基于全基因组关联分析的水稻穗长QTL定位及其候选基因分析

Panicle length QTL mapping and candidate gene analysis based on genome-wide association analysis in rice

分别于2021年和2022年在湖南长沙种植254份水稻3K种质资源,在成熟期测定各种质的穗长。结合种质基因型进行全基因组关联分析,共检测到3个穗长QTL,分布于水稻第1、5、6号染色体,分别命名为qPL-1、qPL-5和qPL-6,相对贡献率为9.06%~28.27%;结合QTL区间内基因功能注释和基因不同单倍型的穗长差异显著性分析结果,最终获得qPL-1、qPL-5和qPL-6的候选基因,其中qPL-6与sped1-D共定位,Os01g0715600、Os05g0132700为调控穗长的新候选基因;对Os01g0715600、Os05g0132700和Os06g0597500的单倍型进行聚合分析,发现这3个基因存在累加效应。

In this study,254 rice 3K germplasm resources were used as research materials,and they were planted in Changsha,Hunan Province,in 2021 and 2022,respectively.The panicle lengths of the various germplasm were measured at heading stage.Combined with germplasm genotypes for genome-wide association study,three panicle length QTL were detected on rice chromosomes 1,5,and 6,namedqPL-1,qPL-5,andqPL-6,respectively.These QTL explained phenotypic variation range from 9.06%to 28.27%of the variation of spike length.The candidate genes ofqPL-1,qPL-5 and qPL-6were finally obtained by combining the gene function annotation in the QTL interval and the significant difference of the panicle length of different haplotypes.With the co-localization ofqPL-6andsped1-D,Os01g0715600and Os05g0132700were identified as the new candidate genes for the regulation of spike length.Polymerization analysis of theelite haplotypes of Os01g0715600,Os05g0132700 and Os06g0597500revealed a superposition effect within the three genes.