Rice yield is a complex trait affected by many related traits.Traditional single-trait genome-wide association studies(GWAS)have limitations when studying complex traits,as they cannot account for the genetic relation...Rice yield is a complex trait affected by many related traits.Traditional single-trait genome-wide association studies(GWAS)have limitations when studying complex traits,as they cannot account for the genetic relationships among multiple traits.Multi-trait GWAS can consider the relationships among multiple traits and identify pleiotropic loci,so it is more suitable for complex traits such as rice yield than single-trait GWAS.In this study,we conducted a multi-trait GWAS on 11 two-trait combinations of yield and yield-related traits with 575 hybrid rice varieties across two environments.All these yield-related traits showed significant genetic correlations with yield(YD),including filled grains per panicle(FGPP),1,000-grain weight(KGW),tillers per plant(TP),primary branch number(PB),secondary branch number(SB),and main panicle length(MPL).In total,we identified 44 pleiotropic quantitative trait loci(p QTLs),including 29 new p QTLs not found in a single-trait GWAS.We then screened 23 p QTLs showing common effects in two traits as key p QTLs.These key p QTLs were subsequently analyzed by haplotype analysis,which identified 13 pleiotropic candidate genes.Finally,we identified two optimal yieldenhancing allele combinations by pyramiding the superior haplotypes:GS3-GL3.1-Os CIPK17 for the YD-KGW combination and GNP12 for the YD-FGPP and YD-SB combinations.This study provides pleiotropic candidate genes and allele combinations that exhibit superior differences in both yield and yield-related traits,offering valuable information for future high-yielding rice breeding.展开更多
基金supported by the Science and Technology Innovation Program of Hunan Province,China(2023NK2001)the Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement,China(2022LZJJ08)the Changsha Science and Technology Project,China(kq2402109)。
文摘Rice yield is a complex trait affected by many related traits.Traditional single-trait genome-wide association studies(GWAS)have limitations when studying complex traits,as they cannot account for the genetic relationships among multiple traits.Multi-trait GWAS can consider the relationships among multiple traits and identify pleiotropic loci,so it is more suitable for complex traits such as rice yield than single-trait GWAS.In this study,we conducted a multi-trait GWAS on 11 two-trait combinations of yield and yield-related traits with 575 hybrid rice varieties across two environments.All these yield-related traits showed significant genetic correlations with yield(YD),including filled grains per panicle(FGPP),1,000-grain weight(KGW),tillers per plant(TP),primary branch number(PB),secondary branch number(SB),and main panicle length(MPL).In total,we identified 44 pleiotropic quantitative trait loci(p QTLs),including 29 new p QTLs not found in a single-trait GWAS.We then screened 23 p QTLs showing common effects in two traits as key p QTLs.These key p QTLs were subsequently analyzed by haplotype analysis,which identified 13 pleiotropic candidate genes.Finally,we identified two optimal yieldenhancing allele combinations by pyramiding the superior haplotypes:GS3-GL3.1-Os CIPK17 for the YD-KGW combination and GNP12 for the YD-FGPP and YD-SB combinations.This study provides pleiotropic candidate genes and allele combinations that exhibit superior differences in both yield and yield-related traits,offering valuable information for future high-yielding rice breeding.
