全基因组关联分析定位水稻分蘖角度QTL

doi:10.16819/j.1001-7216.2024.230904

摘要/Abstract

摘要：

【目的】水稻分蘖角度是影响水稻产量的关键农艺性状，挖掘水稻分蘖角度QTL（基因）及其优势单倍型，有助于构建水稻理想株型。【方法】以333份来自水稻3K资源的核心种质为研究材料，于2020年和2022年分别在湖南农业大学耘园基地和春华基地种植，在抽穗期测量分蘖角度，结合基因型，利用TASSEL 5.2的MLM模型进行全基因组关联分析。【结果】共检测到6个分蘖角度QTL位点，分布在水稻2、5、6、9和12号染色体上，分别命名为qTA2、qTA5、qTA6.1、qTA6.2、qTA9和qTA12，这些QTL的表型贡献率为6.23%~16.22%。除了qTA9与分蘖角度主效QTL TAC1共定位外，其余5个QTL均为新的位点。进一步对5个QTL位点进行候选基因分析，初步筛选到qTA2和qTA6.1的候选基因别为Os02g0817900和Os06g0682800，候选基因Os02g0817900编码水稻细胞色素P450家族蛋白，候选基因Os06g0682800编码锌指结构域蛋白。【结论】本研究挖掘到新的水稻分蘖角度相关位点并对候选基因进行了分析，为分蘖角度新QTL（基因）的克隆以及分蘖角度的遗传改良提供参考。

关键词: 水稻, 分蘖角度, QTL, 候选基因, 单倍型

Abstract:

【Objective】Tiller angle is a critical agronomic trait influencing rice yield. Identifying rice tiller angle QTL (genes) and detecting their elite haplotypes can be beneficial for developing ideal rice varieties. 【Method】333 core germplasms from the rice 3K resources were utilized as research materials. These germplasms were cultivated in Yunyuan and Chunhua of Hunan Agricultural University in 2020 and 2022, respectively. Tiller angles of various germplasms were measured during the heading stage. Genome-wide association analysis was conducted using the MLM model of TASSEL 5.2, combined with the genotypes of the germplasms. 【Results】Six QTL for tiller angle were identified on rice chromosomes 2, 5, 6, 9, and 12, designated as qTA2, qTA5, qTA6.1, qTA6.2, qTA9, and qTA12, respectively. These QTL explained phenotypic variation ranging from 6.23% to 16.22%. Notably, qTA9 co-localized with the major QTL TAC1 for tiller angle, while the other five QTL were newly discovered. Candidate gene analysis was conducted for these five QTL. The candidate genes for qTA2 and qTA6.1 were identified as Os02g0817900 and Os06g0682800, respectively. Os02g0817900 encodes a rice cytochrome P450 family protein, while Os06g0682800 encodes a zinc finger domain protein.【Conclusion】This study successfully identified new QTL for tiller angle in rice and analyzed candidate genes, offering valuable insights for the cloning of tiller angle QTL (genes) and genetic improvement of tiller angle in rice.

Key words: rice (Oryza sativa L.), tiller angle, QTL, candidate gene, haplotype

朱裕敬, 桂金鑫, 龚成云, 罗新阳, 石居斌, 张海清, 贺记外. 全基因组关联分析定位水稻分蘖角度QTL[J]. 中国水稻科学, 2024, 38(3): 266-276.

ZHU Yujing, GUI Jinxin, GONG Chengyun, LUO Xinyang, SHI Jubin, ZHANG Haiqing, HE Jiwai. QTL Mapping for Tiller Angle in Rice by Genome-wide Association Analysis[J]. Chinese Journal OF Rice Science, 2024, 38(3): 266-276.

图/表 9

表1 全基因组关联分析定位水稻分蘖角度QTL

Table 1. List of QTL for tiller angle by GWAS

年份 Year	QTL	染色体 Chr	关联位点 SNP	位置 Position	P值 P value	贡献率 R²(%)
2020	qTA2	2	78 251 484	34 980 561	2.82×10⁻⁵	13.28
	qTA9	9	290 983 508	20 510 958	2.58×10⁻⁵	13.66
	qTA12	12	365 807 909	20 094 246	3.08×10⁻⁶	16.22
2022	qTA5	5	165 535 507	14 410 821	4.36×10⁻⁵	6.23
	qTA6.1	6	208 648 428	27 565 308	1.95×10⁻⁶	8.29
	qTA6.2	6	209 509 442	28 426 322	7.28×10⁻⁶	7.54
	qTA9	9	291 032 810	20 560 260	7.45×10⁻⁸	10.41

图1 水稻种质群体分蘖角度统计分析***P<0.001. ns, P>0.05.

Fig. 1. Statistical analysis of tiller angle in rice germplasms

图2 水稻分蘖角度GWAS分析

Fig. 2. GWAS analysis for tiller angle

表2 水稻分蘖角度候选基因

Table 2. Candidate genes of rice tiller angle

QTL位点 QTL	候选基因 Candidate gene	功能注释 Description
qTA2	Os02g0817600	生长素/吲哚-3-乙酸蛋白
		Auxin/indole-3-acetic acid protein
	Os02g0817900	细胞色素P450家族蛋白
		Cytochrome P450 family protein
qTA6.1	Os06g0663800	叶绿体前体
		Chloroplast precursor
	Os06g0665400	F-box结构域蛋白
		F-box domain containing protein
	Os06g0666500	锌指结构域蛋白
		Zinc finger domain containing protein
	Os06g0679400	Myb转录因子
		Myb-transcription factor
qTA6.2	Os06g0680700	细胞色素P450家族蛋白
		Cytochrome P450 family protein.
	Os06g0682800	锌指结构域蛋白
		Zinc finger domain containing protein
	Os06g0683000	锌指结构域蛋白
		Zinc finger domain containing protein
	Os12g0516900	F-box结构域蛋白
		F-box domain containing protein
qTA12	Os12g0517000	F-box结构域蛋白
		F-box domain containing protein
	Os12g0517100	F-box结构域蛋白
		F-box domain containing protein

表3 候选基因单倍型分组及每种单倍型的SNP组成

Table 3. Candidate gene haplotype group and composition of each haplotype SNP

基因 Gene		单倍型1/种质数 Hap1/Accession number	单倍型2/种质数 Hap2/Accession number	单倍型3/种质数 Hap3/Accession number
Os02g0817900	AACGGACAAT/51	AACGGGCAAT/33	TGATGACGGCGC/81
Os06g0682800		GGGATG/77	GATACCA/70
Os06g0663800		ATGGCCCGC/46	ATTGCCCGC/41	GCGAATTAT/74
Os02g0817600		CGATCC/56	CGCGTT/25	GACGTC/50
Os06g0680700		AATTCAATGAAGCTGAAG/78	GGGGGGGCAGGCGCTGGT/79

图3 分蘖角度候选基因表达量热图及单倍型箱线图

Fig. 3. Expression heat map and box plot for tiller angle candidate gene haplotype

图4 TAC1单倍型分析 A: qTA9中−lg P>4的SNP连锁不平衡分析; B: TAC1的结构示意图以及单倍型，不同小写字母表示差异显著(P<0.05); C: TAC1不同单倍型的亚群组成; D TAC1不同单倍型种质的地理分布

Fig. 4. TAC1 haplotype analysis A, Linkage disequilibrium plot for SNPs with -lg P> 4 in qTA9; B, TAC1 gene structure and haplotype schematic. Different lowercase letters indicate significant differences (P<0.05); C: The subpopulation composition of TAC1 haplotypes; D, Geographical distribution of different haplotypes of TAC1.

图5 Os02g0817900单倍型分析 A: qTA2中−lg P>4的SNP连锁不平衡分析; B: Os02g0817900的结构示意图以及单倍型，不同小写字母表示差异显著(P<0.05); C: Os02g0817900不同单倍型的亚群组成; D: Os02g0817900不同单倍型种质的地理分布。

Fig. 5. Os02g0817900 haplotype analysis A, Linkage disequilibrium plot for SNPs with -lg P> 4 in qTA2; B, Os02g0817900 structure and haplotype schematic. Different lowercase letters indicate significant differences(P<0.05); C, Subpopulation composition of Os02g0817900 haplotypes; D, Geographical distribution of haplotypes of Os02g0817900.

图6 Os06g0682800单倍型分析 A: qTA6中−lg P>4的SNP连锁不平衡分析; B: Os06g0682800的结构示意图以及单倍型，不同小写字母表示差异显著(P<0.05); C: Os06g0682800不同单倍型的亚群组成; D Os06g0682800不同单倍型种质的地理分布

Fig. 6. Os06g0682800 haplotype analysis A, Linkage disequilibrium plot for SNPs with -lg P> 4 in qTA6; B, Os06g0682800 structure and haplotype Schematic. Different lowercase letters indicate significant differences(P<0.05); C, Subpopulation composition of Os06g0682800 haplotypes; D, Geographical distribution of haplotypes of Os06g0682800.

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