A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica

Abstract This study presents a comprehensive study of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diverse panel of indica accessions, each genotyped with 5.2 million markers. GWAS was performed for twelve elements including B, Ca...

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Autores principales:	Suong T. Cu, Nicholas I. Warnock, Julie Pasuquin, Michael Dingkuhn, James Stangoulis
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/582e7c5703ec436684b95b4b43149973
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spelling	oai:doaj.org-article:582e7c5703ec436684b95b4b431499732021-12-02T17:37:28ZA high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica10.1038/s41598-021-98573-w2045-2322https://doaj.org/article/582e7c5703ec436684b95b4b431499732021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98573-whttps://doaj.org/toc/2045-2322Abstract This study presents a comprehensive study of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diverse panel of indica accessions, each genotyped with 5.2 million markers. GWAS was performed for twelve elements including B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn and four agronomic traits including days to 50% flowering, grain yield, plant height and thousand grain weight. GWAS identified 128 loci associated with the grain elements and 57 associated with the agronomic traits. There were sixteen co-localization regions containing QTL for two or more traits. Fourteen grain element quantitative trait loci were stable across growing environments, which can be strong candidates to be used in marker-assisted selection to improve the concentrations of nutritive elements in rice grain. Potential candidate genes were revealed including OsNAS3 linked to the locus that controls the variation of Zn and Co concentrations. The effects of starch synthesis and grain filling on multiple grain elements were elucidated through the likely involvement of OsSUS1 and OsGSSB1 genes. Overall, our study provides crucial insights into the genetic basis of ionomic variations in rice and will facilitate improvement in breeding for trace mineral content.Suong T. CuNicholas I. WarnockJulie PasuquinMichael DingkuhnJames StangoulisNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Suong T. Cu Nicholas I. Warnock Julie Pasuquin Michael Dingkuhn James Stangoulis A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica
description	Abstract This study presents a comprehensive study of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diverse panel of indica accessions, each genotyped with 5.2 million markers. GWAS was performed for twelve elements including B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn and four agronomic traits including days to 50% flowering, grain yield, plant height and thousand grain weight. GWAS identified 128 loci associated with the grain elements and 57 associated with the agronomic traits. There were sixteen co-localization regions containing QTL for two or more traits. Fourteen grain element quantitative trait loci were stable across growing environments, which can be strong candidates to be used in marker-assisted selection to improve the concentrations of nutritive elements in rice grain. Potential candidate genes were revealed including OsNAS3 linked to the locus that controls the variation of Zn and Co concentrations. The effects of starch synthesis and grain filling on multiple grain elements were elucidated through the likely involvement of OsSUS1 and OsGSSB1 genes. Overall, our study provides crucial insights into the genetic basis of ionomic variations in rice and will facilitate improvement in breeding for trace mineral content.
format	article
author	Suong T. Cu Nicholas I. Warnock Julie Pasuquin Michael Dingkuhn James Stangoulis
author_facet	Suong T. Cu Nicholas I. Warnock Julie Pasuquin Michael Dingkuhn James Stangoulis
author_sort	Suong T. Cu
title	A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica
title_short	A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica
title_full	A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica
title_fullStr	A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica
title_full_unstemmed	A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica
title_sort	high-resolution genome-wide association study of the grain ionome and agronomic traits in rice oryza sativa subsp. indica
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/582e7c5703ec436684b95b4b43149973
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A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica

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