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Genome-wide association analysis reveals the optimal genomic regions for pod size in bean
The snap bean is the most commonly grown vegetable legume worldwide, and its pod size is both an important yield and appearance quality trait. However, the improvement of pod size in snap beans grown in China has been largely hindered by a lack of information on the specific genes that determine pod...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10213521/ https://www.ncbi.nlm.nih.gov/pubmed/37251758 http://dx.doi.org/10.3389/fpls.2023.1138988 |
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author | Li, Mao Wu, Xinyi Wang, Baogen Wu, Xiaohua Wang, Ying Wang, Jian Dong, Junyang Wu, Jian Lu, Zhongfu Sun, Yuyan Dong, Wenqi Yang, Jing Li, Guojing |
author_facet | Li, Mao Wu, Xinyi Wang, Baogen Wu, Xiaohua Wang, Ying Wang, Jian Dong, Junyang Wu, Jian Lu, Zhongfu Sun, Yuyan Dong, Wenqi Yang, Jing Li, Guojing |
author_sort | Li, Mao |
collection | PubMed |
description | The snap bean is the most commonly grown vegetable legume worldwide, and its pod size is both an important yield and appearance quality trait. However, the improvement of pod size in snap beans grown in China has been largely hindered by a lack of information on the specific genes that determine pod size. In this study, we identified 88 snap bean accessions and evaluated their pod size traits. Through a genome-wide association study (GWAS), 57 single nucleotide polymorphisms (SNPs) significantly associated with pod size were detected. Candidate gene analysis showed that cytochrome P450 family genes, WRKY, and MYB transcription factors were the predominant candidate genes for pod development, and eight of these 26 candidate genes showed relatively higher expression patterns in flowers and young pods. A significant pod length (PL) SNP and a single pod weight (SPW) SNP were successfully converted into kompetitive allele-specific polymerase chain reaction (KASP) markers and validated in the panel. These results enhance our understanding of the genetic basis of pod size, and also provide genetic resources for the molecular breeding of pod size in snap beans. |
format | Online Article Text |
id | pubmed-10213521 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-102135212023-05-27 Genome-wide association analysis reveals the optimal genomic regions for pod size in bean Li, Mao Wu, Xinyi Wang, Baogen Wu, Xiaohua Wang, Ying Wang, Jian Dong, Junyang Wu, Jian Lu, Zhongfu Sun, Yuyan Dong, Wenqi Yang, Jing Li, Guojing Front Plant Sci Plant Science The snap bean is the most commonly grown vegetable legume worldwide, and its pod size is both an important yield and appearance quality trait. However, the improvement of pod size in snap beans grown in China has been largely hindered by a lack of information on the specific genes that determine pod size. In this study, we identified 88 snap bean accessions and evaluated their pod size traits. Through a genome-wide association study (GWAS), 57 single nucleotide polymorphisms (SNPs) significantly associated with pod size were detected. Candidate gene analysis showed that cytochrome P450 family genes, WRKY, and MYB transcription factors were the predominant candidate genes for pod development, and eight of these 26 candidate genes showed relatively higher expression patterns in flowers and young pods. A significant pod length (PL) SNP and a single pod weight (SPW) SNP were successfully converted into kompetitive allele-specific polymerase chain reaction (KASP) markers and validated in the panel. These results enhance our understanding of the genetic basis of pod size, and also provide genetic resources for the molecular breeding of pod size in snap beans. Frontiers Media S.A. 2023-05-12 /pmc/articles/PMC10213521/ /pubmed/37251758 http://dx.doi.org/10.3389/fpls.2023.1138988 Text en Copyright © 2023 Li, Wu, Wang, Wu, Wang, Wang, Dong, Wu, Lu, Sun, Dong, Yang and Li 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 Li, Mao Wu, Xinyi Wang, Baogen Wu, Xiaohua Wang, Ying Wang, Jian Dong, Junyang Wu, Jian Lu, Zhongfu Sun, Yuyan Dong, Wenqi Yang, Jing Li, Guojing Genome-wide association analysis reveals the optimal genomic regions for pod size in bean |
title | Genome-wide association analysis reveals the optimal genomic regions for pod size in bean |
title_full | Genome-wide association analysis reveals the optimal genomic regions for pod size in bean |
title_fullStr | Genome-wide association analysis reveals the optimal genomic regions for pod size in bean |
title_full_unstemmed | Genome-wide association analysis reveals the optimal genomic regions for pod size in bean |
title_short | Genome-wide association analysis reveals the optimal genomic regions for pod size in bean |
title_sort | genome-wide association analysis reveals the optimal genomic regions for pod size in bean |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10213521/ https://www.ncbi.nlm.nih.gov/pubmed/37251758 http://dx.doi.org/10.3389/fpls.2023.1138988 |
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