Mining of Drought-resistance Related Genes in Rice Based on Genome-wide Association Study

doi:10.13560/j.cnki.biotech.bull.1985.2025-1211

Abstract

Abstract:

Objective Analysis of quantitative trait loci (QTLs) associated with rice leaf wilt degree, providing a reference for screening drought-tolerance candidate genes in rice. Method Using a panel of 300 rice germplasm resources, the leaf rolling index (LRI) and leaf wilt degree (LWD) were investigated under drought stress. Genome-wide association study (GWAS) was employed to map drought tolerance-related quantitative trait loci (QTLs). Result Phenotypic data for LRI and LWD followed a normal distribution. Four QTLs associated with LWD were identified via GWAS. Among these, qLWD4-1 was consistently detected across both investigation periods. Based on haplotype analysis and gene function annotation, four candidate genes for drought tolerance (LOC_Os04g54360, LOC_Os04g54474, LOC_Os04g54560, and LOC_Os04g54570) were screened within the qLWD4-1 locus region. Conclusion This study identified a stably expressed QTL (qLWD4-1) associated with leaf wilt degree across two investigation periods via GWAS, and four drought-resistant candidate genes were determined within this locus.

Key words: rice, drought resistance, genome-wide association study, principal component analysis, quantitative trait loci

SONG Zi-hui, XUE Li, WANG Sen, SUN Jian-chang, HAN Bing, CUI Di, HAN Long-zhi, ZHAO Zheng-wu, MA Xiao-ding. Mining of Drought-resistance Related Genes in Rice Based on Genome-wide Association Study[J]. Biotechnology Bulletin, 2026, 42(8): 97-105.

Figures/Tables 8

References 42

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性状 Trait	调查日期 Investigation date	富源4 Fuyuan 4	群体 Population
性状 Trait	调查日期 Investigation date	均值 Mean	变异范围 Variation range	均值 Mean	标准差 SD	变异系数 CV （%）
叶卷曲指数LRI	7/6	2.91	1-7	3.27	1.61	49.2
	8/4	3.38	1-9	3.74	2.30	61.4
叶枯萎度LWD	7/6	3.08	1-7	3.16	1.31	41.4
	7/13	3.51	1-7	3.66	1.30	35.4
	7/24	3.84	1-7	3.81	1.27	33.3
	8/4	4.54	1-9	4.77	1.98	41.5

性状 Trait	调查日期 Investigation date	富源4 Fuyuan 4	群体 Population
性状 Trait	调查日期 Investigation date	均值 Mean	变异范围 Variation range	均值 Mean	标准差 SD	变异系数 CV （%）
叶卷曲指数LRI	7/6	2.91	1-7	3.27	1.61	49.2
	8/4	3.38	1-9	3.74	2.30	61.4
叶枯萎度LWD	7/6	3.08	1-7	3.16	1.31	41.4
	7/13	3.51	1-7	3.66	1.30	35.4
	7/24	3.84	1-7	3.81	1.27	33.3
	8/4	4.54	1-9	4.77	1.98	41.5

性状Trait	调查日期Investigating date	位点Locus	染色体Chromosomes	物理区间 Physical interval （Mb）	SNP数量 Number of SNPs	峰值SNP Top SNP	变异解释率 PVE （%）
LWD	7/13	qLWD1	1	15.03‒15.49	2	15 289 931	1.20
		qLWD4-1	4	32.06‒32.66	2	32 260 706	1.10
LWD	7/24	qLWD4-2	4	31.79‒32.43	5	32 033 623	1.48
		qLWD4-1	4	32.06‒32.66	3	32 457 574	1.56
		qLWD4-3	4	32.47‒33.04	3	32 843 337	1.29

性状Trait	调查日期Investigating date	位点Locus	染色体Chromosomes	物理区间 Physical interval （Mb）	SNP数量 Number of SNPs	峰值SNP Top SNP	变异解释率 PVE （%）
LWD	7/13	qLWD1	1	15.03‒15.49	2	15 289 931	1.20
		qLWD4-1	4	32.06‒32.66	2	32 260 706	1.10
LWD	7/24	qLWD4-2	4	31.79‒32.43	5	32 033 623	1.48
		qLWD4-1	4	32.06‒32.66	3	32 457 574	1.56
		qLWD4-3	4	32.47‒33.04	3	32 843 337	1.29

候选基因 Candidate gene	单倍型 Haplotype	叶枯萎度 Leaf wilt degree		基因注释Gene annotation
候选基因 Candidate gene	单倍型 Haplotype	7/13	7/24	基因注释Gene annotation
LOC_Os04g54360	Hap_1：ACCTCCGG	-	3.79b	含糖基转移酶8结构域的蛋白质
	Hap_2：ACCTCCGA	-	4.01a	Glycosyl transferase 8 domain containing protein， putative， expressed
	Hap_3：ACTTCCAG	-	3.63b
	Hap_4：ACCTTCAG	-	3.55c
LOC_Os04g54474	Hap_1：GGTAGAG	3.59b	3.73b	bZIP转录因子
	Hap_2：GGTATAG	3.80a	4.02a	The bZIP family of transcription factors
LOC_Os04g54560	Hap_1：CGCCCGCGGCGGACCCGGA	3.52b	3.70b	转移酶家族蛋白 Transferase family protein
	Hap_2：CACCCGCGGCGGACCCGGA	3.78a	4.00a
	Hap_3：CATCCGCGGCGGACCCGGA	3.60ab	3.60b
LOC_Os04g54570	Hap_1：GGCG	3.60b	3.75b	转移酶家族蛋白
	Hap_2：AGCG	3.80a	4.04a	Transferase family protein