棉花产量构成因素性状的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2022.12.001

摘要/Abstract

摘要：

【目的】对铃重、衣分、单株铃数和籽指等棉花产量构成因素性状进行全基因组关联分析（genome-wide association study,GWAS）,发掘与其关联的标记位点、优异等位变异及候选基因,为棉花产量的分子育种提供理论依据。【方法】以408份陆地棉品种（系）资源为材料,利用Cotton SNP 80K芯片,对6个环境的铃重、衣分、单株铃数和籽指4个产量构成因素性状进行基于混合线性模型（mixed linear model,MLM）的全基因组关联分析,检测与产量构成因素性状显著关联的位点、优异等位变异;进一步依据转录组数据的基因表达量,在显著关联的位点侧翼序列1 Mb区间挖掘可能的候选基因。【结果】 4个产量构成因素性状在不同环境下均表现出广泛的表型变异,其中,单株铃数变异系数最大为16.67%—22.66%,各性状的遗传率为48.4%—92.2%;除铃重与衣分间相关性不显著外,其他性状间均呈显著或极显著相关性;基于6个环境各性状表型数据的最佳线性无偏预测值（best linear unbiased prediction,BLUP）,GWAS共检测到分布于基因组的7个区间内23个与目标性状关联的SNP位点,其中,与铃重关联的位点5个,与衣分关联的位点1个,与单株铃数关联的位点9个,与籽指关联的位点8个,有3个位点（TM21094、TM21102和TM57382）同时与多个目标性状关联;鉴定到7个最优SNP位点的优异等位变异,分别为TM21099（TT）、TM57382（GG）、TM78920（CC）、TM53448（TT）、TM59015（AA）、TM43412（GG）和TM69770（AA）;利用转录组数据分析,在基因组的7个区间筛选到158个与产量形成可能的候选基因,GO富集分析和KEGG代谢途径分析发现,候选基因功能类别多样并参与了多种代谢途径。【结论】在陆地棉品种（系）群体中共鉴定到23个与产量构成因素性状关联的SNP位点,筛选到158个可能与产量性状相关的候选基因。

关键词: 陆地棉, 产量构成因素, 全基因组关联分析, 候选基因

Abstract:

【Objective】The loci, elite alleles and candidate genes associated with yield component traits, such as boll weight, lint percentage, number of bolls per plant and seed index, were explored using a genome-wide association analysis (GWAS), which provided a theoretical reference for the molecular breeding of cotton yield.【Method】The GWAS based on a mixed linear model was performed on 408 upland cotton accessions grown in six different environments using the Cotton SNP 80K chip for the four yield component traits, and the significant SNP loci (SNPs) and elite allele were also detected. Finally, on the basis of the gene expression levels of the transcriptome, candidate genes related to the target traits were mined within a 1 Mb genome range of the flanking sequences of the significant SNPs. 【Result】The four yield component traits showed wide phenotypic variations in different environments, with the maximum coefficient of variation for number of bolls per plant being 16.67%-22.66%. The heritability of each trait was between 48.4% and 92.2%. The correlations among traits were significant or highly significant, except between boll weight and lint percentage. A total of 23 significant SNPs distributed in seven different genomic regions associated with the four traits were identified across the 408 cotton accessions in the BLUP. The numbers of loci associated with boll weight, lint percentage, number of bolls per plant and seed index were 5, 1, 9 and 8, respectively, and three loci (TM21094, TM21102, and TM57382) were associated with multiple target traits simultaneously. Seven elite allele types, TM21099(TT), TM57382(GG), TM78920(CC), TM53448(TT), TM59015(AA), TM43412(GG) and TM69770(AA), were identified. A total of 158 candidate genes potentially related to yield formation were selected through an analysis of gene expression patterns in RNA-Seq data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the functions and metabolic pathways of most genes were varied.【Conclusion】In this study, 23 significant SNPs associated with four yield component traits were identified across 408 cotton accessions, and 158 candidate genes were predicted using RNA-Seq.

Key words: Upland cotton, yield components, genome-wide association analysis, candidate genes

王娟, 马晓梅, 周小凤, 王新, 田琴, 李成奇, 董承光. 棉花产量构成因素性状的全基因组关联分析[J]. 中国农业科学, 2022, 55(12): 2265-2277.

WANG Juan, MA XiaoMei, ZHOU XiaoFeng, WANG Xin, TIAN Qin, LI ChengQi, DONG ChengGuang. Genome-Wide Association Study of Yield Component Traits in Upland Cotton (Gossypium hirsutum L.)[J]. Scientia Agricultura Sinica, 2022, 55(12): 2265-2277.

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性状 Trait	环境 Environment	最小值 Min	最大值 Max	平均数 Mean	标准差 SD	变异系数 CV (%)	G	G×E	遗传率 <BOLD>H</BOLD>² (%)
铃重 BW	SHZ13	3.10	7.60	5.57	0.56	10.05	**		78.0
	KRL13	3.90	7.90	5.54	0.56	10.11
	SHZ14	3.80	7.70	5.69	0.59	10.37
	KRL14	4.00	7.50	5.70	0.58	10.18
	SHZ15	3.90	7.10	5.43	0.53	9.76
	KRL15	4.30	8.60	6.19	0.67	10.82
	BLUP	4.22	7.16	5.64	0.41	7.27
衣分 LP	SHZ13	31.90	56.10	43.86	3.26	7.43	**	**	92.2
	KRL13	31.50	50.30	41.73	3.05	7.31
	SHZ14	28.70	48.80	39.99	3.31	8.28
	KRL14	27.50	48.40	39.12	3.46	8.84
	SHZ15	28.10	47.20	39.48	3.43	8.69
	KRL15	28.00	48.20	39.56	3.68	9.30
	BLUP	30.28	48.42	40.84	2.90	7.10
单株铃数 BN	SHZ13	2.30	10.90	4.28	0.94	21.96	**	*	48.8
	KRL13	3.10	9.50	5.50	0.96	17.45
	SHZ14	3.70	11.10	6.16	1.14	18.51
	KRL14	5.10	16.30	7.92	1.56	19.70
	SHZ15	3.00	10.80	5.87	1.33	22.66
	KRL15	4.00	11.30	6.00	1.00	16.67
	BLUP	4.82	8.04	5.95	0.50	8.40
籽指 SI	SHZ13	7.50	16.20	10.13	1.16	11.45	**	**	85.4
	KRL13	8.00	16.70	10.29	1.24	12.05
	SHZ14	8.30	17.80	11.15	1.27	11.39
	KRL14	8.20	18.80	11.16	1.39	12.46
	SHZ15	6.50	16.40	10.53	1.20	11.40
	KRL15	8.10	18.50	11.49	1.36	11.84
	BLUP	8.75	16.17	10.71	1.01	9.43

性状 Trait	SNP位点 SNP locus	染色体 Chromosome	位置 Position (bp)	等位基因 Allele	-log₁₀(<BOLD>P</BOLD>)
铃重 BW	TM21099	A07	70392221	T/C	6.07
	TM21097	A07	70365245	T/C	5.92
	TM21094	A07	70345913	T/C	5.60
	TM58956	D06	1287377	A/G	5.11
	TM21102	A07	70411236	A/G	4.90
衣分LP	TM57382	D05	18043944	A/G	4.74
单株铃数 BN	TM78920	D12	42319440	A/C	6.80
	TM78922	D12	42325933	T/C	6.49
	TM78921	D12	42322642	T/A	6.09
	TM53448	D03	1908727	T/C	5.59
	TM53452	D03	1940517	T/C	5.33
	TM53460	D03	1989801	T/C	5.24
	TM78919	D12	42306456	T/C	5.18
	TM59015	D06	1782860	A/G	5.17
	TM53454	D03	1950689	T/C	5.11
籽指 SI	TM43412	A13	5005690	A/G	6.75
	TM21094	A07	70345913	T/C	5.15
	TM69770	D08	62547519	A/T	5.11
	TM43413	A13	5012761	A/G	4.98
	TM21098	A07	70381299	T/C	4.94
	TM21102	A07	70411236	A/G	4.90
	TM57382	D05	18043944	T/C	4.84
	TM21111	A07	70492663	A/G	4.75

性状 Trait	SNP位点 SNP loci	-log₁₀(P)	等位基因 Allele	优异等位变异 Elite allele	表型效应值 a_i
铃重BW	TM21099	6.07	T/C	TT	0.42
衣分LP	TM57382	4.74	A/G	GG	1.73
单株铃数BN	TM78920	6.80	A/C	CC	0.48
	TM53448	5.59	T/C	TT	0.31
	TM59015	5.17	A/G	AA	0.31
籽指SI	TM43412	6.75	A/G	GG	2.14
籽指SI	TM69770	5.11	A/T	AA	1.74

性状 Trait	SNP位点 SNP locus	染色体 Chr.	SNP位置 SNP position (bp)	目标区间 Target region (bp)	前人研究 Previous studies
铃重 BW	TM21099	A07	70392221	69892221—70892221	BW (q^BW)^[6], LP (q^LP-1)^[6], SI (q^SD)^[6], LP (q^LP-c7-1)^[12], SI (q^SI-7-1)^[7], SI (q^SIA7-2)^[14], SI (A07: 70700387)^[27], SI (TM21134)^[29]
衣分LP	TM57382	D05	18043944	17543944—18543944	BN (q^NB-D5-1)^[24]
单株铃数 BN	TM78920	D12	42319440	41819440—42819440	LY (q^LY-C26-1)^[10], SCY (q^YLD-C26-1)^[10], SCY (q^{SCY-06A-c26-1})^[12]
	TM53448	D03	1908727	1408727—2408727	LP (D03: 1424880)^[27]
	TM59015	D06	1782860	1282860—2282860
籽指 SI	TM43412	A13	5005690	4505690—5505690	SI (A13: 4741980)^[27]
籽指 SI	TM69770	D08	62547519	62047519—63047519