陆地棉吐絮率的限制性两阶段多位点全基因组关联分析及候选基因预测

doi:10.3864/j.issn.0578-1752.2022.02.002

Abstract

Abstract:

【Objective】Boll opening rate (BOR) is one of the most important indicators reflecting the early maturing trait of upland cotton (Gossypium hirsutum L.). The genome-wide association study (GWAS) was applied to dissect the QTL (quantitative trait locus) and its genetic effect for providing a theoretical basis for molecular breeding of early maturing traits in upland cotton. 【Method】The natural population composed of 315 different upland cotton varieties (lines) were used to identify the BOR under three environments. Simultaneously, a total of 9 244 SNP linkage disequilibrium block (SNPLDB) markers with multiple alleles were constructed. Then, the restricted two-stage multi-locus GWAS (RTM-GWAS) was utilized to detect SNPLDB loci significantly associated with BOR, estimate its phenotypic effect value, establish QTL-Allele matrix for significantly associated loci in the population, and further detected the stable major SNPLDB loci and elite haplotypes. Finally, according to the gene expression levels of the two transcriptome data, candidate genes that may be related to the target trait were mined within the 1 Mb genome range of the flanking sequence of the significant SNPLDB loci. 【Result】The variation of BOR was ranged from 37.78% to 100.00% and the broad-sense heritability was 67.03% in the natural population under three environments. The multi-environment variance analysis revealed that the BOR was significantly different among genotype, environment and genotype × environment interaction (P<0.001). A total of 52 SNPLDB loci significantly associated with BOR were detected through the RTM-GWAS procedure, containing 179 alleles or haplotypes, among them, the effect values of 90 increasing alleles or haplotypes ranged from 0.014 to 19.43, and the effect values of 89 decreasing alleles or haplotypes ranged from -21.49 to -0.039. Among the significant SNPLDB loci mentioned above, 6 SNPLDB loci were detected simultaneously in both multi-environment and single environment, which were considered as stable SNPLDB loci significantly associated with BOR. Through the significance analysis of phenotypic traits corresponding to different allelic variations of the above six stable SNPLDB loci, the four favorable alleles were identified as LDB_16_37952328(TT), LDB_5_96395565(AA), LDB_16_49503485(TT), and LDB_4_81118668(TT). Besides, further analysis showed that there were significant differences in the frequency distribution of favorable alleles among varieties (lines) in four different ecological regions. Additionally, a total of 178 genes were annotated and 23 potential candidate genes were predicted in the adjacent regions of 4 stable major SNPLDB loci by transcriptome data analysis. 【Conclusion】A total of 52 SNPLDB loci significantly associated with BOR were identified, of which 4 loci were stable major SNPLDB loci. Furthermore, it was predicted that 23 genes might be related to the BOR of upland cotton. These SNPLDBs loci and candidate genes will provide a theoretical basis for marker-assisted breeding of early maturity in upland cotton.

Key words: Upland cotton, boll opening rate, RTM-GWAS, QTL allele matrix, candidate genes

XIE XiaoYu, WANG KaiHong, QIN XiaoXiao, WANG CaiXiang, SHI ChunHui, NING XinZhu, YANG YongLin, QIN JiangHong, LI ChaoZhou, MA Qi, SU JunJi. Restricted Two-Stage Multi-Locus Genome-Wide Association Analysis and Candidate Gene Prediction of Boll Opening Rate in Upland Cotton[J].Scientia Agricultura Sinica, 2022, 55(2): 248-264.

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https://www.chinaagrisci.com/EN/Y2022/V55/I2/248

Figures/Tables 8

Table 1

Table 2

Table 3

SNPLDB loci significantly associated with boll opening rate in upland cotton"

位点 Loci	染色体 Chr.	位置 Position (bp)	-lg(P)	表型变异 PV (%)	共同环境^a Common environments
LDB_16_37952328	16 (D03)	37952328	46.14	1.90	AY-15 (11.49)、SHZ-14 (5.91)
LDB_5_96395565	5 (A05)	96395565	22.69	0.40	AY-15 (7.42)
LDB_16_49503485	16 (D03)	49503485	17.79	0.91	AY-15 (8.49)
LDB_10_6908012	10 (A10)	6908012	16.70	0.87	AY-15 (8.75)
LDB_15_9697358	15 (D02)	9697358	13.52	1.89	AY-15 (8.41)
LDB_21_22036171	21 (D08)	22036171	13.44	1.34
LDB_4_81118668	4 (A04)	81118668	11.80	0.91	AY-15 (4.58)
LDB_3_6725154_6746183	3 (A03)	6725154	11.63	1.21
LDB_1_57527637_57527855	1 (A01)	57527637	10.44	1.11
LDB_16_36553916_36554161	16 (D03)	36553916	9.81	1.72
LDB_11_119047116	11 (A11)	119047116	9.76	0.86
LDB_19_52309050_52309284	19 (D06)	52309050	7.97	1.54
LDB_17_51465593	17 (D04)	51465593	7.93	0.51
LDB_13_54999733	13 (A13)	54999733	7.36	0.61
位点 Loci	染色体 Chr.	位置 Position (bp)	-lg(P)	表型变异 PV (%)	共同环境^a Common environments
LDB_20_6608424	20 (D07)	6608424	6.63
LDB_7_94884564_94884800	7 (A07)	94884564	6.34
LDB_19_53788858	19 (D06)	53788858	6.25	0.27
LDB_9_58666084_58666088	9 (A09)	58666084	6.06	1.12
LDB_6_41226103	6 (A06)	41226103	5.52	9.00
LDB_15_46384945_46385146	15 (D02)	46384945	5.17	0.36
LDB_15_67139952_67140180	15 (D02)	67139952	5.14	1.68
LDB_25_27281705	25 (D12)	27281705	5.10
LDB_23_6012092	23 (D10)	6012092	4.94	0.18
LDB_1_33221331	1 (A01)	33221331	4.06	0.38
LDB_12_96771402	12 (A12)	96771402	3.84	0.97
LDB_15_65780303	15 (D02)	65780303	3.65	0.67
LDB_22_48423583	22 (D09)	48423583	3.64	0.88
LDB_14_45778715_45778973	14 (D01)	45778715	3.58	1.08
LDB_21_5030313_5030325	21 (D08)	5030313	3.55	0.15
LDB_25_39776065	25 (D12)	39776065	3.47	0.37
LDB_26_45642548	26 (D13)	45642548	3.42		SHZ-14 (1.77)
LDB_5_30493466	5 (A05)	30493466	3.20
LDB_12_103902963	12 (A12)	103902963	3.15	0.39
LDB_3_42046528_42046540	3 (A03)	42046528	2.86
LDB_10_70110862_70110882	10 (A10)	70110862	2.51
LDB_13_72681594_72681843	13 (A13)	72681594	2.46	0.21
LDB_19_39327466	19 (D06)	39327466	2.43
LDB_11_18062977	11 (A11)	18062977	2.42	0.44
LDB_8_113962673	8 (A08)	113962673	2.30
LDB_23_24053424	23 (D10)	24053424	2.25	0.43
LDB_21_25090078	21 (D08)	25090078	2.19	0.47
LDB_6_108270563	6 (A06)	108270563	2.05
LDB_25_1835041	25 (D12)	1835041	1.86	0.18
LDB_2_4064617	2 (A02)	4064617	1.76	0.29
LDB_18_52473670	18 (D05)	52473670	1.71	0.32
LDB_13_62696637	13 (A13)	62696637	1.62	0.30
LDB_8_8677270	8 (A08)	8677270	1.56
LDB_24_59986795	24 (D11)	59986795	1.48
LDB_17_1478345	17 (D04)	1478345	1.39	0.42
LDB_5_23314512	5 (A05)	23314512	1.34
LDB_15_17739938	15 (D02)	17739938	1.34
LDB_17_53762505_53762526	17 (D04)	53762505	1.33		AY-14 (4.68)

Table 3

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 4

Candidate genes related to BOR in upland cotton"

组别 Group	候选基因 Candidate gene	基因名称 Gene name	基因功能注释 Gene function annotation
a类 Group a	GH_D03G1078	SWEET10	双向糖转运体SWEET10 Bidirectional sugar transporter SWEET10
	GH_D03G1058	slc25a24	钙结合线粒体载体蛋白 SCAMC-1 Calcium-binding mitochondrial carrier protein SCaMC-1
	GH_D03G1629	IRL5	植物细胞内Ras-group相关LRR蛋白5 Plant intracellular Ras-group-related LRR protein 5
	GH_D03G1059	NA	NA
	GH_D03G1067	Bicc1	蛋白双尾C同源物1 Protein bicaudal C homolog 1
	GH_D03G1594	RABD2C	Ras-related蛋白质RABD2c Ras-related protein RABD2c
	GH_D03G1618	NA	假定的转化酶抑制剂 Putative invertase inhibitor
	GH_A04G1255	RRP6L3	蛋白质RRP6-like 3 Protein RRP6-like 3
	GH_D03G1643	ABCB2	ABC转运体B家族成员2 ABC transporter B family member 2
b类 Group b	GH_D03G1586	HOS1	E3泛素蛋白连接酶HOS1 E3 ubiquitin-protein ligase HOS1
	GH_D03G1616	BRG3	可能与BOI相关的E3泛素蛋白连接酶3 Probable BOI-related E3 ubiquitin-protein ligase 3
	GH_A04G1248	P3H1	脯氨酰3-羟化酶 1 Prolyl 3-hydroxylase 1
	GH_D03G1644	HSF8	热休克因子蛋白HSF8 Heat shock factor protein HSF8
c类 Group c	GH_D03G1617	UPF1	无意义转录本1同源物的调节器 Regulator of nonsense transcripts 1 homolog
	GH_D03G1083	NA	NA
	GH_D03G1610	caskin2	Caskin-2
	GH_A04G1266	SPL6	Squamosa启动子结合样蛋白6 Squamosa promoter-binding-like protein 6
	GH_D03G1087	PAP27	可能失活的紫色酸性磷酸酶27 Probable inactive purple acid phosphatase 27
	GH_D03G1608	At2g01680	含锚蛋白重复蛋白At2g01680 Ankyrin repeat-containing protein At2g01680
	GH_D03G1063	GLO1	过氧化物酶体(S)-2-羟基氧化酶 Peroxisomal (S)-2-hydroxy-acid oxidase GLO1
	GH_D03G1085	IRX15	蛋白质不规则木质部15 Protein IRREGULAR XYLEM 15
	GH_A05G3660	At3g52300	ATP合酶亚基d,线粒体 ATP synthase subunit d, mitochondrial
	GH_A05G3680	NA	NA

Table 4

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性状 Trait	方差来源 Variance	平方和 SS	均方 MS	F值 F- value	P值 P-value	遗传力 H²(%)
吐絮率 BOR	环境Environment	321981.19	160990.59	1084.69	<0.0001	67.03
	基因型Genotype	288095.59	917.50	6.18	<0.0001
	环境×基因型Environment ×Genotype	237515.09	378.21	2.55	<0.0001

Restricted Two-Stage Multi-Locus Genome-Wide Association Analysis and Candidate Gene Prediction of Boll Opening Rate in Upland Cotton

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环境 Env.	吐絮率BOR(%)																平均数 Mean (%)	变幅 Range (%)	变异系数 CV (%)
环境 Env.	13	19	25	31	37	43	49	55	61	67	73	79	85	91	97	N	平均数 Mean (%)	变幅 Range (%)	变异系数 CV (%)
AY-14							3	5	6	19	31	85	133	33		315	80.62	46.73—90.00	9.86
AY-15	4	5	11	23	25	32	35	43	36	22	24	20	19	9	7	315	55.99	10.42—100.00	34.60
SHZ-14					1	1	3	16	28	41	63	62	57	34	9	315	70.80	37.78—98.05	14.42
综合 Syn.					1	2	9	24	48	58	80	44	37	12		315	70.76	39.27—91.32	14.25

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