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Liang L, Wang D, Xu D, Xiao J, Tang W, Song X, Yu G, Liang Z, Xie M, Xu Z, Sun B, Tang Y, Huang Z, Lai Y, Li H. Comparative phylogenetic analysis of the mediator complex subunit in asparagus bean (Vigna unguiculata ssp. sesquipedialis) and its expression profile under cold stress. BMC Genomics 2024; 25:149. [PMID: 38321384 PMCID: PMC10848533 DOI: 10.1186/s12864-024-10060-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND The mediator complex subunits (MED) constitutes a multiprotein complex, with each subunit intricately involved in crucial aspects of plant growth, development, and responses to stress. Nevertheless, scant reports pertain to the VunMED gene within the context of asparagus bean (Vigna unguiculata ssp. sesquipedialis). Establishing the identification and exploring the responsiveness of VunMED to cold stress forms a robust foundation for the cultivation of cold-tolerant asparagus bean cultivars. RESULTS Within this study, a comprehensive genome-wide identification of VunMED genes was executed in the asparagus bean cultivar 'Ningjiang3', resulting in the discovery of 36 distinct VunMED genes. A phylogenetic analysis encompassing 232 MED genes from diverse species, including Arabidopsis, tomatoes, soybeans, mung beans, cowpeas, and asparagus beans, underscored the highly conserved nature of MED gene sequences. Throughout evolutionary processes, each VunMED gene underwent purification and neutral selection, with the exception of VunMED19a. Notably, VunMED9/10b/12/13/17/23 exhibited structural variations discernible across four cowpea species. Divergent patterns of temporal and spatial expression were evident among VunMED genes, with a prominent role attributed to most genes during early fruit development. Additionally, an analysis of promoter cis-acting elements was performed, followed by qRT-PCR assessments on roots, stems, and leaves to gauge relative expression after exposure to cold stress and subsequent recovery. Both treatments induced transcriptional alterations in VunMED genes, with particularly pronounced effects observed in root-based genes following cold stress. Elucidating the interrelationships between subunits involved a preliminary understanding facilitated by correlation and principal component analyses. CONCLUSIONS This study elucidates the pivotal contribution of VunMED genes to the growth, development, and response to cold stress in asparagus beans. Furthermore, it offers a valuable point of reference regarding the individual roles of MED subunits.
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Affiliation(s)
- Le Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dongmei Xu
- Mianyang Academy of Agricultural Sciences, Mianyang, 621000, China
| | - Jiachang Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wen Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xueping Song
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guofeng Yu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zongxu Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minghui Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zeping Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunsong Lai
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
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Yan H, Sun M, Zhang Z, Jin Y, Zhang A, Lin C, Wu B, He M, Xu B, Wang J, Qin P, Mendieta JP, Nie G, Wang J, Jones CS, Feng G, Srivastava RK, Zhang X, Bombarely A, Luo D, Jin L, Peng Y, Wang X, Ji Y, Tian S, Huang L. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nat Genet 2023; 55:507-518. [PMID: 36864101 PMCID: PMC10011142 DOI: 10.1038/s41588-023-01302-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/18/2023] [Indexed: 03/04/2023]
Abstract
Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.
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Affiliation(s)
- Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | | | - Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ailing Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chuang Lin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jing Wang
- Key Laboratory of Bio-Source and Environmental Conservation, School of Life Science, Sichuan University, Chengdu, China
| | - Peng Qin
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | | | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Aureliano Bombarely
- Instituto de Biologia Molecular y Celular de Plantas, UPV-CSIC, Valencia, Spain
| | - Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yang Ji
- Sichuan Animal Science Academy, Chengdu, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, China.
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
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Zhang H, Zheng D, Yin L, Song F, Jiang M. Functional Analysis of OsMED16 and OsMED25 in Response to Biotic and Abiotic Stresses in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:652453. [PMID: 33868352 PMCID: PMC8044553 DOI: 10.3389/fpls.2021.652453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/08/2021] [Indexed: 05/19/2023]
Abstract
Mediator complex is a multiprotein complex that regulates RNA polymerase II-mediated transcription. Moreover, it functions in several signaling pathways, including those involved in response to biotic and abiotic stresses. We used virus-induced gene silencing (VIGS) to study the functions of two genes, namely OsMED16 and OsMED25 in response to biotic and abiotic stresses in rice. Both genes were differentially induced by Magnaporthe grisea (M. grisea), the causative agent of blast disease, hormone treatment, and abiotic stress. We found that both BMV: OsMED16- and BMV: OsMED25-infiltrated seedlings reduced the resistance to M. grisea by regulating the accumulation of H2O2 and expression of defense-related genes. Furthermore, BMV: OsMED16-infiltrated seedlings decreased the tolerance to cold by increasing the malondialdehyde (MDA) content and reducing the expression of cold-responsive genes.
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Affiliation(s)
- Huijuan Zhang
- College of Life Science, Taizhou University, Taizhou, China
| | - Dewei Zheng
- College of Life Science, Taizhou University, Taizhou, China
| | - Longfei Yin
- College of Life Science, Taizhou University, Taizhou, China
| | - Fengming Song
- National Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ming Jiang
- College of Life Science, Taizhou University, Taizhou, China
- *Correspondence: Ming Jiang,
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Malik N, Ranjan R, Parida SK, Agarwal P, Tyagi AK. Mediator subunit OsMED14_1 plays an important role in rice development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1411-1429. [PMID: 31702850 DOI: 10.1111/tpj.14605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 05/06/2023]
Abstract
Mediator, a multisubunit co-activator complex, regulates transcription in eukaryotes and is involved in diverse processes in Arabidopsis through its different subunits. Here, we have explored developmental aspects of one of the rice Mediator subunit gene OsMED14_1. We analyzed its expression pattern through RNA in situ hybridization and pOsMED14_1:GUS transgenics that showed its expression in roots, leaves, anthers and seeds prominently at younger stages, indicating possible involvement of this subunit in multiple aspects of rice development. To understand the developmental roles of OsMED14_1 in rice, we generated and studied RNAi-based knockdown rice plants that showed multiple effects including less height, narrower leaves and culms with reduced vasculature, lesser lateral root branching, defective microspore development, reduced panicle branching and seed set, and smaller seeds. Histological analyses showed that slender organs were caused by reduction in both cell number and cell size in OsMED14_1 knockdown plants. Flow cytometric analyses and expression analyses of cell cycle-related genes revealed that defective cell-cycle progression led to these defects. Expression analyses of auxin-related genes and indole-3-acetic acid (IAA) immunolocalization study indicated altered auxin level in these knockdown plants. Reduction of lateral root branching in knockdown plants was corrected by exogenous IAA supplement. OsMED14_1 physically interacts with transcription factors YABBY5, TAPETUM DEGENERATION RETARDATION (TDR) and MADS29, possibly regulating auxin homeostasis and ultimately leading to lateral organ/leaf, microspore and seed development.
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Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
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