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Maple R, Zhu P, Hepworth J, Wang JW, Dean C. Flowering time: From physiology, through genetics to mechanism. PLANT PHYSIOLOGY 2024; 195:190-212. [PMID: 38417841 PMCID: PMC11060688 DOI: 10.1093/plphys/kiae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/12/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024]
Abstract
Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.
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Affiliation(s)
- Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pan Zhu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jo Hepworth
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Yuan B, Qi G, Yuan C, Wang Y, Zhao H, Li Y, Wang Y, Dong L, Dong Y, Liu X. Major genetic locus with pleiotropism determined seed-related traits in cultivated and wild soybeans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:125. [PMID: 37165285 DOI: 10.1007/s00122-023-04358-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Here, a novel pleiotropic QTL qSS14 simultaneously regulating four seed size traits and two consistently detected QTLs qSW17 and qSLW02 were identified across multiple years. Seed-related traits were the key agronomic traits that have been artificially selected during the domestication of wild soybean. Identifying the genetic loci and genes that regulate seed size could clarify the genetic variations in seed-related traits and provide novel insights into high-yield soybean breeding. In this study, we used a high-density genetic map constructed by F10 RIL populations from a cross between Glycine max and Glycine soja to detect additive QTLs for seven seed-related traits over the last three years. As a result, we identified one novel pleiotropic QTL, qSS14, that simultaneously controlled four seed size traits (100-seed weight, seed length, seed width, and seed thickness) and two consistently detected QTLs, qSW17, and qSLW02, in multiple years of phenotypic data. Furthermore, we predicted two, two and three candidate genes within these three critical loci based on the parental resequencing data and gene function annotations. And the relative expression of four candidate genes GLYMA_14G155100, GLYMA_17G061000, GLYMA_02G273100, and GLYMA_02G273300 showed significant differences among parents and the extreme materials through qRT-PCR analysis. These findings could facilitate the determination of beneficial genes in wild soybean and contribute to our understanding of the soybean domestication process.
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Affiliation(s)
- Baoqi Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Guangxun Qi
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yingnan Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Lingchao Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yingshan Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China.
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China.
| | - Xiaodong Liu
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China.
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China.
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Han X, Shi Q, He Z, Song W, Chen Q, Qi Z. Transcriptome-wide N 6-methyladenosine (m 6A) methylation in soybean under Meloidogyne incognita infection. ABIOTECH 2022; 3:197-211. [PMID: 36313932 PMCID: PMC9590533 DOI: 10.1007/s42994-022-00077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/30/2022] [Indexed: 02/02/2023]
Abstract
N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3' end of coding sequences and in 3' UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00077-2.
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Affiliation(s)
- Xue Han
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Qianqian Shi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Ziyi He
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Wenwen Song
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
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