Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).

Sesame (Sesamum indicum L.) is an important and ancient oilseed crop. Sesame seed coat color is related to biochemical functions involved in protein and oil metabolism, and antioxidant content. Because of its complication, the genetic basis of sesame seed coat color remains poorly understood. To elu...

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Autores principales:	Chengqi Cui, Yanyang Liu, Yan Liu, Xianghua Cui, Zhiyu Sun, Zhenwei Du, Ke Wu, Xiaolin Jiang, Hongxian Mei, Yongzhan Zheng
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bc7f8b3663774daab3f4bb07facbde75
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spelling	oai:doaj.org-article:bc7f8b3663774daab3f4bb07facbde752021-11-25T05:54:14ZGenome-wide association study of seed coat color in sesame (Sesamum indicum L.).1932-620310.1371/journal.pone.0251526https://doaj.org/article/bc7f8b3663774daab3f4bb07facbde752021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0251526https://doaj.org/toc/1932-6203Sesame (Sesamum indicum L.) is an important and ancient oilseed crop. Sesame seed coat color is related to biochemical functions involved in protein and oil metabolism, and antioxidant content. Because of its complication, the genetic basis of sesame seed coat color remains poorly understood. To elucidate the factors affecting the genetic architecture of seed coat color, 366 sesame germplasm lines were evaluated for seed coat color in 12 environments. The genome-wide association studies (GWAS) for three seed coat color space values, best linear unbiased prediction (BLUP) values from a multi-environment trial analysis and principal component scores (PCs) of three seed coat color space values were conducted. GWAS for three seed coat color space values identified a total of 224 significant single nucleotide polymorphisms (SNPs, P < 2.34×10-7), with phenotypic variation explained (PVE) ranging from 1.01% to 22.10%, and 35 significant SNPs were detected in more than 6 environments. Based on BLUP values, 119 significant SNPs were identified, with PVE ranging from 8.83 to 31.98%. Comparing the results of the GWAS using phenotypic data from different environments and the BLUP values, all significant SNPs detected in more than 6 environments were also detected using the BLUP values. GWAS for PCs identified 197 significant SNPs, and 30 were detected in more than 6 environments. GWAS results for PCs were consistent with those for three color space values. Out of 224 significant SNPs, 22 were located in the confidence intervals of previous reported quantitative trait loci (QTLs). Finally, 92 candidate genes were identified in the vicinity of the 4 SNPs that were most significantly associated with sesame seed coat color. The results in this paper will provide new insights into the genetic basis of sesame seed coat color, and should be useful for molecular breeding in sesame.Chengqi CuiYanyang LiuYan LiuXianghua CuiZhiyu SunZhenwei DuKe WuXiaolin JiangHongxian MeiYongzhan ZhengPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0251526 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chengqi Cui Yanyang Liu Yan Liu Xianghua Cui Zhiyu Sun Zhenwei Du Ke Wu Xiaolin Jiang Hongxian Mei Yongzhan Zheng Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).
description	Sesame (Sesamum indicum L.) is an important and ancient oilseed crop. Sesame seed coat color is related to biochemical functions involved in protein and oil metabolism, and antioxidant content. Because of its complication, the genetic basis of sesame seed coat color remains poorly understood. To elucidate the factors affecting the genetic architecture of seed coat color, 366 sesame germplasm lines were evaluated for seed coat color in 12 environments. The genome-wide association studies (GWAS) for three seed coat color space values, best linear unbiased prediction (BLUP) values from a multi-environment trial analysis and principal component scores (PCs) of three seed coat color space values were conducted. GWAS for three seed coat color space values identified a total of 224 significant single nucleotide polymorphisms (SNPs, P < 2.34×10-7), with phenotypic variation explained (PVE) ranging from 1.01% to 22.10%, and 35 significant SNPs were detected in more than 6 environments. Based on BLUP values, 119 significant SNPs were identified, with PVE ranging from 8.83 to 31.98%. Comparing the results of the GWAS using phenotypic data from different environments and the BLUP values, all significant SNPs detected in more than 6 environments were also detected using the BLUP values. GWAS for PCs identified 197 significant SNPs, and 30 were detected in more than 6 environments. GWAS results for PCs were consistent with those for three color space values. Out of 224 significant SNPs, 22 were located in the confidence intervals of previous reported quantitative trait loci (QTLs). Finally, 92 candidate genes were identified in the vicinity of the 4 SNPs that were most significantly associated with sesame seed coat color. The results in this paper will provide new insights into the genetic basis of sesame seed coat color, and should be useful for molecular breeding in sesame.
format	article
author	Chengqi Cui Yanyang Liu Yan Liu Xianghua Cui Zhiyu Sun Zhenwei Du Ke Wu Xiaolin Jiang Hongxian Mei Yongzhan Zheng
author_facet	Chengqi Cui Yanyang Liu Yan Liu Xianghua Cui Zhiyu Sun Zhenwei Du Ke Wu Xiaolin Jiang Hongxian Mei Yongzhan Zheng
author_sort	Chengqi Cui
title	Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).
title_short	Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).
title_full	Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).
title_fullStr	Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).
title_full_unstemmed	Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).
title_sort	genome-wide association study of seed coat color in sesame (sesamum indicum l.).
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/bc7f8b3663774daab3f4bb07facbde75
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Genome-wide association study of seed coat color in sesame (Sesamum indicum L.).

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