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Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population

Rice grain size plays a crucial role in determining grain quality and yield. In this study, two multiparent advanced generation intercross (MAGIC) populations, DC1 and BIM, were evaluated for grain size across three environments and genotyped with 55K array-based SNP detection and genotype-by-sequen...

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Autores principales: Ponce, Kimberly, Zhang, Ya, Guo, Longbiao, Leng, Yujia, Ye, Guoyou
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193545/
https://www.ncbi.nlm.nih.gov/pubmed/32391027
http://dx.doi.org/10.3389/fpls.2020.00395
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author Ponce, Kimberly
Zhang, Ya
Guo, Longbiao
Leng, Yujia
Ye, Guoyou
author_facet Ponce, Kimberly
Zhang, Ya
Guo, Longbiao
Leng, Yujia
Ye, Guoyou
author_sort Ponce, Kimberly
collection PubMed
description Rice grain size plays a crucial role in determining grain quality and yield. In this study, two multiparent advanced generation intercross (MAGIC) populations, DC1 and BIM, were evaluated for grain size across three environments and genotyped with 55K array-based SNP detection and genotype-by-sequencing (GBS), respectively, to identify QTLs and SNPs associated with grain length, grain width, grain length–width ratio, grain thickness, and thousand grain weight. A total of 18 QTLs were identified for the five grain size-related traits and explained 6.43–63.35% of the total phenotypic variance. Twelve of these QTLs colocalized with the cloned genes, GS3, GW5/qSW5, GW7/GL7/SLG7, and GW8/OsSPL16, of which the first two genes showed the strongest effect for grain length and grain width, respectively. Four potential new genes were also identified from the QTLs, which exhibited both genetic background independency and environment stability and could be validated in future studies. Moreover, the significant SNP markers identified are valuable for direct utilization in marker-assisted breeding to improve rice grain size.
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spelling pubmed-71935452020-05-08 Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population Ponce, Kimberly Zhang, Ya Guo, Longbiao Leng, Yujia Ye, Guoyou Front Plant Sci Plant Science Rice grain size plays a crucial role in determining grain quality and yield. In this study, two multiparent advanced generation intercross (MAGIC) populations, DC1 and BIM, were evaluated for grain size across three environments and genotyped with 55K array-based SNP detection and genotype-by-sequencing (GBS), respectively, to identify QTLs and SNPs associated with grain length, grain width, grain length–width ratio, grain thickness, and thousand grain weight. A total of 18 QTLs were identified for the five grain size-related traits and explained 6.43–63.35% of the total phenotypic variance. Twelve of these QTLs colocalized with the cloned genes, GS3, GW5/qSW5, GW7/GL7/SLG7, and GW8/OsSPL16, of which the first two genes showed the strongest effect for grain length and grain width, respectively. Four potential new genes were also identified from the QTLs, which exhibited both genetic background independency and environment stability and could be validated in future studies. Moreover, the significant SNP markers identified are valuable for direct utilization in marker-assisted breeding to improve rice grain size. Frontiers Media S.A. 2020-04-24 /pmc/articles/PMC7193545/ /pubmed/32391027 http://dx.doi.org/10.3389/fpls.2020.00395 Text en Copyright © 2020 Ponce, Zhang, Guo, Leng and Ye. http://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
Ponce, Kimberly
Zhang, Ya
Guo, Longbiao
Leng, Yujia
Ye, Guoyou
Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population
title Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population
title_full Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population
title_fullStr Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population
title_full_unstemmed Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population
title_short Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population
title_sort genome-wide association study of grain size traits in indica rice multiparent advanced generation intercross (magic) population
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193545/
https://www.ncbi.nlm.nih.gov/pubmed/32391027
http://dx.doi.org/10.3389/fpls.2020.00395
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