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Recent Advances in Plant Molecular Science in China 2021 (Closed)

A topical collection in International Journal of Molecular Sciences (ISSN 1422-0067). This collection belongs to the section "Molecular Plant Sciences".

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Editors

Prof. Dr. Changning Liu

E-Mail Website
Collection Editor
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
Interests: bioinformatics; disease; long non coding RNA; plant biology
Special Issues, Collections and Topics in MDPI journals
Dr. Ke Wang

E-Mail Website
Collection Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: wheat; genetic transformation; gene editing; molecular genetics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jin Xu

E-Mail Website
Collection Editor
College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China
Interests: trace elements; plant metal transporters; transcriptional regulation; phytohormones; signaling transduction
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

This Topical Collection aims to provide a comprehensive overview of recent advances in plant molecular science in China by inviting contributions from Chinese research institutes/laboratories that consolidate our understanding of this area. Potential topics regarding plants include, but are not limited to: biophysics, biochemistry, and molecular biology; cell biology; physiology; genomics/epigenomics; proteomics and metabolomics; bioactive phytochemicals; plant–microbe interactions; developmental biology; pests and diseases; synthetic biology; computational biology, and the development of new technologies in plant sciences. In this collection, we welcome submissions for comprehensive reviews or new research advancements in—but not limited to—all of the above-mentioned areas.

Dr. Changning Liu
Dr. Ke Wang
Prof. Dr. Jin Xu
Collection Editors

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Published Papers (31 papers)

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2022

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14 pages, 3223 KiB  
Article
Comparative Transcriptome Analysis Reveals the Gene Expression and Regulatory Characteristics of Broad-Spectrum Immunity to Leaf Rust in a Wheat–Agropyron cristatum 2P Addition Line
by Xiajie Ji, Taiguo Liu, Shirui Xu, Zongyao Wang, Haiming Han, Shenghui Zhou, Baojin Guo, Jinpeng Zhang, Xinming Yang, Xiuquan Li, Lihui Li and Weihua Liu
Int. J. Mol. Sci. 2022, 23(13), 7370; https://doi.org/10.3390/ijms23137370 - 01 Jul 2022
Cited by 4 | Viewed by 1856
Abstract
Wheat leaf rust (caused by Puccinia triticina Erikss.) is among the major diseases of common wheat. The lack of resistance genes to leaf rust has limited the development of wheat cultivars. Wheat–Agropyron cristatum (A. cristatum) 2P addition line II-9-3 has [...] Read more.
Wheat leaf rust (caused by Puccinia triticina Erikss.) is among the major diseases of common wheat. The lack of resistance genes to leaf rust has limited the development of wheat cultivars. Wheat–Agropyron cristatum (A. cristatum) 2P addition line II-9-3 has been shown to provide broad-spectrum immunity to leaf rust. To identify the specific A. cristatum resistance genes and related regulatory pathways in II-9-3, we conducted a comparative transcriptome analysis of inoculated and uninoculated leaves of the resistant addition line II-9-3 and the susceptible cultivar Fukuhokomugi (Fukuho). The results showed that there were 66 A. cristatum differentially expressed genes (DEGs) and 1389 wheat DEGs in II-9-3 during P. triticina infection. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and gene set enrichment analysis (GSEA) revealed that the DEGs of II-9-3 were associated with plant–pathogen interaction, MAPK signaling pathway–plant, plant hormone signal transduction, glutathione metabolism, and phenylpropanoid biosynthesis. Furthermore, many defense-related A. cristatum genes, such as two NLR genes, seven receptor kinase-encoding genes, and four transcription factor-encoding genes, were identified. Our results indicated that the key step of resistance to leaf rust involves, firstly, the gene expression of chromosome 2P upstream of the immune pathway and, secondly, the effect of chromosome 2P on the co-expression of wheat genes in II-9-3. The disease resistance regulatory pathways and related genes in the addition line II-9-3 thus could play a critical role in the effective utilization of innovative resources for leaf rust resistance in wheat breeding. Full article
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18 pages, 4021 KiB  
Article
Two B-Box Proteins, MaBBX20 and MaBBX51, Coordinate Light-Induced Anthocyanin Biosynthesis in Grape Hyacinth
by Han Zhang, Jiangyu Wang, Shuting Tian, Wenhui Hao and Lingjuan Du
Int. J. Mol. Sci. 2022, 23(10), 5678; https://doi.org/10.3390/ijms23105678 - 19 May 2022
Cited by 4 | Viewed by 1636
Abstract
Floral colour is an important agronomic trait that influences the commercial value of ornamental plants. Anthocyanins are a class of flavonoids and confer diverse colours, and elucidating the molecular mechanisms that regulate their pigmentation could facilitate artificial manipulation of flower colour in ornamental [...] Read more.
Floral colour is an important agronomic trait that influences the commercial value of ornamental plants. Anthocyanins are a class of flavonoids and confer diverse colours, and elucidating the molecular mechanisms that regulate their pigmentation could facilitate artificial manipulation of flower colour in ornamental plants. Here, we investigated the regulatory mechanism of light-induced anthocyanin biosynthesis during flower colouration in grape hyacinth (Muscari spp.). We studied the function of two B-box proteins, MaBBX20 and MaBBX51. The qPCR revealed that MaBBX20 and MaBBX51 were associated with light-induced anthocyanin biosynthesis. Both MaBBX20 and MaBBX51 are transcript factors and are specifically localised in the nucleus. Besides, overexpression of MaBBX20 in tobacco slightly increased the anthocyanin content of the petals, but reduced in MaBBX51 overexpression lines. The yeast one-hybrid assays indicated that MaBBX20 and MaBBX51 did not directly bind to the MaMybA or MaDFR promoters, but MaHY5 did. The BiFC assay revealed that MaBBX20 and MaBBX51 physically interact with MaHY5. A dual luciferase assay further confirmed that the MaBBX20–MaHY5 complex can strongly activate the MaMybA and MaDFR transcription in tobacco. Moreover, MaBBX51 hampered MaBBX20–MaHY5 complex formation and repressed MaMybA and MaDFR transcription by physically interacting with MaHY5 and MaBBX20. Overall, the results suggest that MaBBX20 positively regulates light-induced anthocyanin biosynthesis in grape hyacinth, whereas MaBBX51 is a negative regulator. Full article
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40 pages, 15887 KiB  
Review
Insecticidal Triterpenes in Meliaceae: Plant Species, Molecules, and Activities: Part II (Cipadessa, Melia)
by Meihong Lin, Xiaoyang Bi, Lijuan Zhou and Jiguang Huang
Int. J. Mol. Sci. 2022, 23(10), 5329; https://doi.org/10.3390/ijms23105329 - 10 May 2022
Cited by 11 | Viewed by 2275
Abstract
Plant-originated triterpenes are important insecticidal molecules. Research on the insecticidal activity of molecules from Meliaceae plants has always been a hotspot due to the molecules from this family showing a variety of insecticidal activities with diverse mechanisms of action. In this paper, we [...] Read more.
Plant-originated triterpenes are important insecticidal molecules. Research on the insecticidal activity of molecules from Meliaceae plants has always been a hotspot due to the molecules from this family showing a variety of insecticidal activities with diverse mechanisms of action. In this paper, we discussed 116 triterpenoid molecules with insecticidal activity from 22 plant species of five genera (Cipadessa, Entandrophragma, Guarea, Khaya, and Melia) in Meliaceae. In these genera, the insecticidal activities of plants from Entandrophragma and Melia have attracted substantial research attention in recent years. Specifically, the insecticidal activities of plants from Melia have been systemically studied for several decades. In total, the 116 insecticidal chemicals consisted of 34 ring-intact limonoids, 31 ring-seco limonoids, 48 rearranged limonoids, and 3 tetracyclic triterpenes. Furthermore, the 34 ring-intact limonoids included 29 trichilin-class chemicals, 3 azadirone-class chemicals, and 1 cedrelone-class and 1 havanensin-class limonoid. The 31 ring-seco limonoids consisted of 16 C-seco group chemicals, 8 B,D-seco group chemicals, 4 A,B-seco group chemicals, and 3 D-seco group chemicals. Furthermore, among the 48 rearranged limonoids, 46 were 2,30-linkage group chemicals and 2 were 10,11-linkage group chemicals. Specifically, the 46 chemicals belonging to the 2,30-linkage group could be subdivided into 24 mexicanolide-class chemicals and 22 phragmalin-class chemicals. Additionally, the three tetracyclic triterpenes were three protolimonoids. To sum up, 80 chemicals isolated from 19 plant species exhibited antifeedant activity toward 14 insect species; 18 chemicals isolated from 17 plant species exhibited poisonous activity toward 10 insect species; 16 chemicals isolated from 11 plant species possessed growth-regulatory activity toward 8 insect species. In particular, toosendanin was the most effective antifeedant and insect growth-regulatory agent. The antifeedant activity of toosendanin was significant. Owing to its high effect, toosendanin has been commercially applied. Three other molecules, 1,3-dicinnamoyl-11-hydroxymeliacarpin, 1-cinnamoyl-3-methacryl-11-hydroxymeliacarpin, and 1-cinnamoyl-3-acetyl-11-hydroxymeliacarpin, isolated from Meliaazedarach, exhibited a highly poisonous effect on Spodoptera littoralis; thus, they deserve further attention. Full article
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13 pages, 6383 KiB  
Review
Mechanisms Underlying Soybean Response to Phosphorus Deficiency through Integration of Omics Analysis
by Xiaohui Mo, Guoxuan Liu, Zeyu Zhang, Xing Lu, Cuiyue Liang and Jiang Tian
Int. J. Mol. Sci. 2022, 23(9), 4592; https://doi.org/10.3390/ijms23094592 - 21 Apr 2022
Cited by 13 | Viewed by 2788
Abstract
Low phosphorus (P) availability limits soybean growth and yield. A set of potential strategies for plant responses to P deficiency have been elucidated in the past decades, especially in model plants such as Arabidopsis thaliana and rice (Oryza sativa). Recently, substantial [...] Read more.
Low phosphorus (P) availability limits soybean growth and yield. A set of potential strategies for plant responses to P deficiency have been elucidated in the past decades, especially in model plants such as Arabidopsis thaliana and rice (Oryza sativa). Recently, substantial efforts focus on the mechanisms underlying P deficiency improvement in legume crops, especially in soybeans (Glycine max). This review summarizes recent advances in the morphological, metabolic, and molecular responses of soybean to phosphate (Pi) starvation through the combined analysis of transcriptomics, proteomics, and metabolomics. Furthermore, we highlight the functions of the key factors controlling root growth and P homeostasis, base on which, a P signaling network in soybean was subsequently presumed. This review also discusses current barriers and depicts perspectives in engineering soybean cultivars with high P efficiency. Full article
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20 pages, 6273 KiB  
Article
Multidimensional Gene Regulatory Landscape of Motor Organ Pulvinus in the Model Legume Medicago truncatula
by Quanzi Bai, Wenjing Yang, Guochen Qin, Baolin Zhao, Liangliang He, Xuan Zhang, Weiyue Zhao, Dian Zhou, Ye Liu, Yu Liu, Hua He, Million Tadege, Yan Xiong, Changning Liu and Jianghua Chen
Int. J. Mol. Sci. 2022, 23(8), 4439; https://doi.org/10.3390/ijms23084439 - 18 Apr 2022
Cited by 5 | Viewed by 5209
Abstract
Nyctinastic leaf movement of Fabaceae is driven by the tiny motor organ pulvinus located at the base of the leaf or leaflet. Despite the increased understanding of the essential role of ELONGATED PETIOLULE1 (ELP1)/PETIOLE LIKE PULVINUS (PLP) orthologs [...] Read more.
Nyctinastic leaf movement of Fabaceae is driven by the tiny motor organ pulvinus located at the base of the leaf or leaflet. Despite the increased understanding of the essential role of ELONGATED PETIOLULE1 (ELP1)/PETIOLE LIKE PULVINUS (PLP) orthologs in determining pulvinus identity in legumes, key regulatory components and molecular mechanisms underlying this movement remain largely unclear. Here, we used WT pulvinus and the equivalent tissue in the elp1 mutant to carry out transcriptome and proteome experiments. The omics data indicated that there are multiple cell biological processes altered at the gene expression and protein abundance level during the pulvinus development. In addition, comparative analysis of different leaf tissues provided clues to illuminate the possible common primordium between pulvinus and petiole, as well as the function of ELP1. Furthermore, the auxin pathway, cell wall composition and chloroplast distribution were altered in elp1 mutants, verifying their important roles in pulvinus development. This study provides a comprehensive insight into the motor organ of the model legume Medicago truncatula and further supplies a rich dataset to facilitate the identification of novel players involved in nyctinastic movement. Full article
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15 pages, 4331 KiB  
Article
Isolation and Functional Characterization of a LEAFY Gene in Mango (Mangifera indica L.)
by Yihan Wang, Haixia Yu, Xinhua He, Tingting Lu, Xing Huang and Cong Luo
Int. J. Mol. Sci. 2022, 23(7), 3974; https://doi.org/10.3390/ijms23073974 - 02 Apr 2022
Cited by 11 | Viewed by 2271
Abstract
LEAFY (LFY) plays an important role in the flowering process of plants, controlling flowering time and mediating floral meristem differentiation. Owing to its considerable importance, the mango LFY gene (MiLFY; GenBank accession no. HQ585988) was isolated, and its expression [...] Read more.
LEAFY (LFY) plays an important role in the flowering process of plants, controlling flowering time and mediating floral meristem differentiation. Owing to its considerable importance, the mango LFY gene (MiLFY; GenBank accession no. HQ585988) was isolated, and its expression pattern and function were characterized in the present study. The cDNA sequence of MiLFY was 1152 bp, and it encoded a 383 amino acid protein. MiLFY was expressed in all tested tissues and was highly expressed in flowers and buds. Temporal expression analysis showed that MiLFY expression was correlated with floral development stage, and two relative expression peaks were detected in the early stages of floral transition and floral organ differentiation. Moreover, 35S::GFP-MiLFY fusion protein was shown to be localized to the nucleus of cells. Overexpression of MiLFY in Arabidopsis promoted early flowering and the conversion of lateral meristems into terminal flowers. In addition, transgenic plants exhibited obvious morphological changes, such as differences in cauline leaf shape, and the number of lateral branches. When driven by the MiLFY promoter, GFP was highly expressed in leaves, floral organs, stems, and roots, during the flowering period. Exogenous gibberellin (GA3) treatment downregulated MiLFY promoter expression, but paclobutrazol (PPP333) upregulated it. Bimolecular fluorescence complementation (BiFC) assays showed that the MiLFY protein can interact with zinc-finger protein 4 (ZFP4) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (MiSOC1D). Taken together, these results indicate that MiLFY plays a pivotal role in controlling mango flowering, and that it is regulated by gibberellin and paclobutrazol. Full article
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20 pages, 9547 KiB  
Article
Transcriptome Analysis of Populus euphratica under Salt Treatment and PeERF1 Gene Enhances Salt Tolerance in Transgenic Populus alba × Populus glandulosa
by Xiao-Lan Ge, Lei Zhang, Jiu-Jun Du, Shuang-Shuang Wen, Guan-Zheng Qu and Jian-Jun Hu
Int. J. Mol. Sci. 2022, 23(7), 3727; https://doi.org/10.3390/ijms23073727 - 28 Mar 2022
Cited by 8 | Viewed by 2506
Abstract
Populus euphratica is mainly distributed in desert environments with dry and hot climate in summer and cold in winter. Compared with other poplars, P. euphratica is more resistant to salt stress. It is critical to investigate the transcriptome and molecular basis of salt [...] Read more.
Populus euphratica is mainly distributed in desert environments with dry and hot climate in summer and cold in winter. Compared with other poplars, P. euphratica is more resistant to salt stress. It is critical to investigate the transcriptome and molecular basis of salt tolerance in order to uncover stress-related genes. In this study, salt-tolerant treatment of P. euphratica resulted in an increase in osmo-regulatory substances and recovery of antioxidant enzymes. To improve the mining efficiency of candidate genes, the analysis combining both the transcriptome WGCNA and the former GWAS results was selected, and a range of key regulatory factors with salt resistance were found. The PeERF1 gene was highly connected in the turquoise modules with significant differences in salt stress traits, and the expression levels were significantly different in each treatment. For further functional verification of PeERF1, we obtained stable overexpression and dominant suppression transgenic lines by transforming into Populus alba × Populusglandulosa. The growth and physiological characteristics of the PeERF1 overexpressed plants were better than that of the wild type under salt stress. Transcriptome analysis of leaves of transgenic lines and WT revealed that highly enriched GO terms in DEGs were associated with stress responses, including abiotic stimuli responses, chemical responses, and oxidative stress responses. The result is helpful for in-depth analysis of the salt tolerance mechanism of poplar. This work provides important genes for poplar breeding with salt tolerance. Full article
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12 pages, 3866 KiB  
Article
Overexpression of SgDREB2C from Stylosanthes guianensis Leads to Increased Drought Tolerance in Transgenic Arabidopsis
by Yun Han, Leilei Xiang, Zhigang Song and Shaoyun Lu
Int. J. Mol. Sci. 2022, 23(7), 3520; https://doi.org/10.3390/ijms23073520 - 24 Mar 2022
Cited by 5 | Viewed by 1802
Abstract
Stylosanthes guianensis is an excellent forage legume in subtropical and tropical regions with drought tolerance, but little is known about its drought tolerance mechanism. Dehydration responsive element binding proteins (DREBs) are responsive to abiotic stresses. A SgDREB2C was cloned from S. guianensis, [...] Read more.
Stylosanthes guianensis is an excellent forage legume in subtropical and tropical regions with drought tolerance, but little is known about its drought tolerance mechanism. Dehydration responsive element binding proteins (DREBs) are responsive to abiotic stresses. A SgDREB2C was cloned from S. guianensis, while SgDREB2C protein was localized at nucleus. SgDREB2C transcript was induced by dehydration treatment. Transgenic Arabidopsis overexpressing SgDREB2C showed enhanced osmotic and drought tolerance with higher levels of relative germination rate, seedlings survival rate and Fv/Fm and lower levels of ion leakage compared with WT after osmotic and drought stress treatments. In addition, higher levels of superoxide dismutase (SOD) and ascorbate peroxidase (APX) activities and stress responsive gene (COR15A, COR47) transcripts were observed in transgenic Arabidopsis than in WT under drought stress. These results suggest that SgDREB2C regulated drought tolerance, which was associated with increased SOD and APX activities and stress-responsive gene expression under drought stress. Full article
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18 pages, 5619 KiB  
Article
Genome-Wide Identification, Classification, and Expression Analysis of the HD-Zip Transcription Factor Family in Apple (Malus domestica Borkh.)
by Kai Liu, Xiaolei Han, Zhaolin Liang, Jiadi Yan, Peihua Cong and Caixia Zhang
Int. J. Mol. Sci. 2022, 23(5), 2632; https://doi.org/10.3390/ijms23052632 - 27 Feb 2022
Cited by 4 | Viewed by 2327
Abstract
Homeodomain-leucine zipper (HD-Zip) family genes are considered to play an important role in plant growth and stress tolerance. However, a genome-wide analysis of HD-Zip genes in apples (Malus domestica Borkh.) has not been performed. We detected 48 MdHDZ genes in [...] Read more.
Homeodomain-leucine zipper (HD-Zip) family genes are considered to play an important role in plant growth and stress tolerance. However, a genome-wide analysis of HD-Zip genes in apples (Malus domestica Borkh.) has not been performed. We detected 48 MdHDZ genes in the apple genome, and categorized them into three subfamilies on the basis of phylogenetic analysis. The chromosomal locations, gene/protein structures, and physiological and biochemical properties of these genes were analyzed. Synteny analysis revealed that segmental duplications were key in the expansion of the apple HD-Zip family. According to an analysis of cis-regulatory elements and tissue-specific expression patterns, MdHDZ genes may be widely involved in the regulation of apple growth and tolerance to environmental stresses. Furthermore, the transcript levels of apple HD-Zip I and II genes were up-regulated in response to fungal treatments. Expression of apple HD-Zip Ⅲ genes was enhanced during adventitious bud regeneration. This suggested possible roles of these genes in regulating the apple response to fungal infection, as well as adventitious bud regeneration. The current results may help us to better understand the evolution and function of apple HD-ZIP genes, and thus facilitate further research on plant resistance to fungal infection and in vitro regeneration. Full article
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15 pages, 2861 KiB  
Article
CabHLH79 Acts Upstream of CaNAC035 to Regulate Cold Stress in Pepper
by Ziyu Wang, Yumeng Zhang, Huifang Hu, Lang Chen, Huafeng Zhang and Rugang Chen
Int. J. Mol. Sci. 2022, 23(5), 2537; https://doi.org/10.3390/ijms23052537 - 25 Feb 2022
Cited by 9 | Viewed by 2110
Abstract
Cold stress is one of the main restricting factors affecting plant growth and agricultural production. Complex cold signaling pathways induce the expression of hundreds of cold-sensitive genes. The NAC transcription factor CaNAC035 has previously been reported to significantly influence the response of pepper [...] Read more.
Cold stress is one of the main restricting factors affecting plant growth and agricultural production. Complex cold signaling pathways induce the expression of hundreds of cold-sensitive genes. The NAC transcription factor CaNAC035 has previously been reported to significantly influence the response of pepper to cold stress. Here, using Yeast one-hybrid (Y1H) library screened to search for other relevant molecular factors, we identified that CabHLH79 directly binds to the CaNAC035 promoter. Different basic helix–loop–helix (bHLH) transcription factors (TFs) in plants significantly respond to multiple plant stresses, but the mechanism of bHLHs in the cold tolerance of pepper is still unclear. This study investigated the functional characterization of CabHLH79 in the regulation of cold resistance in pepper. Down-regulation of CabHLH79 in pepper by virus-induced gene silencing (VIGS) increased its sensitivity to low temperature, whereas overexpression of CabHLH79 in pepper or Arabidopsis enhanced cold resistance. Compared with control plants, VIGS mediated of CabHLH79 had lower enzyme activity and related gene expression levels, accompanied by higher reactive oxygen species (ROS) accumulation, relative electrolyte leakage (REL), and malondialdehyde accumulation (MDA) contents. Transient overexpression of CabHLH79 pepper positively regulated cold stress response genes and ROS genes, which reduced REL and MDA contents. Similarly, ectopic expression of CabHLH79 in Arabidopsis showed less ROS accumulation, and higher enzymes activities and expression levels. These results indicated that CabHLH79 enhanced cold tolerance by enhancing the expression of ROS-related and other cold stress tolerance-related genes. Taken together, our results showed a multifaceted module of bHLH79-NAC035 in the cold stress of pepper. Full article
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15 pages, 2632 KiB  
Article
Functional Redundancy of FLOWERING LOCUS T 3b in Soybean Flowering Time Regulation
by Qiang Su, Li Chen, Yupeng Cai, Yingying Chen, Shan Yuan, Min Li, Jialing Zhang, Shi Sun, Tianfu Han and Wensheng Hou
Int. J. Mol. Sci. 2022, 23(5), 2497; https://doi.org/10.3390/ijms23052497 - 24 Feb 2022
Cited by 8 | Viewed by 2011
Abstract
Photoperiodic flowering is an important agronomic trait that determines adaptability and yield in soybean and is strongly influenced by FLOWERING LOCUS T (FT) genes. Due to the presence of multiple FT homologs in the genome, their functions in soybean are not [...] Read more.
Photoperiodic flowering is an important agronomic trait that determines adaptability and yield in soybean and is strongly influenced by FLOWERING LOCUS T (FT) genes. Due to the presence of multiple FT homologs in the genome, their functions in soybean are not fully understood. Here, we show that GmFT3b exhibits functional redundancy in regulating soybean photoperiodic flowering. Bioinformatic analysis revealed that GmFT3b is a typical floral inducer FT homolog and that the protein is localized to the nucleus. Moreover, GmFT3b expression was induced by photoperiod and circadian rhythm and was more responsive to long-day (LD) conditions. We generated a homozygous ft3b knockout and three GmFT3b-overexpressing soybean lines for evaluation under different photoperiods. There were no significant differences in flowering time between the wild-type, the GmFT3b overexpressors, and the ft3b knockouts under natural long-day, short-day, or LD conditions. Although the downstream flowering-related genes GmFUL1 (a, b), GmAP1d, and GmLFY1 were slightly down-regulated in ft3b plants, the floral inducers GmFT5a and GmFT5b were highly expressed, indicating potential compensation for the loss of GmFT3b. We suggest that GmFT3b acts redundantly in flowering time regulation and may be compensated by other FT homologs in soybean. Full article
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15 pages, 6666 KiB  
Article
Combined BSA-Seq Based Mapping and RNA-Seq Profiling Reveal Candidate Genes Associated with Plant Architecture in Brassica napus
by Shenhua Ye, Lei Yan, Xiaowei Ma, Yanping Chen, Lumei Wu, Tiantian Ma, Lun Zhao, Bin Yi, Chaozhi Ma, Jinxing Tu, Jinxiong Shen, Tingdong Fu and Jing Wen
Int. J. Mol. Sci. 2022, 23(5), 2472; https://doi.org/10.3390/ijms23052472 - 23 Feb 2022
Cited by 17 | Viewed by 3042
Abstract
Plant architecture involves important agronomic traits affecting crop yield, resistance to lodging, and fitness for mechanical harvesting in Brassica napus. Breeding high-yield varieties with plant architecture suitable for mechanical harvesting is the main goal of rapeseed breeders. Here, we report an accession [...] Read more.
Plant architecture involves important agronomic traits affecting crop yield, resistance to lodging, and fitness for mechanical harvesting in Brassica napus. Breeding high-yield varieties with plant architecture suitable for mechanical harvesting is the main goal of rapeseed breeders. Here, we report an accession of B. napus (4942C-5), which has a dwarf and compact plant architecture in contrast to cultivated varieties. A BC8 population was constructed by crossing a normal plant architecture line, 8008, with the recurrent parent 4942C-5. To investigate the molecular mechanisms underlying plant architecture, we performed phytohormone profiling, bulk segregant analysis sequencing (BSA-Seq), and RNA sequencing (RNA-Seq) in BC8 plants with contrasting plant architecture. Genetic analysis indicated the plant architecture traits of 4942C-5 were recessive traits controlled by multiple genes. The content of auxin (IAA), gibberellin (GA), and abscisic acid (ABA) differed significantly between plants with contrasting plant architecture in the BC8 population. Based on BSA-Seq analysis, we identified five candidate intervals on chromosome A01, namely those of 0 to 6.33 Mb, 6.45 to 6.48 Mb, 6.51 to 6.53 Mb, 6.77 to 6.79 Mb, and 7 to 7.01 Mb regions. The RNA-Seq analysis revealed a total of 4378 differentially expressed genes (DEGs), of which 2801 were up-regulated and 1577 were down-regulated. There, further analysis showed that genes involved in plant hormone biosynthesis and signal transduction, cell structure, and the phenylpropanoid pathway might play a pivotal role in the morphogenesis of plant architecture. Association analysis of BSA-Seq and RNA-Seq suggested that seven DEGs involved in plant hormone signal transduction and a WUSCHEL-related homeobox (WOX) gene (BnaA01g01910D) might be candidate genes responsible for the dwarf and compact phenotype in 4942C-5. These findings provide a foundation for elucidating the mechanisms underlying rapeseed plant architecture and should contribute to breed new varieties suitable for mechanization. Full article
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17 pages, 3552 KiB  
Article
Global N6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress
by Yinxiao Wang, Fengping Du, Yingbo Li, Juan Wang, Xiuqin Zhao, Zhikang Li, Jianlong Xu, Wensheng Wang and Binying Fu
Int. J. Mol. Sci. 2022, 23(4), 2091; https://doi.org/10.3390/ijms23042091 - 14 Feb 2022
Cited by 13 | Viewed by 2438
Abstract
N6-methyladenosine (m6A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m6A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation [...] Read more.
N6-methyladenosine (m6A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m6A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m6A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m6A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m6A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m6A sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased m6A methylation levels only in the shoots or roots under salt stress, implying m6A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m6A modifications and gene expression changes revealed that m6A changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of m6A modifications on rice salt tolerance. Full article
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14 pages, 2651 KiB  
Article
Identification of the Regulatory Genes of UV-B-Induced Anthocyanin Biosynthesis in Pepper Fruit
by Yihao Wang, Sujun Liu, Haoran Wang, Yingxue Zhang, Wenjie Li, Jinkui Liu, Qing Cheng, Liang Sun and Huolin Shen
Int. J. Mol. Sci. 2022, 23(4), 1960; https://doi.org/10.3390/ijms23041960 - 10 Feb 2022
Cited by 13 | Viewed by 2389
Abstract
Fruit peels of certain pepper (Capsicum annum L.) varieties accumulate a large amount of anthocyanins and exhibit purple color under medium-wave ultraviolet (UV-B) conditions, which severely impacts the commodity value of peppers. However, the regulatory mechanism of the above process has not [...] Read more.
Fruit peels of certain pepper (Capsicum annum L.) varieties accumulate a large amount of anthocyanins and exhibit purple color under medium-wave ultraviolet (UV-B) conditions, which severely impacts the commodity value of peppers. However, the regulatory mechanism of the above process has not been well studied so far. To explore which key genes are involved in this regulatory mechanism, pepper variety 19Q6100, the fruit peels of which turn purple under UV-B conditions, was investigated in this study. Transcription factors with expression levels significantly impacted by UV-B were identified by RNA-seq. Those genes may be involved in the regulation of UV-B-induced anthocyanin biosynthesis. Yeast one-hybrid results revealed that seven transcription factors, CabHLH143, CaMYB113, CabHLH137, CaMYBG, CaWRKY41, CaWRKY44 and CaWRKY53 directly bound to the putative promotor regions of the structural genes in the anthocyanin biosynthesis pathway. CaMYB113 was found to interact with CabHLH143 and CaHY5 by yeast two-hybrid assay, and those three genes may participate collaboratively in UV-B-induced anthocyanin biosynthesis in pepper fruit. Virus-induced gene silencing (VIGS) indicated that fruit peels of CaMYB113-silenced plants were unable to turn purple under UV-B conditions. These findings could deepen our understanding of UV-B-induced anthocyanin biosynthesis in pepper. Full article
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15 pages, 5457 KiB  
Article
Screening of Differentially Expressed Genes and Localization Analysis of Female Gametophyte at the Free Nuclear Mitosis Stage in Pinus tabuliformis Carr.
by Zaixin Gong, Hailin Hu, Li Xu, Yuanyuan Zhao and Caixia Zheng
Int. J. Mol. Sci. 2022, 23(3), 1915; https://doi.org/10.3390/ijms23031915 - 08 Feb 2022
Viewed by 1777
Abstract
Female sterility is a common phenomenon in the plant world, and systematic research has not been carried out in gymnosperms. In this study, the ovules of No. 28 sterile line and No. 15 fertile line Pinus tabuliformis were used as materials, and a [...] Read more.
Female sterility is a common phenomenon in the plant world, and systematic research has not been carried out in gymnosperms. In this study, the ovules of No. 28 sterile line and No. 15 fertile line Pinus tabuliformis were used as materials, and a total of 18 cDNA libraries were sequenced by the HiSeqTM 4000 platform to analyze the differentially expressed genes (DEGs) and simple sequence repeats (SSRs) between the two lines. In addition, this study further analyzed the DEGs involved in the signal transduction of plant hormones, revealing that the signal pathways related to auxin, cytokinin, and gibberellin were blocked in the sterile ovule. Additionally, real-time fluorescent quantitative PCR verified that the expression trend of DEGs related to plant hormones was consistent with the results of high-throughput sequencing. Frozen sections and fluorescence in situ hybridization (FISH) were used to study the temporal and spatial expression patterns of PtRab in the ovules of P. tabuliformis. It was found that PtRab was significantly expressed in female gametophytes and rarely expressed in the surrounding diploid tissues. This study further explained the molecular regulation mechanism of female sterility in P. tabuliformis, preliminarily mining the key factors of ovule abortion in gymnosperms at the transcriptional level. Full article
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20 pages, 4932 KiB  
Article
Genome-Wide Analysis of BpYABs and Function Identification Involving in the Leaf and Silique Development in Transgenic Arabidopsis
by Feng Tang, Dan Zhang, Naizhi Chen, Xianjun Peng and Shihua Shen
Int. J. Mol. Sci. 2022, 23(3), 1670; https://doi.org/10.3390/ijms23031670 - 31 Jan 2022
Cited by 1 | Viewed by 1982
Abstract
YABs play an important role in the leaf development of the paper mulberry (Broussonetia papyrifera) and of the heterophylly. Thus, we investigated the function of BpYABs. Gene cloning, phylogenetic analysis, motif identification, subcellular localization, transactivation activity assay, qRT-PCR, in situ hybridization, [...] Read more.
YABs play an important role in the leaf development of the paper mulberry (Broussonetia papyrifera) and of the heterophylly. Thus, we investigated the function of BpYABs. Gene cloning, phylogenetic analysis, motif identification, subcellular localization, transactivation activity assay, qRT-PCR, in situ hybridization, and ectopic expression were used in our study. Six BpYABs were isolated, and four of them had transcriptional activity. BpYAB1, BpYAB3, BpYAB4, and BpYAB5 were localized to the nucleus. BpYAB1 was only expressed in the flower, while BpYAB6 was not expressed in any detected tissues; the four remaining BpYABs were expressed in the bud, leaf and flower, and their expression level decreased with leaf development. Further in situ hybridization showed that BpYAB3 and BpYAB5 were expressed in the vascular tissues and lamina, but neither showed the adaxial–abaxial polarity distribution pattern in the mature leaf lamina. Ectopic expression of BpYAB2, BpYAB3, BpYAB4 and BpYAB5 induced increased expression of AtWOX1 and caused the leaf of Arabidopsis to become smaller and curl downwards. Ectopic expression also led to shorter siliques and smaller seeds, but not for BpYAB5. These results suggest that BpYABs have functional divergency and redundancy in regulating leaf and silique development. Full article
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15 pages, 17046 KiB  
Article
Fine Mapping and Candidate Gene Prediction of Tuber Shape Controlling Ro Locus Based on Integrating Genetic and Transcriptomic Analyses in Potato
by Guiyan Fan, Qianru Wang, Jianfei Xu, Na Chen, Wenwen Zhu, Shaoguang Duan, Xiaohui Yang, Walter S. De Jong, Yangdong Guo, Liping Jin and Guangcun Li
Int. J. Mol. Sci. 2022, 23(3), 1470; https://doi.org/10.3390/ijms23031470 - 27 Jan 2022
Cited by 6 | Viewed by 2202
Abstract
Tuber shape is one of the most important quality traits in potato appearance. Since poor or irregular shape results in higher costs for processing and influences the consumers’ willingness to purchase, breeding for shape uniformity and shallow eye depth is highly important. Previous [...] Read more.
Tuber shape is one of the most important quality traits in potato appearance. Since poor or irregular shape results in higher costs for processing and influences the consumers’ willingness to purchase, breeding for shape uniformity and shallow eye depth is highly important. Previous studies showed that the major round tuber shape controlling locus, the Ro locus, is located on chromosome 10. However, fine mapping and cloning of tuber shape genes have not been reported. In this study, the analyses of tissue sectioning and transcriptome sequencing showed that the developmental differences between round and elongated tuber shapes begin as early as the hook stage of the stolon. To fine map tuber shape genes, a high-density genetic linkage map of the Ro region on chromosome 10 based on a diploid segregating population was constructed. The total length of the genetic linkage map was 25.8 cM and the average marker interval was 1.98 cM. Combined with phenotypic data collected from 2014 to 2017, one major quantitative trait locus (QTL) for tuber shape was identified, which explained 61.7–72.9% of the tuber shape variation. Through the results of genotyping and phenotypic investigation of recombinant individuals, Ro was fine mapped in a 193.43 kb interval, which contained 18 genes. Five candidate genes were preliminarily predicted based on tissue sections and transcriptome sequencing. This study provides an important basis for cloning Ro gene(s). Full article
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11 pages, 2409 KiB  
Article
The Regulation of Nitrate Reductases in Response to Abiotic Stress in Arabidopsis
by Xianli Tang, Yang Peng, Zheng Li, Hongwei Guo, Xinli Xia, Bosheng Li and Weilun Yin
Int. J. Mol. Sci. 2022, 23(3), 1202; https://doi.org/10.3390/ijms23031202 - 21 Jan 2022
Cited by 13 | Viewed by 2498
Abstract
The two homologous genes, NIA1 and NIA2, encode nitrate reductases in Arabidopsis, which govern the reduction of nitrate to nitrite. This step is the rate-limiting step of the nitrate assimilation and utilization. Therefore, the regulation of NIA1 and NIA2 is important [...] Read more.
The two homologous genes, NIA1 and NIA2, encode nitrate reductases in Arabidopsis, which govern the reduction of nitrate to nitrite. This step is the rate-limiting step of the nitrate assimilation and utilization. Therefore, the regulation of NIA1 and NIA2 is important for plant development and growth. Although they are similar in sequence and structure, their regulations are different. Genetic analysis uncovers that NIA1, rather than NIA2, plays a predominant role in adopting to ABA stress. Although both long-term stress conditions can cause an improvement in NIA1 levels, a decrease in NIA1 levels under short-term treatments seems to be necessary for plants to switch from the growth status into the adopting status. Interestingly, the downregulation of the NR is distinct under different stress conditions. Under ABA treatment, the NR proteins are degraded via a 26S-proteasome dependent manner, while the transcriptional regulation is the main manner to rapidly reduce the NIA1 levels under nitrogen deficiency and NaCl stress conditions. These results indicate that under stress conditions, the regulation of NIA1 is complex, and it plays a key role in regulating the balance between growth and adaptation. Full article
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16 pages, 11917 KiB  
Article
Co-Silencing of the Voltage-Gated Calcium Channel β Subunit and High-Voltage Activated α1 Subunit by dsRNA Soaking Resulted in Enhanced Defects in Locomotion, Stylet Thrusting, Chemotaxis, Protein Secretion, and Reproduction in Ditylenchus destructor
by Mingwei An, Xueling Chen, Zhuhong Yang, Jianyu Zhou, Shan Ye and Zhong Ding
Int. J. Mol. Sci. 2022, 23(2), 784; https://doi.org/10.3390/ijms23020784 - 11 Jan 2022
Cited by 2 | Viewed by 1553
Abstract
The voltage-gated calcium channel (VGCC) β subunit (Cavβ) protein is a kind of cytosolic auxiliary subunit that plays an important role in regulating the surface expression and gating characteristics of high-voltage-activated (HVA) calcium channels. Ditylenchus destructor is an important plant-parasitic nematode. [...] Read more.
The voltage-gated calcium channel (VGCC) β subunit (Cavβ) protein is a kind of cytosolic auxiliary subunit that plays an important role in regulating the surface expression and gating characteristics of high-voltage-activated (HVA) calcium channels. Ditylenchus destructor is an important plant-parasitic nematode. In the present study, the putative Cavβ subunit gene of D. destructor, namely, DdCavβ, was subjected to molecular characterization. In situ hybridization assays showed that DdCavβ was expressed in all nematode tissues. Transcriptional analyses showed that DdCavβ was expressed during each developmental stage of D. destructor, and the highest expression level was recorded in the third-stage juveniles. The crucial role of DdCavβ was verified by dsRNA soaking-mediated RNA interference (RNAi). Silencing of DdCavβ or HVA Cavα1 alone and co-silencing of the DdCavβ and HVA Cavα1 genes resulted in defective locomotion, stylet thrusting, chemotaxis, protein secretion and reproduction in D. destructor. Co-silencing of the HVA Cavα1 and Cavβ subunits showed stronger interference effects than single-gene silencing. This study provides insights for further study of VGCCs in plant-parasitic nematodes. Full article
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20 pages, 6946 KiB  
Article
Bidirectional lncRNA Transfer between Cuscuta Parasites and Their Host Plant
by Yuguo Wu, Dong Luo, Longfa Fang, Qiang Zhou, Wenxian Liu and Zhipeng Liu
Int. J. Mol. Sci. 2022, 23(1), 561; https://doi.org/10.3390/ijms23010561 - 05 Jan 2022
Cited by 7 | Viewed by 2638
Abstract
Dodder species (Cuscuta spp.) are holoparasites that have extensive material exchange with their host plants through vascular connections. Recent studies on cross-species transfer have provided breakthrough insights, but little is known about the interaction mechanisms of the inter-plant mobile substances in parasitic [...] Read more.
Dodder species (Cuscuta spp.) are holoparasites that have extensive material exchange with their host plants through vascular connections. Recent studies on cross-species transfer have provided breakthrough insights, but little is known about the interaction mechanisms of the inter-plant mobile substances in parasitic systems. We sequenced the transcriptomes of dodder growing on soybean hosts to characterize the long non-coding RNA (lncRNA) transfer between the two species, and found that lncRNAs can move in high numbers (365 dodder lncRNAs and 14 soybean lncRNAs) in a bidirectional manner. Reverse transcription-polymerase chain reaction further confirmed that individual lncRNAs were trafficked in the dodder–soybean parasitic system. To reveal the potential functions of mobile transcripts, the Gene Ontology terms of mobile lncRNA target genes were predicted, and mobile dodder target genes were found to be mainly enriched in “metabolic process”, “catalytic activity”, “signaling”, and “response to stimulus” categories, whereas mobile soybean target genes were enriched in organelle-related categories, indicating that specific mobile lncRNAs may be important in regulating dodder parasitism. Our findings reveal that lncRNAs are transferred between dodder and its host soybean plants, which may act as critical regulators to coordinate the host–dodder interaction at the whole parasitic level. Full article
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2021

Jump to: 2022

18 pages, 3337 KiB  
Article
Functions of COP1/SPA E3 Ubiquitin Ligase Mediated by MpCRY in the Liverwort Marchantia polymorpha under Blue Light
by Li Zhang, Tianhong Li, Shengzhong Su, Hao Peng, Sudi Li, Ke Li, Luyao Ji, Yaoyun Xing, Junchuan Zhang, Xinglin Du, Mingdi Bian, Yuying Liao, Zhenming Yang and Zecheng Zuo
Int. J. Mol. Sci. 2022, 23(1), 158; https://doi.org/10.3390/ijms23010158 - 23 Dec 2021
Cited by 3 | Viewed by 2817
Abstract
COP1/SPA1 complex in Arabidopsis inhibits photomorphogenesis through the ubiquitination of multiple photo-responsive transcription factors in darkness, but such inhibiting function of COP1/SPA1 complex would be suppressed by cryptochromes in blue light. Extensive studies have been conducted on these mechanisms in Arabidopsis whereas little [...] Read more.
COP1/SPA1 complex in Arabidopsis inhibits photomorphogenesis through the ubiquitination of multiple photo-responsive transcription factors in darkness, but such inhibiting function of COP1/SPA1 complex would be suppressed by cryptochromes in blue light. Extensive studies have been conducted on these mechanisms in Arabidopsis whereas little attention has been focused on whether another branch of land plants bryophyte utilizes this blue-light regulatory pathway. To study this problem, we conducted a study in the liverwort Marchantia polymorpha and obtained a MpSPA knock-out mutant, in which Mpspa exhibits the phenotype of an increased percentage of individuals with asymmetrical thallus growth, similar to MpCRY knock-out mutant. We also verified interactions of MpSPA with MpCRY (in a blue light-independent way) and with MpCOP1. Concomitantly, both MpSPA and MpCOP1 could interact with MpHY5, and MpSPA can promote MpCOP1 to ubiquitinate MpHY5 but MpCRY does not regulate the ubiquitination of MpHY5 by MpCOP1/MpSPA complex. These data suggest that COP1/SPA ubiquitinating HY5 is conserved in Marchantia polymorpha, but dissimilar to CRY in Arabidopsis, MpCRY is not an inhibitor of this process under blue light. Full article
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13 pages, 5507 KiB  
Article
Transcriptome Analysis of Salt Stress in Hibiscus hamabo Sieb. et Zucc Based on Pacbio Full-Length Transcriptome Sequencing
by Longjie Ni, Zhiquan Wang, Xiangdong Liu, Shuting Wu, Jianfeng Hua, Yunlong Yin, Huogen Li and Chunsun Gu
Int. J. Mol. Sci. 2022, 23(1), 138; https://doi.org/10.3390/ijms23010138 - 23 Dec 2021
Cited by 5 | Viewed by 2803
Abstract
Hibiscus hamabo Sieb. et Zucc is an important semi-mangrove plant with great morphological features and strong salt resistance. In this study, by combining single molecule real time and next-generation sequencing technologies, we explored the transcriptomic changes in the roots of salt stressed H [...] Read more.
Hibiscus hamabo Sieb. et Zucc is an important semi-mangrove plant with great morphological features and strong salt resistance. In this study, by combining single molecule real time and next-generation sequencing technologies, we explored the transcriptomic changes in the roots of salt stressed H. hamabo. A total of 94,562 unigenes were obtained by clustering the same isoforms using the PacBio RSII platform, and 2269 differentially expressed genes were obtained under salt stress using the Illumina platform. There were 519 differentially expressed genes co-expressed at each treatment time point under salt stress, and these genes were found to be enriched in ion signal transduction and plant hormone signal transduction. We used Arabidopsis thaliana (L.) Heynh. transformation to confirm the function of the HhWRKY79 gene and discovered that overexpression enhanced salt tolerance. The full-length transcripts generated in this study provide a full characterization of the transcriptome of H. hamabo and may be useful in mining new salt stress-related genes specific to this species, while facilitating the understanding of the salt tolerance mechanisms. Full article
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20 pages, 5902 KiB  
Article
Genome-Wide Analysis of the Soybean Calmodulin-Binding Protein 60 Family and Identification of GmCBP60A-1 Responses to Drought and Salt Stresses
by Qian Yu, Ya-Li Liu, Guo-Zhong Sun, Yuan-Xia Liu, Jun Chen, Yong-Bin Zhou, Ming Chen, You-Zhi Ma, Zhao-Shi Xu and Jin-Hao Lan
Int. J. Mol. Sci. 2021, 22(24), 13501; https://doi.org/10.3390/ijms222413501 - 16 Dec 2021
Cited by 12 | Viewed by 2589
Abstract
Calmodulin-binding protein 60 (CBP60) members constitute a plant-specific protein family that plays an important role in plant growth and development. In the soybean genome, nineteen CBP60 members were identified and analyzed for their corresponding sequences and structures to explore their functions. Among GmCBP60A-1, [...] Read more.
Calmodulin-binding protein 60 (CBP60) members constitute a plant-specific protein family that plays an important role in plant growth and development. In the soybean genome, nineteen CBP60 members were identified and analyzed for their corresponding sequences and structures to explore their functions. Among GmCBP60A-1, which primarily locates in the cytomembrane, was significantly induced by drought and salt stresses. The overexpression of GmCBP60A-1 enhanced drought and salt tolerance in Arabidopsis, which showed better state in the germination of seeds and the root growth of seedlings. In the soybean hairy roots experiment, the overexpression of GmCBP60A-1 increased proline content, lowered water loss rate and malondialdehyde (MDA) content, all of which likely enhanced the drought and salt tolerance of soybean seedlings. Under stress conditions, drought and salt response-related genes showed significant differences in expression in hairy root soybean plants of GmCBP60A-1-overexpressing and hairy root soybean plants of RNAi. The present study identified GmCBP60A-1 as an important gene in response to salt and drought stresses based on the functional analysis of this gene and its potential underlying mechanisms in soybean stress-tolerance. Full article
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15 pages, 24769 KiB  
Article
Identification of Co-Expressed Genes Related to Theacrine Synthesis in Tea Flowers at Different Developmental Stages
by Xiaomin Chen, Shuxian Shao, Ruxing Yang, Mengya Gu, Pengjie Wang, Feng Zhao and Naixing Ye
Int. J. Mol. Sci. 2021, 22(24), 13394; https://doi.org/10.3390/ijms222413394 - 13 Dec 2021
Cited by 8 | Viewed by 2254
Abstract
Jiaocheng kucha is the first reported tea germplasm resource which contains theacrine founded in Fujian Province. Currently, the anabolic mechanism of theacrine within tea leaves is clear, but there are few studies focused on its flowers. In order to further explore the mechanism [...] Read more.
Jiaocheng kucha is the first reported tea germplasm resource which contains theacrine founded in Fujian Province. Currently, the anabolic mechanism of theacrine within tea leaves is clear, but there are few studies focused on its flowers. In order to further explore the mechanism of theacrine synthesis and related genes in flowers, current study applied Jiaocheng kucha flowers (JC) as test materials and Fuding Dabaicha flowers (FD) as control materials to make transcriptome sequencing, and determination of purine alkaloid content in three different developmental periods (flower bud stage, whitening stage and full opening stage). The results showed that the flower in all stages of JC contained theacrine. The theacrine in the flower bud stage was significantly higher than in the other stages. The differentially expressed genes (DEGs) at three different developmental stages were screened from the transcriptome data, and were in a total of 5642, 8640 and 8465. These DEGs related to the synthesis of theacrine were primarily annotated to the pathways of purine alkaloids. Among them, the number of DEGs in xanthine synthesis pathway was the largest and upregulated in JC, while it was the smallest in caffeine synthesis pathway and downregulated in JC. Further weighted gene co-expression network (WGCNA) indicated that ADSL (CsTGY03G0002327), ADSL (CsTGY09G0001824) and UAZ (CsTGY06G0002694) may be a hub gene for the regulation of theacrine metabolism in JC. Our results will contribute to the identification of candidate genes related to the synthesis of theacrine in tea flowers, and explore the molecular mechanism of theacrine synthesis in JC at different developmental stages. Full article
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17 pages, 4305 KiB  
Article
Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar
by Xuechun Wang, Nan Chao, Aijing Zhang, Jiaqi Kang, Xiangning Jiang and Ying Gai
Int. J. Mol. Sci. 2021, 22(24), 13366; https://doi.org/10.3390/ijms222413366 - 13 Dec 2021
Cited by 6 | Viewed by 2035
Abstract
Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We [...] Read more.
Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus. Full article
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18 pages, 2497 KiB  
Review
The Flavonoid Biosynthesis Network in Plants
by Weixin Liu, Yi Feng, Suhang Yu, Zhengqi Fan, Xinlei Li, Jiyuan Li and Hengfu Yin
Int. J. Mol. Sci. 2021, 22(23), 12824; https://doi.org/10.3390/ijms222312824 - 26 Nov 2021
Cited by 252 | Viewed by 14594
Abstract
Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are [...] Read more.
Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses. Full article
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21 pages, 3616 KiB  
Article
High-Throughput and Accurate Determination of Transgene Copy Number and Zygosity in Transgenic Maize: From DNA Extraction to Data Analysis
by Fang Liu, Jinkui Cheng, Xuhua Liu and Xi-Qing Wang
Int. J. Mol. Sci. 2021, 22(22), 12487; https://doi.org/10.3390/ijms222212487 - 19 Nov 2021
Cited by 3 | Viewed by 2095
Abstract
It is vital to develop high-throughput methods to determine transgene copy numbers initially and zygosity during subsequent breeding. In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were [...] Read more.
It is vital to develop high-throughput methods to determine transgene copy numbers initially and zygosity during subsequent breeding. In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were observed. These SNPs significantly increased the PCR efficiency, while the newly developed hmg gene assay (hmg-taq-F2/R2) excluding these SNPs reduced the efficiency into normal ranges. The TaqMan amplification efficiency of bar and hmg with newly developed primers was calculated as 0.993 and 1.000, respectively. The inter-assay coefficient of variation (CV) values for the bar and hmg genes varied from 1.18 to 2.94%. The copy numbers of the transgene bar using new TaqMan assays were identical to those using dPCR. Significantly, the precision of one repetition reached 96.7% of that of three repetitions of single-copy plants analyzed by simple random sampling, and the actual accuracy reached 95.8%, confirmed by T1 and T2 progeny. With the high-throughput DNA extraction and automated data analysis procedures developed in this study, nearly 2700 samples could be analyzed within eight hours by two persons. The combined results suggested that the new hmg gene assay developed here could be a universal maize reference gene system, and the new assay has high throughput and high accuracy for large-scale screening of maize varieties around the world. Full article
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21 pages, 8730 KiB  
Article
Garlic Volatile Diallyl Disulfide Induced Cucumber Resistance to Downy Mildew
by Fan Yang, Hui Wang, Chengchen Zhi, Birong Chen, Yujie Zheng, Lijun Qiao, Jingcao Gao, Yupeng Pan and Zhihui Cheng
Int. J. Mol. Sci. 2021, 22(22), 12328; https://doi.org/10.3390/ijms222212328 - 15 Nov 2021
Cited by 7 | Viewed by 2241
Abstract
Allicin compositions in garlic are used widely as fungicides in modern agriculture, in which diallyl disulfide (DADS) is a major compound. Downy mildew, caused by Pseudoperonospora cubensis (P. cubensis), is one of the most destructive diseases and causes severe yield losses [...] Read more.
Allicin compositions in garlic are used widely as fungicides in modern agriculture, in which diallyl disulfide (DADS) is a major compound. Downy mildew, caused by Pseudoperonospora cubensis (P. cubensis), is one of the most destructive diseases and causes severe yield losses in cucumbers. To explore the potential mechanism of DADS-induced cucumber resistance to downy mildew, cucumber seedlings were treated with DADS and then inoculated with P. cubensis at a 10-day interval. Symptom observation showed that DADS significantly induced cucumber resistance to downy mildew. Furthermore, both lignin and H2O2 were significantly increased by DADS treatment to responding P. cubensis infection. Simultaneously, the enzyme activities of peroxidase (POD) in DADS-treated seedlings were significantly promoted. Meanwhile, both the auxin (IAA) and salicylic acid (SA) contents were increased, and their related differentially expressed genes (DEGs) were up-regulated when treated with DADS. Transcriptome profiling showed that many DEGs were involved in the biological processes of defense responses, in which DEGs on the pathways of ‘phenylpropanoid biosynthesis’, ‘phenylalanine metabolism’, ‘MAPK signaling’, and ‘plant hormone signal transduction’ were significantly up-regulated in DADS-treated cucumbers uninoculated with the pathogen. Based on the results of several physiological indices and transcriptomes, a potential molecular mechanism of DADS-induced cucumber resistance to downy mildew was proposed and discussed. The results of this study might give new insight into the exploration of the induced resistance mechanism of cucumber to downy mildew and provide useful information for the subsequent mining of resistance genes in cucumber. Full article
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17 pages, 4142 KiB  
Article
Silencing a Simple Extracellular Leucine-Rich Repeat Gene OsI-BAK1 Enhances the Resistance of Rice to Brown Planthopper Nilaparvata lugens
by Miaofen Ye, Peng Kuai, Shuting Chen, Na Lin, Meng Ye, Lingfei Hu and Yonggen Lou
Int. J. Mol. Sci. 2021, 22(22), 12182; https://doi.org/10.3390/ijms222212182 - 10 Nov 2021
Cited by 2 | Viewed by 2100
Abstract
Many plant proteins with extracellular leucine-rich repeat (eLRR) domains play an important role in plant immunity. However, the role of one class of eLRR plant proteins—the simple eLRR proteins—in plant defenses against herbivores remains largely unknown. Here, we found that a simple eLRR [...] Read more.
Many plant proteins with extracellular leucine-rich repeat (eLRR) domains play an important role in plant immunity. However, the role of one class of eLRR plant proteins—the simple eLRR proteins—in plant defenses against herbivores remains largely unknown. Here, we found that a simple eLRR protein OsI-BAK1 in rice localizes to the plasma membrane. Its expression was induced by mechanical wounding, the infestation of gravid females of brown planthopper (BPH) Nilaparvata lugens or white-backed planthopper Sogatella furcifera and treatment with methyl jasmonate or abscisic acid. Silencing OsI-BAK1 (ir-ibak1) in rice enhanced the BPH-induced transcript levels of three defense-related WRKY genes (OsWRKY24, OsWRKY53 and OsWRKY70) but decreased the induced levels of ethylene. Bioassays revealed that the hatching rate was significantly lower in BPH eggs laid on ir-ibak1 plants than wild-type (WT) plants; moreover, gravid BPH females preferred to oviposit on WT plants over ir-ibak1 plants. The exogenous application of ethephon on ir-ibak1 plants eliminated the BPH oviposition preference between WT and ir-ibak1 plants but had no effect on the hatching rate of BPH eggs. These findings suggest that OsI-BAK1 acts as a negative modulator of defense responses in rice to BPH and that BPH might exploit this modulator for its own benefit. Full article
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15 pages, 4500 KiB  
Article
Rhizosphere Microbiomes of Potato Cultivated under Bacillus subtilis Treatment Influence the Quality of Potato Tubers
by Jian Song, Zhi-Qiang Kong, Dan-Dan Zhang, Jie-Yin Chen, Xiao-Feng Dai and Ran Li
Int. J. Mol. Sci. 2021, 22(21), 12065; https://doi.org/10.3390/ijms222112065 - 08 Nov 2021
Cited by 12 | Viewed by 2885
Abstract
Plants serve as a niche for the growth and proliferation of a diversity of microorganisms. Soil microorganisms, which closely interact with plants, are increasingly being recognized as factors important to plant health. In this study, we explored the use of high-throughput DNA sequencing [...] Read more.
Plants serve as a niche for the growth and proliferation of a diversity of microorganisms. Soil microorganisms, which closely interact with plants, are increasingly being recognized as factors important to plant health. In this study, we explored the use of high-throughput DNA sequencing of the fungal ITS and bacterial 16S for characterization of the fungal and bacterial microbiomes following biocontrol treatment (DT) with Bacillus subtilis strain Bv17 relative to treatments without biocontrol (DC) during the potato growth cycle at three time points. A total of 5631 operational taxonomic units (OTUs) were identified from the 16S data, and 2236 OTUs were identified from the ITS data. The number of bacterial and fungal OTU in DT was higher than in DC and gradually increased during potato growth. In addition, indices such as Ace, Chao, Shannon, and Simpson were higher in DT than in DC, indicating greater richness and community diversity in soil following the biocontrol treatment. Additionally, the potato tuber yields improved without a measurable change in the bacterial communities following the B. subtilis strain Bv17 treatment. These results suggest that soil microbial communities in the rhizosphere are differentially affected by the biocontrol treatment while improving potato yield, providing a strong basis for biocontrol utilization in crop production. Full article
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23 pages, 4320 KiB  
Article
Adaptive Responses of Citrus grandis Leaves to Copper Toxicity Revealed by RNA-Seq and Physiology
by Fenglin Wu, Huiyu Huang, Mingyi Peng, Yinhua Lai, Qianqian Ren, Jiang Zhang, Zengrong Huang, Lintong Yang, Christopher Rensing and Lisong Chen
Int. J. Mol. Sci. 2021, 22(21), 12023; https://doi.org/10.3390/ijms222112023 - 06 Nov 2021
Cited by 20 | Viewed by 2122
Abstract
Copper (Cu)-toxic effects on Citrus grandis growth and Cu uptake, as well as gene expression and physiological parameters in leaves were investigated. Using RNA-Seq, 715 upregulated and 573 downregulated genes were identified in leaves of C. grandis seedlings exposed to Cu-toxicity (LCGSEC). Cu-toxicity [...] Read more.
Copper (Cu)-toxic effects on Citrus grandis growth and Cu uptake, as well as gene expression and physiological parameters in leaves were investigated. Using RNA-Seq, 715 upregulated and 573 downregulated genes were identified in leaves of C. grandis seedlings exposed to Cu-toxicity (LCGSEC). Cu-toxicity altered the expression of 52 genes related to cell wall metabolism, thus impairing cell wall metabolism and lowering leaf growth. Cu-toxicity downregulated the expression of photosynthetic electron transport-related genes, thus reducing CO2 assimilation. Some genes involved in thermal energy dissipation, photorespiration, reactive oxygen species scavenging and cell redox homeostasis and some antioxidants (reduced glutathione, phytochelatins, metallothioneins, l-tryptophan and total phenolics) were upregulated in LCGSEC, but they could not protect LCGSEC from oxidative damage. Several adaptive responses might occur in LCGSEC. LCGSEC displayed both enhanced capacities to maintain homeostasis of Cu via reducing Cu uptake by leaves and preventing release of vacuolar Cu into the cytoplasm, and to improve internal detoxification of Cu by accumulating Cu chelators (lignin, reduced glutathione, phytochelatins, metallothioneins, l-tryptophan and total phenolics). The capacities to maintain both energy homeostasis and Ca homeostasis might be upregulated in LCGSEC. Cu-toxicity increased abscisates (auxins) level, thus stimulating stomatal closure and lowering water loss (enhancing water use efficiency and photosynthesis). Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review. 

Title:
Genome-wide characterization and analysis of MYB transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii)
Zhenyu Huang
Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences

 Abstract: MYB transcription factor family plays an important role in plant metabolism, physiology, and growth. Berry color is one of the important factors that determine grape quality. However, the MYB transcription factor family’s function in anthocyanin synthesis of grape berry has not been studied systematically. We identified 138 MYB transcription factors from spine grape, which is the only Chinese wild grape with white berries. First, we screened six candidate genes by bioinformatics analysis and expression analysis. We found one of the candidate genes, VdMYB014, belonged to III subfamily and interacted with genes related to anthocyanin synthesis through phylogenetic analysis and interaction network prediction. Therefore, we speculated that VdMYB014 participated in the anthocyanin synthesis process. To confirm this, we transiently expressed VdMYB014 in grape and Arabidopsis transformation. Compared with the control, transgenic materials can accumulate more anthocyanins. These results provide a good base to study the function of the VdMYB family in anthocyanin synthesis of grape berry.
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