Genome-wide Association Analysis and Candidate Gene Prediction for Rice Drought Tolerance at Seedling Stage
HUANG Shipeng
HE Huqiang
LI Guangzhao
CHEN Chuanxin
ZHONG Tuo
XIE Jianbo
ZHOU Xiangwan
WANG Dan
XIAO Yinghui
Abstract：Taking 355 rice germplasms from RDP-Ⅱ as materials,taking the yellow leaf rate after re-watering as the drought tolerance evaluation index,combined with the population genotype data,genome-wide association analysis(GWAS)was carried out,and the candidate genes related to drought tolerance were analyzed,so as to provide excellent germplasm resources and gene resources for the breeding of drought tolerant rice.The results showed that in RDP-Ⅱ population,the yellow leaf rate of tropical japonica rice was the lowest,and that of Osbeck rice was the highest;Seventeen SNP loci related to drought tolerance were identified by GWAS,and distributed on chromosomes 1,2,3,6,7,8,11 and 12 of rice.Candidate genes were predicted in the 10 kb region near the peak SNP,and 33 candidate genes related to drought tolerance were screened,mainly including genes encoding protein kinases,transposon proteins,etc.Based on gene function annotation,8 candidate genes were selected for gene expression analysis in drought tolerant germplasm and drought intolerant germplasm,and OsCTFdt and OsPEX1 genes with significant difference in expression level were identified,which positively and negatively regulated the drought tolerance of rice at seedling stage,respectively.OsCTFdt and OsPEX1 genes had 4 haplotypes respectively,and the yellow leaf rate of the dominant haplotype was significantly lower than that of other haplotypes.
Keywords：RiceDrought tolerance at seedling stageGenome wide association analysisCandidate gene predictionHaplotype
Publication Date：2025-07-15
Online Publishing Date：2026-09-12(First online date of this platform, not the publication date of the document)
Pages：9( 12-20 )