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

Abstract

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

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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References 51

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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

Genome-Wide Association Study of Yield Component Traits in Upland Cotton (Gossypium hirsutum L.)

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