class of transcription factors widely present in plants. As an important economic crop, research on the effects of safflower ARFs on endogenous auxin and effective components is relatively limited. In this study, a total of 23 ARF genes were identified from the safflower genome. Sequence alignment and domain analysis indicated the presence of conserved B3 and Auxin_resp domains in these ARFs. Phylogenetic analysis indicated that CtARF could be classified into five subfamilies, a conclusion also supported by gene structure, consensus motifs, and domain compositions. Transcriptome data showed that ARFs are expressed in all flower colors, but the expression levels of ARF family members vary among different flower colors. CtARF19 had relatively higher expression in deep red flowers, CtARF3 had higher expression in white flowers, CtARF2/12 had higher expression in yellow flowers, and CtARF21/22 had higher expression in light red flowers. Protein–protein interaction network analysis indicated that ARF family members (CtARF2/3/4/5/15/18/19/22) are located within the interaction network. Cis-acting element analysis suggested that CtARF genes may be regulated by hormone treatment (AuxRR-core) and abiotic stress, and the results of qRT-PCR also confirmed this. Additionally, the content of endogenous auxin and active components in safflower with different flower colors significantly changed upon treatment with hormones that affect IAA content. In summary, our study provides valuable insights into the biological functions of CtARF genes under exogenous hormone conditions and their effects on active components. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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20 pages, 6460 KiB

Open AccessArticle

Multiomics Studies on the Effects of High-Temperature Stress on Male Sterility in Gossypium barbadense

by Jiangbo Li, Xiaojuan Deng, Man Gao, Tao Lv, Yongsheng Cai, Yanying Qu, Quanjia Chen and Kai Zheng

Int. J. Mol. Sci. 2025, 26(8), 3693; https://doi.org/10.3390/ijms26083693 - 14 Apr 2025

Viewed by 193

Abstract

High-temperature (HT) stress has been recognized as one of the main factors restricting the normal growth and development of cotton and severely affects fiber quality and yield. To elucidate the regulatory mechanism of male sterility-related hormones in Gossypium barbadense under HT stress, we [...] Read more.

High-temperature (HT) stress has been recognized as one of the main factors restricting the normal growth and development of cotton and severely affects fiber quality and yield. To elucidate the regulatory mechanism of male sterility-related hormones in Gossypium barbadense under HT stress, we explored candidate genes closely related to male sterility in G. barbadense. We studied the expression profiles of hormones and genes in the anthers of G. barbadense GB150 under HT stress by combining transcriptomic and metabolomic analyses. Through a combined analysis of the transcriptional metabolism of the anthers of G. barbadense GB150, we determined the contents of ABA, JA, SA, IAA, tZR, and GA₂₀ and the expression of genes related to biosynthetic pathways and signal transduction pathways. The results revealed that the ABA and JA contents significantly increased after HT; the IAA, tZR, and GA₂₀ contents significantly decreased; and the SA content did not significantly change after HT. We then used weighted gene coexpression network analysis (WGCNA) to further analyze the interactions among hormones, transcription factors, and core genes and constructed hormone coexpression networks and genome-wide coexpression networks. Through these network analyses, we ultimately identified 10 candidate genes closely related to male sterility in G. barbadense. Using qRT-PCR, resequencing data from 221 G. barbadense materials revealed that ALA4 (Arabidopsis thaliana has been proven to be associated with male fertility) and SBP1 (two stop gains in the gene structure) may play important roles in the process of male sterility in G. barbadense. The results of this study provide a theoretical basis for the molecular mechanism of male sterility in G. barbadense. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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13 pages, 2137 KiB

Open AccessArticle

Genome-Wide Association Study and Candidate Gene Mining of Husk Number Trait in Maize

by Yancui Wang, Shukai Wang, Dusheng Lu, Ming Chen, Baokun Li, Zhenhong Li, Haixiao Su, Jing Sun, Pingping Xu and Cuixia Chen

Int. J. Mol. Sci. 2025, 26(7), 3437; https://doi.org/10.3390/ijms26073437 - 7 Apr 2025

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Abstract

Husk number (HN) trait is an important factor affecting maize kernel dehydration rate after the physiological maturity stage. In general, a reasonable reduction in HN is a key target sought for breeding maize varieties that are suitable for mechanized harvesting. In this study, [...] Read more.

Husk number (HN) trait is an important factor affecting maize kernel dehydration rate after the physiological maturity stage. In general, a reasonable reduction in HN is a key target sought for breeding maize varieties that are suitable for mechanized harvesting. In this study, the HN of a maize natural population panel containing 232 inbred lines was analyzed, and the results showed a broad-sense heritability of 0.89, along with a wide range of phenotypic variation. With the best linear unbiased prediction (BLUP) values across the three environments, a genome-wide association study (GWAS) was conducted using 995,106 single-nucleotide polymorphism (SNP) markers. A total of 16 SNPs significantly associated with HN were identified by the mixed linear model and general linear model using the TASSEL 5.0 software program. A local linkage disequilibrium (LD) study was performed to infer the candidate interval around the lead SNPs. A total of 19 functionally annotated genes were identified. The candidate genes were divided into multiple functional types, including transcriptional regulation, signal transduction, and metabolic and cellular transport. These results provide hints for the understanding of the genetic basis of the HN trait and for the breeding of maize varieties with fewer HN and faster dehydration rate. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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18 pages, 4562 KiB

Open AccessArticle

Breeding D1-Type Hybrid Japonica Rice in Diverse Upland Rainfed Environments

by Chunli Wang, Juan Li, Qian Zhu, Junjie Li, Cui Zhang, Ruke Hong, Dajun Huang, Zhonglin Zhang, Jin Xu, Dandan Li, Jiancheng Wen, Chengyun Li, Youyong Zhu, Dongsun Lee and Lijuan Chen

Int. J. Mol. Sci. 2025, 26(7), 3246; https://doi.org/10.3390/ijms26073246 - 31 Mar 2025

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Abstract

‘Dianheyou615’ (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance [...] Read more.

‘Dianheyou615’ (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance of the D1-type hybrid japonica rice remain unclear. In this study, a comprehensive analysis of ‘DHY615’’s agronomic performance, genetic genealogy, and molecular genetic foundation was conducted to dissect its desirable traits for upland rainfed cultivation across diverse ecological environments. The main findings indicate that ‘DHY615’ possesses 6432 heterozygous SNPs, with 57.48% and 14.43% located in the promoter and coding regions, respectively, potentially affecting key phenotypic traits. High-impact SNPs variants and numerous well-known functional genes were identified, such as OsAAP6, GS3, Sd1, Rf1, BADH2, BPh14, Rymv1, OsFRO1, NRT1.1B, SKC1, OsNCED2, and qUVR-10, which are likely linked to traits including plant architecture, grain yield, grain quality, and resistance to various biotic and abiotic stresses (e.g., disease, cold, drought, salt, high iron, and high UV radiation). Notably, ‘Nan615’ harbors a greater number of functional allele variants compared to ‘H479A’, which potentially explaining its superior grain yield and remarkable adaptability. This study offers novel and valuable insights into the molecular genetic foundation of the plateau D1-type hybrid japonica rice, underscoring its potential for sustainable rice production across diverse ecological zones, especially with its unparalleled high-altitude adaptability to rainfed upland planting. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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13 pages, 1769 KiB

Open AccessArticle

Fine Mapping of the QTL qRLP12 That Controls Root Length Under Polyethylene glycol-Induced Drought Stress During the Early Seedling Stage of Sesame

by Junchao Liang, Yanxin Deng, Xiaowen Yan, Zhiqi Wang, Pan Zeng, Meiwang Le, Hongying Zhou and Jian Sun

Int. J. Mol. Sci. 2025, 26(7), 2886; https://doi.org/10.3390/ijms26072886 - 22 Mar 2025

Viewed by 316

Abstract

A deeper root system can improve the efficiency of water and nutrient absorption from soil; therefore, genetic improvements to the root length of crops are essential for yield stability under drought stress. We previously identified a stable quantitative trait locus (QTL) qRLP12 for [...] Read more.

A deeper root system can improve the efficiency of water and nutrient absorption from soil; therefore, genetic improvements to the root length of crops are essential for yield stability under drought stress. We previously identified a stable quantitative trait locus (QTL) qRLP12 for root length under polyethylene glycol (PEG)-induced drought stress in a Jinhuangma (JHM, sensitive)/Zhushanbai (ZSB, tolerant) recombinant inbred line (RIL) population. To validate and fine map this QTL, in this study, a secondary F₂ population was constructed, and the genetic effect of the target QTL was validated by comparing the phenotype data of different genotypes. Using newly developed markers, 14 genotypes of recombinant F₂ individuals were obtained. A phenotypic analysis of homozygous recombinant progeny lines narrowed qRLP12 to a 91 kb region. Seven putative predicted genes were identified in the target region, among which LOC105165547, a callose synthase gene, was the only one containing nonsynonymous variations in the coding region between two parents. Quantitative real-time PCR analysis revealed that LOC105165547 was significantly induced by PEG stress in the qRLP12+ line. These indicated that LOC105165547 might be the candidate gene for qRLP12, which is responsible for root length subjected to PEG stress. Our results provide a favored gene resource for improving root length under drought stress in sesame. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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18 pages, 19918 KiB

Open AccessArticle

Integrated Transcriptome and Metabolome Analyses Reveal Candidate Genes Associate with Phenolic Compound Biosynthesis in Different Varieties of Perilla frutescens

by Hong Ye, Jiaxin Mu, Tong Yang, Qi Shen and Yukun Wang

Int. J. Mol. Sci. 2025, 26(7), 2841; https://doi.org/10.3390/ijms26072841 - 21 Mar 2025

Viewed by 294

Abstract

Perilla frutescens (Perilla) has great potential for utilization in food and medicine due to the abundance of secondary metabolites, especially phenolic compounds. However, the molecular mechanism underlying phenolic compound synthesis in perilla remains poorly understood. By targeted metabolome analysis, we found nine differentially [...] Read more.

Perilla frutescens (Perilla) has great potential for utilization in food and medicine due to the abundance of secondary metabolites, especially phenolic compounds. However, the molecular mechanism underlying phenolic compound synthesis in perilla remains poorly understood. By targeted metabolome analysis, we found nine differentially accumulated metabolites among QS2, QS6, and QO7 leaves and nine unique metabolites which only exist in QS6. Furthermore, transcriptome analysis showed the differential expression genes (DEGs) were significantly enriched into phenylpropanoid- and flavonoid-related pathways. Moreover, the integrated transcriptome and metabolome analyses indicated 14 candidates highly correlated with phenolic compound biosynthesis. In addition, phenylpropanoid- and flavonoid-biosynthesis-related DEGs, including one PAL, one CYP73A, one 4CL, two CHI, two F3H, one FLS, three CHS, two CYP75B1, one ANS, and two DFR, were isolated. The results in this study provide useful information for the metabolic regulation of phenolic compounds and serve as essential gene resources for future breeding programs. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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14 pages, 14455 KiB

Open AccessArticle

NAC047/052/104 Synergistically Regulate the Dark-Induced Leaf Senescence in Non-Heading Chinese Cabbage

by Bing Yang, Dingyu Zhang, Zitong Meng, Yijiang Yin, Xiao Yang, Mengqin Cao, Ruixin Li, Yishan Song and Hongfang Zhu

Int. J. Mol. Sci. 2025, 26(5), 2340; https://doi.org/10.3390/ijms26052340 - 6 Mar 2025

Viewed by 433

Abstract

Non-heading Chinese cabbage (NHCC) is an important vegetable, and its leaves are harvested for consumption. Thus, the initiation and progression of leaf senescence in NHCC directly impact its yield and quality. In multiple plant species, NAC transcription factors are known to act as [...] Read more.

Non-heading Chinese cabbage (NHCC) is an important vegetable, and its leaves are harvested for consumption. Thus, the initiation and progression of leaf senescence in NHCC directly impact its yield and quality. In multiple plant species, NAC transcription factors are known to act as critical regulators of leaf senescence. However, in NHCC, the NAC transcription factors contributing to leaf senescence regulation remain to be identified, and the mechanisms underlying dark-induced leaf senescence remain unclear. To explore the molecular mechanisms of leaf senescence in NHCC, we stored NHCC away from light and subsequently examined dark-induced transcriptional alterations via RNA sequencing. Interestingly, three NAC transcription factors, BrNAC047, BrNAC052, and BrNAC104, were found to be potently activated by darkness. Subsequently, the virus-induced gene silencing of BrNAC047, BrNAC052, and BrNAC104 demonstrated that these three NACs act as positive regulators of dark-induced leaf senescence in NHCC. Dual-luciferase assays further confirmed that BrNAC047, BrNAC052, and BrNAC104 directly activate the promoters of certain senescence-associated genes. This study uncovers the molecular signaling pathways governing dark-induced leaf senescence in NHCC, highlighting the role of three key regulators and offering valuable molecular targets for delaying leaf senescence in NHCC. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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19 pages, 9076 KiB

Open AccessArticle

Functional Study of GbSMXL8-Mediated Strigolactone Signaling Pathway in Regulating Cotton Fiber Elongation and Plant Growth

by Lingyu Chen, Wennuo Xu, Lingyu Zhang, Qin Chen, Yongsheng Cai, Quanjia Chen and Kai Zheng

Int. J. Mol. Sci. 2025, 26(5), 2293; https://doi.org/10.3390/ijms26052293 - 5 Mar 2025

Viewed by 544

Abstract

The novel plant hormone strigolactones (SL) are involved significantly in plant growth and development. Its key members SMXL6, 7, 8 can modulate SL signal reception and response negatively and can regulate plant branching remarkably. There are relatively scarce studies of cotton [...] Read more.

The novel plant hormone strigolactones (SL) are involved significantly in plant growth and development. Its key members SMXL6, 7, 8 can modulate SL signal reception and response negatively and can regulate plant branching remarkably. There are relatively scarce studies of cotton SMXL gene family, and this study was carried out to clarify the role of GbSMXL8 in cotton fiber development. Phylogenetic analysis identified 48 cotton SMXL genes, which were divided into SMXL-I (SMXL 1, 2), SMXL-II (SMXL 3) and SMXL-III (SMXL6, 7, 8) groups. The results of the cis-element analysis indicated that the SMXL gene could respond to hormones and the environment to modulate cotton growth process. A candidate gene GbSMXL8 was screened out based on the expression difference in extreme varieties of Gossypium barbadense. Tissue-specific analysis indicated that GbSMXL8 was mainly expressed in roots, 20D, 25D, and 35D and was involved in SL signaling pathways. In vitro ovule culture experiments showed that exogenous SLs (GR24) could promote the fiber elongation of G. barbadense, and GbSMXL8 expression was increased after GR24 treatment, indicating that GbSMXL8 was specifically responsive to GR24 in regulating fiber growth. GbSMXL8 knockout resulted in creased length and number of epidermal hairs and the length of fiber, indicating the interference role of GbSMXL8 gene with the development of cotton fiber. The GbSMXL8 transgenic plant was detected with a higher chlorophyll content and photosynthetic rate than those of the control plant, producing a direct impact on plant growth, yield, and biomass accumulation. GbSMXL8 gene knockout could increase plant height, accelerate growth rate, and lengthen fiber length. Intervening GbSMXL8 may mediate cotton growth, plant type formation and fiber elongation. In conclusion, the present study uncovers the function of GbSMXL8-mediated SL signal in cotton, providing theoretical insight for future breeding of new cotton varieties. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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21 pages, 10126 KiB

Open AccessArticle

Phylogeny and Functional Differentiation of the Terpene Synthase Gene Family in Angiosperms with Emphasis on Rosa chinensis

by Qi Li, Yifang Peng, Tao Zhao, Qijing Dong, Qian Yang, Xiaoyu Liu and Yu Han

Int. J. Mol. Sci. 2025, 26(5), 2113; https://doi.org/10.3390/ijms26052113 - 27 Feb 2025

Viewed by 559

Abstract

Terpenes are pivotal for plant growth, development, and adaptation to environmental stresses. With the advent of extensive genomic data and sophisticated bioinformatics tools, new insights into the evolutionary dynamics and functional diversification of terpene synthases (TPSs) have emerged. Despite genome-wide identifications of the [...] Read more.

Terpenes are pivotal for plant growth, development, and adaptation to environmental stresses. With the advent of extensive genomic data and sophisticated bioinformatics tools, new insights into the evolutionary dynamics and functional diversification of terpene synthases (TPSs) have emerged. Despite genome-wide identifications of the TPS family in certain species, comprehensive cross-species analyses remain scarce. In this study, we conducted a genome-wide identification and subgroup classification of TPS families across 115 angiosperms with available genomic sequences. Our phylogenomic synteny network analysis elucidated the complex evolutionary history of TPS genes, revealing notable expansions and contractions among subgroups. Specifically, TPS-a showed significant expansion, while TPS-b was variably lost in some Poaceae, indicating adaptive responses. TPS-c maintained considerable conservation across species, whereas TPS-e/f diverged into distinct evolutionary trajectories despite functional overlap, with TPS-e further splitting into two angiosperm-specific clades. The TPS-g subgroup displayed lineage-restricted distribution, primarily in super-rosids and monocots. Notably, TPS-d and TPS-h subgroups were absent in angiosperms. Employing Rosa chinensis as a case study, we identified RcTPS23, a conserved bifunctional terpene synthase, highlighting the utility of cross-species synteny data in functional prediction. This comprehensive analysis elucidates the phylogenetic and functional landscape of TPS subgroups in angiosperms, providing a robust framework for predicting TPS function and guiding further functional investigations. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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14 pages, 3496 KiB

Open AccessArticle

Transcriptome Analysis and Resistance Identification of bar and BPH9 Co-Transformation Rice

by Sanhe Li, Changyan Li, Jianyu Wang, Lei Zhou, Bian Wu, Zaihui Zhou, Xiaolei Fan, Aiqing You and Kai Liu

Int. J. Mol. Sci. 2025, 26(4), 1762; https://doi.org/10.3390/ijms26041762 - 19 Feb 2025

Viewed by 433

Abstract

Insect pests and weeds are the two major biotic factors affecting crop yield in the modern agricultural system. In this study, a brown planthopper (BPH) resistance gene (BPH9) and glufosinate tolerance gene (bar) were stacked into a single T-DNA [...] Read more.

Insect pests and weeds are the two major biotic factors affecting crop yield in the modern agricultural system. In this study, a brown planthopper (BPH) resistance gene (BPH9) and glufosinate tolerance gene (bar) were stacked into a single T-DNA cassette and transformed into an indica rice (Oryza sativa L.) line H23. The present study employed a gene stacking process that combines more than one gene/trait into an individual transgenic plant to meet the increasing cropping demands under complex conditions. The transgenic rice H23 (H23R) co-expressing bar and BPH9 genes demonstrated both glufosinate tolerance and BPH resistance. We utilized transcriptome data to reveal the mechanism of BPH9-mediated brown planthopper resistance and to analyze the impact of exogenous transgenic fragments on upstream and downstream genes at insertion sites. The evaluation of insect resistance and glufosinate tolerance confirmed H23R as an excellent double-resistant transgenic rice. These findings indicate that H23R can satisfy insect management and weed control in the modern rice agricultural system. However, a deregulation study will help with prospective commercial planting. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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19 pages, 7048 KiB

Open AccessArticle

The Mulberry WRKY Transcription Factor MaWRKYIIc7 Participates in Regulating Plant Drought Stress Tolerance

by Xueqiang Su, Manli Zhao, Rong Zhou, Cuimin Xu, Ran Zhang, Ruixue Li and Taichu Wang

Int. J. Mol. Sci. 2025, 26(4), 1714; https://doi.org/10.3390/ijms26041714 - 17 Feb 2025

Viewed by 489

Abstract

The sericulture industry is an important component of the agricultural industry. Drought stress can cause yellowing, premature ageing, and the shrinkage of mulberry (Morus alba L.) leaves, greatly damaging their quality and restricting the high-quality development of the sericulture industry. WRKY transcription [...] Read more.

The sericulture industry is an important component of the agricultural industry. Drought stress can cause yellowing, premature ageing, and the shrinkage of mulberry (Morus alba L.) leaves, greatly damaging their quality and restricting the high-quality development of the sericulture industry. WRKY transcription factors play important roles in the plant drought stress response. In this study, we found that MaWRKYIIc7 of the mulberry WRKY TFs, had significantly higher expression levels in leaves than in other tissues and was induced to be expressed under drought stress. The MaWRKYIIc7 protein is located in the nucleus and plasma membrane, and its transcriptional activity depends mainly on the N-terminal sequence. The overexpression of MaWRKYIIc7 in Arabidopsis resulted in better drought tolerance. An analysis of the transient overexpression of MaWRKYIIc7 in mulberry seedlings under drought stress revealed that the transgenic seedlings presented decreased stomatal opening, decreased MDA content, increased ROS clearance ability, and increased the expression of ABA biosynthesis-related genes. The Y1H and Dual-luc results indicate that MaWRKYIIc7 can bind W-boxes to positively regulate MaNCED1 and MaRD29A, synergistically regulating the drought tolerance of mulberry. Overall, our research suggests that MaWRKYIIc7 can increase plant drought tolerance by promoting ROS clearance, adjusting stomatal opening, and activating the ABA signalling pathway. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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16 pages, 3104 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Mediator Complex Subunit Gene Family in Cassava

by Lingling Zhou, Shuhui Sun, Linlong Zhu, Xian Chen, Ran Xu, Lian Wu and Shuang Gu

Int. J. Mol. Sci. 2025, 26(4), 1666; https://doi.org/10.3390/ijms26041666 - 15 Feb 2025

Viewed by 563

Abstract

The Mediator complex (MED) functions as a co-activator in plants, transmitting transcriptional signals to regulate gene expression, including responses to environmental stresses. While the MED gene family has been identified in several species, it has not yet been reported in cassava. In this [...] Read more.

The Mediator complex (MED) functions as a co-activator in plants, transmitting transcriptional signals to regulate gene expression, including responses to environmental stresses. While the MED gene family has been identified in several species, it has not yet been reported in cassava. In this study, we identified 32 members of the MeMED gene family in cassava (Manihot esculenta Crantz) distributed across 13 chromosomes. These genes were categorized into distinct Mediator subunits based on their similarity to Arabidopsis modules. Promoter analysis revealed the presence of various cis-regulatory elements, which likely play key roles in regulating plant growth, development, and stress responses. RNA-seq data showed tissue-specific expression patterns for the MeMED genes, with significant expression observed in leaves, roots, petioles, stems, friable embryogenic callus, and shoot apical meristems. Further RT-qPCR analysis under various abiotic stress conditions—including drought, exogenous hydrogen peroxide, cold, heat, and salt—demonstrated that 10 selected MeMED genes exhibited significant differential expression, indicating their potential functional involvement in stress adaptation. These findings offer insights into the biological roles of the MeMED gene family in cassava, with implications for improving stress tolerance in future breeding programs. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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22 pages, 8556 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profile of Farnesyl Pyrophosphate Synthase (FPS) Gene Family in Euphorbia Hirta L.

by Xinyi Bian, Tingkai Wu, Runrun Qiang, Zhi Deng, Fazal Rehman, Qiyu Han, Dong Xu, Yuan Yuan, Xiaobo Wang, Zewei An, Wenguan Wu, Huasen Wang and Han Cheng

Int. J. Mol. Sci. 2025, 26(2), 798; https://doi.org/10.3390/ijms26020798 - 18 Jan 2025

Viewed by 908

Abstract

The biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are essential for sesquiterpenes and triterpenes, respectively, is primarily governed by the mevalonate pathway, wherein farnesyl pyrophosphate synthase (FPS) plays a pivotal role. This study identified eight members of the [...] Read more.

The biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are essential for sesquiterpenes and triterpenes, respectively, is primarily governed by the mevalonate pathway, wherein farnesyl pyrophosphate synthase (FPS) plays a pivotal role. This study identified eight members of the FPS gene family in Euphorbia hirta, designated EhFPS1–EhFPS8, through bioinformatics analysis, revealing their distribution across several chromosomes and a notable tandem gene cluster. The genes exhibited strong hydrophilic properties and key functional motifs crucial for enzyme activity. An in-depth analysis of the EhFPS genes highlighted their significant involvement in isoprenoid metabolism and lipid biosynthesis, with expression patterns influenced by hormones such as jasmonic acid and salicylic acid. Tissue-specific analysis demonstrated that certain FPS genes, particularly EhFPS1, EhFPS2, and EhFPS7, showed elevated expression levels in latex, suggesting their critical roles in terpenoid biosynthesis. Furthermore, subcellular localization studies have indicated that these proteins are primarily found in the cytoplasm, reinforcing their function in metabolic processes. These findings provide a foundational understanding of the FPS genes in E. hirta, including their gene structures, conserved domains, and evolutionary relationships. This study elucidates the potential roles of these genes in response to environmental factors, hormone signaling, and stress adaptation, thereby paving the way for future functional analyses aimed at exploring the regulation of terpenoid biosynthesis and enhancing stress tolerance in this species. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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22 pages, 7428 KiB

Open AccessArticle

Genome-Wide Identification, Phylogenetic Evolution, and Abiotic Stress Response Analyses of the Late Embryogenesis Abundant Gene Family in the Alpine Cold-Tolerant Medicinal Notopterygium Species

by Xuanye Wu, Xiaojing He, Xiaoling Wang, Puyuan Liu, Shaoheng Ai, Xiumeng Liu, Zhonghu Li and Xiaojuan Wang

Int. J. Mol. Sci. 2025, 26(2), 519; https://doi.org/10.3390/ijms26020519 - 9 Jan 2025

Viewed by 790

Abstract

Late embryogenesis abundant (LEA) proteins are a class of proteins associated with osmotic regulation and plant tolerance to abiotic stress. However, studies on the LEA gene family in the alpine cold-tolerant herb are still limited, and the phylogenetic evolution and biological functions of [...] Read more.

Late embryogenesis abundant (LEA) proteins are a class of proteins associated with osmotic regulation and plant tolerance to abiotic stress. However, studies on the LEA gene family in the alpine cold-tolerant herb are still limited, and the phylogenetic evolution and biological functions of its family members remain unclear. In this study, we conducted genome-wide identification, phylogenetic evolution, and abiotic stress response analyses of LEA family genes in Notopterygium species, alpine cold-tolerant medicinal herbs in the Qinghai–Tibet Plateau and adjacent regions. The gene family identification analysis showed that 23, 20, and 20 LEA genes were identified in three Notopterygium species, N. franchetii, N. incisum, and N. forrestii, respectively. All of these genes can be classified into six LEA subfamilies: LEA_1, LEA_2, LEA_5, LEA_6, DHN (Dehydrin), and SMP (seed maturation protein). The LEA proteins in the three Notopterygium species exhibited significant variations in the number of amino acids, physical and chemical properties, subcellular localization, and secondary structure characteristics, primarily demonstrating high hydrophilicity, different stability, and specific subcellular distribution patterns. Meanwhile, we found that the members of the same LEA subfamily shared similar exon–intron structures and conserved motifs. Interestingly, the chromosome distributions of LEA genes in Notopterygium species were scattered. The results of the collinearity analysis indicate that the expansion of the LEA gene family is primarily driven by gene duplication. A Ka/Ks analysis showed that paralogous gene pairs were under negative selection in Notopterygium species. A promoter cis-acting element analysis showed that most LEA genes possessed multiple cis-elements connected to plant growth and development, stress response, and plant hormone signal transduction. An expression pattern analysis demonstrated the species-specific and tissue-specific expression of NinLEAs. Experiments on abiotic stress responses indicated that the NinLEAs play a crucial role in the response to high-temperature and drought stresses in N. franchetii leaves and roots. These results provide novel insights for further understanding the functions of the LEA gene family in the alpine cold-tolerant Notopterygium species and also offer a scientific basis for in-depth research on the abiotic stress response mechanisms and stress-resistant breeding. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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12 pages, 2634 KiB

Open AccessArticle

Novel Allelic Mutations in Dw3 Gene That Affect the Height of Sorghum Plants

by Ping Wang, Bingbing Liang, Zhengjun Li, Chunyu Wang, Lixia Zhang and Xiaochun Lu

Int. J. Mol. Sci. 2024, 25(22), 12000; https://doi.org/10.3390/ijms252212000 - 8 Nov 2024

Viewed by 1000

Abstract

Breeding for dwarfing traits in sorghum is crucial. However, only three genes (Dw1–Dw3) that control plant height have been mapped. In this study, 634 sorghum cultivars were collected to investigate plant height and genotypes. Four were genotyped Dw1DW2Dw3 (wild [...] Read more.

Breeding for dwarfing traits in sorghum is crucial. However, only three genes (Dw1–Dw3) that control plant height have been mapped. In this study, 634 sorghum cultivars were collected to investigate plant height and genotypes. Four were genotyped Dw1DW2Dw3 (wild type) but with different plant heights, and they were selected to construct two populations and map new dwarf genes. Bulked segregant analysis with whole-genome resequencing of the two populations identified the candidate gene in one same genomic region—on chromosome 7. Then, it was narrowed down to a region containing nine genes. Amino acid and DNA sequence analysis of the parent and offspring plants revealed that two novel allelic mutations in the Dw3 gene play a role in reducing the plant height—8R262 or 8R417, including 1 bp substitution and 2 bp deletions. Furthermore, we sequenced 19 cultivars that primarily exhibited a “one-dwarf” hybrid or wild-type and presumed another allelic mutation via the amino acid alignment of 8R019, 8R100, and 8R402, which was another one-base substitution. These results indicate that multiple types of allelic mutations in the Dw3 gene should be considered when identified or applied. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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20 pages, 9529 KiB

Open AccessArticle

Transcriptomic and Metabolomic Profiling Reveals the Variations in Carbohydrate Metabolism between Two Blueberry Cultivars

by Haiyan Yang, Zhiwen Wei, Yaqiong Wu, Chunhong Zhang, Lianfei Lyu, Wenlong Wu and Weilin Li

Int. J. Mol. Sci. 2024, 25(1), 293; https://doi.org/10.3390/ijms25010293 - 25 Dec 2023

Cited by 5 | Viewed by 1896

Abstract

Blueberry is a high-quality fruit tree with significant nutritional and economic value, but the intricate mechanism of sugar accumulation in its fruit remains unclear. In this study, the ripe fruits of blueberry cultivars ‘Anna’ and ‘Misty’ were utilized as experimental materials, and physiological [...] Read more.

Blueberry is a high-quality fruit tree with significant nutritional and economic value, but the intricate mechanism of sugar accumulation in its fruit remains unclear. In this study, the ripe fruits of blueberry cultivars ‘Anna’ and ‘Misty’ were utilized as experimental materials, and physiological and multi-omics methodologies were applied to analyze the regulatory mechanisms of the difference in sugar content between them. The results demonstrated that the ‘Anna’ fruit was smaller and had less hardness than the ‘Misty’ fruit, as well as higher sugar content, antioxidant capability, and lower active substance content. A total of 7067 differentially expressed genes (DEGs) (3674 up-regulated and 3393 down-regulated) and 140 differentially abundant metabolites (DAMs) (82 up-regulated and 58 down-regulated) were identified between the fruits of the two cultivars. According to KEGG analysis, DEGs were primarily abundant in phenylpropanoid synthesis and hormone signal transduction pathways, whereas DAMs were primarily enriched in ascorbate and aldarate metabolism, phenylpropanoid biosynthesis, and the pentose phosphate pathway. A combined multi-omics study showed that 116 DEGs and 3 DAMs in starch and sucrose metabolism (48 DEGs and 1 DAM), glycolysis and gluconeogenesis (54 DEGs and 1 DAM), and the pentose phosphate pathway (14 DEGs and 1 DAM) were significantly enriched. These findings suggest that blueberries predominantly increase sugar accumulation by activating carbon metabolism network pathways. Moreover, we identified critical transcription factors linked to the sugar response. This study presents new understandings regarding the molecular mechanisms underlying blueberry sugar accumulation and will be helpful in improving blueberry fruit quality through breeding. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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19 pages, 4878 KiB

Open AccessArticle

Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways

by Beena Alam, Ruixian Liu, Juwu Gong, Junwen Li, Haoliang Yan, Qun Ge, Xianghui Xiao, Jingtao Pan, Haihong Shang, Yuzhen Shi, Youlu Yuan and Wankui Gong

Int. J. Mol. Sci. 2023, 24(23), 16595; https://doi.org/10.3390/ijms242316595 - 22 Nov 2023

Cited by 1 | Viewed by 1629

Abstract

Upland cotton is the fifth-largest oil crop in the world, with an average supply of nearly 20% of vegetable oil production. Cottonseed oil is also an ideal alternative raw material to be efficiently converted into biodiesel. However, the improvement in kernel oil content [...] Read more.

Upland cotton is the fifth-largest oil crop in the world, with an average supply of nearly 20% of vegetable oil production. Cottonseed oil is also an ideal alternative raw material to be efficiently converted into biodiesel. However, the improvement in kernel oil content (KOC) of cottonseed has not received sufficient attention from researchers for a long time, due to the fact that the main product of cotton planting is fiber. Previous studies have tagged QTLs and identified individual candidate genes that regulate KOC of cottonseed. The regulatory mechanism of oil metabolism and accumulation of cottonseed are still elusive. In the current study, two high-density genetic maps (HDGMs), which were constructed based on a recombinant inbred line (RIL) population consisting of 231 individuals, were used to identify KOC QTLs. A total of forty-three stable QTLs were detected via these two HDGM strategies. Bioinformatic analysis of all the genes harbored in the marker intervals of the stable QTLs revealed that a total of fifty-one genes were involved in the pathways related to lipid biosynthesis. Functional analysis via coexpression network and RNA-seq revealed that the hub genes in the co-expression network that also catalyze the key steps of fatty acid synthesis, lipid metabolism and oil body formation pathways (ACX4, LACS4, KCR1, and SQD1) could jointly orchestrate oil accumulation in cottonseed. This study will strengthen our understanding of oil metabolism and accumulation in cottonseed and contribute to KOC improvement in cottonseed in the future, enhancing the security and stability of worldwide food supply. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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21 pages, 9447 KiB

Open AccessArticle

Transcriptome and Physiological Analysis of Rapeseed Tolerance to Post-Flowering Temperature Increase

by Javier Canales, José F. Verdejo and Daniel F. Calderini

Int. J. Mol. Sci. 2023, 24(21), 15593; https://doi.org/10.3390/ijms242115593 - 26 Oct 2023

Cited by 1 | Viewed by 1858

Abstract

Climate-change-induced temperature fluctuations pose a significant threat to crop production, particularly in the Southern Hemisphere. This study investigates the transcriptome and physiological responses of rapeseed to post-flowering temperature increases, providing valuable insights into the molecular mechanisms underlying rapeseed tolerance to heat stress. Two [...] Read more.

Climate-change-induced temperature fluctuations pose a significant threat to crop production, particularly in the Southern Hemisphere. This study investigates the transcriptome and physiological responses of rapeseed to post-flowering temperature increases, providing valuable insights into the molecular mechanisms underlying rapeseed tolerance to heat stress. Two rapeseed genotypes, Lumen and Solar, were assessed under control and heat stress conditions in field experiments conducted in Valdivia, Chile. Results showed that seed yield and seed number were negatively affected by heat stress, with genotype-specific responses. Lumen exhibited an average of 9.3% seed yield reduction, whereas Solar showed a 28.7% reduction. RNA-seq analysis of siliques and seeds revealed tissue-specific responses to heat stress, with siliques being more sensitive to temperature stress. Hierarchical clustering analysis identified distinct gene clusters reflecting different aspects of heat stress adaptation in siliques, with a role for protein folding in maintaining silique development and seed quality under high-temperature conditions. In seeds, three distinct patterns of heat-responsive gene expression were observed, with genes involved in protein folding and response to heat showing genotype-specific expression. Gene coexpression network analysis revealed major modules for rapeseed yield and quality, as well as the trade-off between seed number and seed weight. Overall, this study contributes to understanding the molecular mechanisms underlying rapeseed tolerance to heat stress and can inform crop improvement strategies targeting yield optimization under changing environmental conditions. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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21 pages, 7324 KiB

Open AccessArticle

Integrated Transcriptomic and Metabolomic Analysis Reveal the Underlying Mechanism of Anthocyanin Biosynthesis in Toona sinensis Leaves

by Jing Xu, Yanru Fan, Xiaojiao Han, Huanhuan Pan, Jianhua Dai, Yi Wei, Renying Zhuo and Jun Liu

Int. J. Mol. Sci. 2023, 24(20), 15459; https://doi.org/10.3390/ijms242015459 - 23 Oct 2023

Cited by 6 | Viewed by 2271

Abstract

Toona sinensis, commonly known as Chinese Toon, is a plant species that possesses noteworthy value as a tree and vegetable. Its tender young buds exhibit a diverse range of colors, primarily determined by the presence and composition of anthocyanins and flavonoids. However, [...] Read more.

Toona sinensis, commonly known as Chinese Toon, is a plant species that possesses noteworthy value as a tree and vegetable. Its tender young buds exhibit a diverse range of colors, primarily determined by the presence and composition of anthocyanins and flavonoids. However, the underlying mechanisms of anthocyanin biosynthesis in Toona sinensis have been rarely reported. To explore the related genes and metabolites associated with composition of leaf color, we conducted an analysis of the transcriptome and metabolome of five distinct Toona clones. The results showed that differentially expressed genes and metabolites involved in anthocyanin biosynthesis pathway were mainly enriched. A conjoint analysis of transcripts and metabolites was carried out in JFC (red) and LFC (green), resulting in the identification of 510 genes and 23 anthocyanin-related metabolites with a positive correlation coefficient greater than 0.8. Among these genes and metabolites, 23 transcription factors and phytohormone-related genes showed strong coefficients with 13 anthocyanin derivates, which mainly belonged to the stable types of delphinidin, cyanidin, peonidin. The core derivative was found to be Cyanidin-3-O-arabinoside, which was present in JFC at 520.93 times the abundance compared to LFC. Additionally, the regulatory network and relative expression levels of genes revealed that the structural genes DFR, ANS, and UFGT1 might be directly or indirectly regulated by the transcription factors SOC1 (MADS-box), CPC (MYB), and bHLH162 (bHLH) to control the accumulation of anthocyanin. The expression of these genes was significantly higher in red clones compared to green clones. Furthermore, RNA-seq results accurately reflected the true expression levels of genes. Overall, this study provides a foundation for future research aimed at manipulating anthocyanin biosynthesis to improve plant coloration or to derive human health benefits. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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16 pages, 2625 KiB

Open AccessArticle

Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO₄ Treatments in Broussonetia papyrifera

by Mengdi Chen, Zhengbo Wang, Ziyuan Hao, Hongying Li, Qi Feng, Xue Yang, Xiaojiao Han and Xiping Zhao

Int. J. Mol. Sci. 2023, 24(20), 15087; https://doi.org/10.3390/ijms242015087 - 11 Oct 2023

Cited by 7 | Viewed by 1515

Abstract

Real-time quantitative PCR (RT-qPCR) has a high sensitivity and strong specificity, and is widely used in the analysis of gene expression. Selecting appropriate internal reference genes is the key to accurately analyzing the expression changes of target genes by RT-qPCR. To find out [...] Read more.

Real-time quantitative PCR (RT-qPCR) has a high sensitivity and strong specificity, and is widely used in the analysis of gene expression. Selecting appropriate internal reference genes is the key to accurately analyzing the expression changes of target genes by RT-qPCR. To find out the most suitable internal reference genes for studying the gene expression in Broussonetia papyrifera under abiotic stresses (including drought, salt, and ZnSO₄ treatments), seven different tissues of B. papyrifera, as well as the roots, stems, and leaves of B. papyrifera under the abiotic stresses were used as test materials, and 15 candidate internal reference genes were screened based on the transcriptome data via RT-qPCR. Then, the expression stability of the candidate genes was comprehensively evaluated through the software geNorm (v3.5), NormFinder (v0.953), BestKeeper (v1.0), and RefFinder. The best internal reference genes and their combinations were screened out according to the analysis results. rRNA and Actin were the best reference genes under drought stress. Under salt stress, DOUB, HSP, NADH, and rRNA were the most stable reference genes. Under heavy metal stress, HSP and NADH were the most suitable reference genes. EIF3 and Actin were the most suitable internal reference genes in the different tissues of B. papyrifera. In addition, HSP, rRNA, NADH, and UBC were the most suitable internal reference genes for the abiotic stresses and the different tissues of B. papyrifera. The expression patterns of DREB and POD were analyzed by using the selected stable and unstable reference genes. This further verified the reliability of the screened internal reference genes. This study lays the foundation for the functional analysis and regulatory mechanism research of genes in B. papyrifera. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

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