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Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses

Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybe...

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Autores principales: Song, Jian, Wang, Xuewen, Huang, Lan, Li, Zhongfeng, Ren, Honglei, Wang, Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9721362/
https://www.ncbi.nlm.nih.gov/pubmed/36479521
http://dx.doi.org/10.3389/fpls.2022.1017672
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author Song, Jian
Wang, Xuewen
Huang, Lan
Li, Zhongfeng
Ren, Honglei
Wang, Jun
author_facet Song, Jian
Wang, Xuewen
Huang, Lan
Li, Zhongfeng
Ren, Honglei
Wang, Jun
author_sort Song, Jian
collection PubMed
description Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.
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spelling pubmed-97213622022-12-06 Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses Song, Jian Wang, Xuewen Huang, Lan Li, Zhongfeng Ren, Honglei Wang, Jun Front Plant Sci Plant Science Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic. Frontiers Media S.A. 2022-11-21 /pmc/articles/PMC9721362/ /pubmed/36479521 http://dx.doi.org/10.3389/fpls.2022.1017672 Text en Copyright © 2022 Song, Wang, Huang, Li, Ren and Wang https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Song, Jian
Wang, Xuewen
Huang, Lan
Li, Zhongfeng
Ren, Honglei
Wang, Jun
Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses
title Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses
title_full Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses
title_fullStr Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses
title_full_unstemmed Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses
title_short Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses
title_sort genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9721362/
https://www.ncbi.nlm.nih.gov/pubmed/36479521
http://dx.doi.org/10.3389/fpls.2022.1017672
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