Genome‑wide Association Analysis and Candidate Gene Prediction for Rice Drought Tolerance at Seedling Stage

doi:10.15933/j.cnki.1004-3268.2025.07.002

Abstract

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.

Key words: Rice, Drought tolerance at seedling stage, Genome wide association analysis, Candidate gene prediction, Haplotype

摘要： 以水稻多样性群体RDP-Ⅱ中的355份种质为材料，以干旱复水后的黄叶率为耐旱评价指标，结合群体基因型数据进行全基因组关联分析（GWAS），并对耐旱相关候选基因进行分析，旨在为耐旱水稻培育提供优异种质资源及基因资源。结果表明，在RDP-Ⅱ群体中热带粳稻黄叶率最低，奥斯稻黄叶率最高。通过GWAS鉴定到17个耐旱相关SNP（单核苷酸多态性）位点，分布在水稻第1、2、3、6、7、8、11、12号染色体上，对峰值SNP附近10 kb区段进行候选基因预测，筛选出33个耐旱相关候选基因，主要包括蛋白激酶、转座子蛋白基因等。基于基因功能注释，挑选其中8个候选基因分别在耐旱种质和不耐旱种质中进行表达量分析，鉴定到表达差异显著的基因OsCTFdt、OsPEX1，分别正调控和负调控水稻苗期耐旱性。OsCTFdt、OsPEX1基因分别有4种单倍型，且优势单倍型的黄叶率均显著低于其他单倍型。

关键词: 水稻, 苗期耐旱性, 全基因组关联分析, 候选基因预测, 单倍型

CLC Number:

S511

HUANG Shipeng, HE Huqiang, LI Guangzhao, CHEN Chuanxin, ZHONG Tuo, XIE Jianbo, ZHOU Xiangwan, WANG Dan, XIAO Yinghui. Genome‑wide Association Analysis and Candidate Gene Prediction for Rice Drought Tolerance at Seedling Stage[J]. Journal of Henan Agricultural Sciences, 2025, 54(7): 12-20.

黄世鹏, 何虎强, 李光照, 陈传鑫, 钟拓, 谢剑波, 周湘晚, 王丹, 肖应辉. 水稻苗期耐旱性全基因组关联分析及候选基因预测[J]. 河南农业科学, 2025, 54(7): 12-20.

Figures/Tables 7

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