Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential

Abstract Rice yield per plant has a complex genetic architecture, which is mainly determined by its three component traits: the number of grains per panicle (GPP), kilo-grain weight (KGW), and tillers per plant (TP). Exploring ideotype breeding based on selection for genetically less complex compone...

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Autores principales:	Jing Su, Kai Xu, Zirong Li, Yuan Hu, Zhongli Hu, Xingfei Zheng, Shufeng Song, Zhonghai Tang, Lanzhi Li
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a3b4cacad5f3418dbdde89276c6f5ec5
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spelling	oai:doaj.org-article:a3b4cacad5f3418dbdde89276c6f5ec52021-12-02T14:02:54ZGenome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential10.1038/s41598-021-86389-72045-2322https://doaj.org/article/a3b4cacad5f3418dbdde89276c6f5ec52021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86389-7https://doaj.org/toc/2045-2322Abstract Rice yield per plant has a complex genetic architecture, which is mainly determined by its three component traits: the number of grains per panicle (GPP), kilo-grain weight (KGW), and tillers per plant (TP). Exploring ideotype breeding based on selection for genetically less complex component traits is an alternative route for further improving rice production. To understand the genetic basis of the relationship between rice yield and component traits, we investigated the four traits of two rice hybrid populations (575 + 1495 F1) in different environments and conducted meta-analyses of genome-wide association study (meta-GWAS). In total, 3589 significant loci for three components traits were detected, while only 3 loci for yield were detected. It indicated that rice yield is mainly controlled by minor-effect loci and hardly to be identified. Selecting quantitative trait locus/gene affected component traits to further enhance yield is recommended. Mendelian randomization design is adopted to investigate the genetic effects of loci on yield through component traits and estimate the genetic relationship between rice yield and its component traits by these loci. The loci for GPP or TP mainly had a positive genetic effect on yield, but the loci for KGW with different direction effects (positive effect or negative effect). Additionally, TP (Beta = 1.865) has a greater effect on yield than KGW (Beta = 1.016) and GPP (Beta = 0.086). Five significant loci for component traits that had an indirect effect on yield were identified. Pyramiding superior alleles of the five loci revealed improved yield. A combination of direct and indirect effects may better contribute to the yield potential of rice. Our findings provided a rationale for using component traits as indirect indices to enhanced rice yield, which will be helpful for further understanding the genetic basis of yield and provide valuable information for improving rice yield potential.Jing SuKai XuZirong LiYuan HuZhongli HuXingfei ZhengShufeng SongZhonghai TangLanzhi LiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jing Su Kai Xu Zirong Li Yuan Hu Zhongli Hu Xingfei Zheng Shufeng Song Zhonghai Tang Lanzhi Li Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
description	Abstract Rice yield per plant has a complex genetic architecture, which is mainly determined by its three component traits: the number of grains per panicle (GPP), kilo-grain weight (KGW), and tillers per plant (TP). Exploring ideotype breeding based on selection for genetically less complex component traits is an alternative route for further improving rice production. To understand the genetic basis of the relationship between rice yield and component traits, we investigated the four traits of two rice hybrid populations (575 + 1495 F1) in different environments and conducted meta-analyses of genome-wide association study (meta-GWAS). In total, 3589 significant loci for three components traits were detected, while only 3 loci for yield were detected. It indicated that rice yield is mainly controlled by minor-effect loci and hardly to be identified. Selecting quantitative trait locus/gene affected component traits to further enhance yield is recommended. Mendelian randomization design is adopted to investigate the genetic effects of loci on yield through component traits and estimate the genetic relationship between rice yield and its component traits by these loci. The loci for GPP or TP mainly had a positive genetic effect on yield, but the loci for KGW with different direction effects (positive effect or negative effect). Additionally, TP (Beta = 1.865) has a greater effect on yield than KGW (Beta = 1.016) and GPP (Beta = 0.086). Five significant loci for component traits that had an indirect effect on yield were identified. Pyramiding superior alleles of the five loci revealed improved yield. A combination of direct and indirect effects may better contribute to the yield potential of rice. Our findings provided a rationale for using component traits as indirect indices to enhanced rice yield, which will be helpful for further understanding the genetic basis of yield and provide valuable information for improving rice yield potential.
format	article
author	Jing Su Kai Xu Zirong Li Yuan Hu Zhongli Hu Xingfei Zheng Shufeng Song Zhonghai Tang Lanzhi Li
author_facet	Jing Su Kai Xu Zirong Li Yuan Hu Zhongli Hu Xingfei Zheng Shufeng Song Zhonghai Tang Lanzhi Li
author_sort	Jing Su
title	Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
title_short	Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
title_full	Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
title_fullStr	Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
title_full_unstemmed	Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
title_sort	genome-wide association study and mendelian randomization analysis provide insights for improving rice yield potential
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/a3b4cacad5f3418dbdde89276c6f5ec5
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Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential

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