葡萄果粒质量相关性状全基因组关联分析

doi:10.3864/j.issn.0578-1752.2023.08.011

Abstract

Abstract:

【Objective】Grape berry size is one of important factors affecting grape appearance and the final productivity. It is a complex quantitative trait regulated by multiple genes. Mining the key genetic regulatory loci and the underlying genes for berry size related traits would help to improve grape yield. 【Method】In this study, 150 diverse grapevine varieties were selected as materials. The berry weight, seed number per berry, and seed weight were measured in 2019 and 2020, respectively. Based on high-density genotype data obtained by resequencing, the genome-wide association studies (GWAS) were carried out to detect significantly associated SNPs and to predict important candidate genes.【Result】The three measured traits exhibited extensive phenotypic variation with 39.55%-68.89% of phenotypic variation coefficients; the phenotypic distribution of the observed three traits in the population showed continuous quantitative genetic characteristics; a significant positive correlation between each trait were observed in two years; based on the phenotypic data collected in two years, a total of 150 significant SNPs were detected for berry weight. In 2019, 99 SNPs were detected, each of which contributed the phenotypic variation from 14.48% to 25.59%; in 2020, 73 SNPs were detected, explaining 16.08%-26.83% of phenotypic variation; among these SNPs, 24 were detected repeatedly in both two years, mainly located on chromosome 1, 5, 11 and 16. Compared with the trait of berry weight, less SNPs significantly associated with the seed number were detected. A significant SNP was detected in 2019, and the phenotypic explanation value was 24.29%; in 2020, 17 significant SNPs were detected, which all located on chromosome 18; 1 and 2 SNPs located on chromosome 18 significantly associated with seed weight were detected in 2019 and 2020, respectively, accounting for 23.59%-48.29% of phenotypic variation. Within the genomic region of SNPs detected repeatedly for two years, 11 candidate genes related to berry weight were screened out based on the functional annotation, including ethylene signal pathway genes (VIT_05s0049g00490, VIT_05s0049g00500, VIT_05s0049g00510 and VIT_16s0100g00400), gibberellin signal pathway genes (VIT_11s0016g04630 and VIT_16s0022g02310), auxin responsive protein gene (VIT_11s0016g05640) and some important transcription factor genes (VIT_05s0049g00460, VIT_11s0016g05660 and VIT_16s0022g02330). A candidate gene VIT_18s0041g01880 (encoding a MADS box protein VviAGL11) associated with seed content was identified on chromosome 18, and different SNP genotypes on this gene significantly affected the grape berry seed number and weight. 【Conclusion】A total of 150 SNPs significantly associated with berry weight were detected in two years, mainly located on chromosomes 1, 5, 11 and 16; A total of 19 significant SNPs associated with seed content were detected, mainly located on chromosome 18. Based on the results of gene annotation and genotype analysis, 11 candidate genes that might be involved in the regulation of grape berry weight including VIT_11s0016g04630 and VIT_16s0022g02310 were selected; the candidate gene VIT_18s0041g01880 was determined significantly correlated with seed content.

Key words: grape, berry size, genome-wide association studies, candidate gene

WANG HuiLing, YAN AiLing, WANG XiaoYue, LIU ZhenHua, REN JianCheng, XU HaiYing, SUN Lei. Genome-Wide Association Studies for Grape Berry Weight Related Traits[J].Scientia Agricultura Sinica, 2023, 56(8): 1561-1573.

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References 41

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性状 Trait	年份 Year	变异范围 Variation range	均值±标准差 Mean±SD	偏度 Skewness	峰度 Kurtosis	变异系数 CV (%)
果实单粒重 Berry weight (BW, g)	2019	0.91-11.91	5.62±2.37	-0.02	-0.71	42.17
果实单粒重 Berry weight (BW, g)	2020	1.5-11.7	5.92±2.44	-0.004	-0.72	41.22
种子数 Seed number (SN)	2019	0-4.75	2.23±1.15	-0.69	-0.17	51.57
种子数 Seed number (SN)	2020	0-4	2.20±0.87	-0.52	0.15	39.55
种子质量 Seed weight (SW, g)	2019	0-1.00	0.34±0.22	-0.13	-0.66	64.71
种子质量 Seed weight (SW, g)	2020	0-1.32	0.45±0.31	0.11	-0.97	68.89

性状Trait	2019BW	2019SN	2019SW	2020BW	2020SN	2020SW
2019BW	1	0.442**	0.561**	0.858**	0.166	0.526**
2019SN		1	0.584**	0.407**	0.550**	0.561**
2019SW			1	0.494**	0.360**	0.823**
2020BW				1	0.212*	0.529**
2020SN					1	0.537**
2020SW						1

性状 Trait	染色体 Chr	位置 Position	P值 P value		贡献率R² (%)		基因型 Genotype
性状 Trait	染色体 Chr	位置 Position	2019	2020	2019	2020	基因型 Genotype
单粒重 Berry weight	1	22639484	2.48E-10	1.94E-09	23.45	23.30	T/ A
	5	7537999	6.37E-11	4.89E-10	21.59	22.03	G/A
	5	9220655	6.91E-10	5.16E-10	22.19	23.47	A/G
	11	3961705	1.44E-09	7.32E-10	21.88	24.67	T/C
	11	4206358	1.97E-09	1.31E-10	17.40	21.14	T/G
	11	4206905	1.88E-10	4.3E-11	23.35	26.73	T/A
	11	4207208	1.03E-09	2.53E-10	22.20	25.79	G/A
	11	4207295	8.32E-10	1.29E-10	21.32	25.17	A/G
	11	4208224	1.47E-09	2.31E-10	22.27	26.51	G/A
	11	4211568	6.47E-10	1.50E-10	22.79	26.40	A/G
	11	4212068	3.21E-11	6.20E-12	23.95	27.69	T/C
	11	4337558	1.61E-10	2.89E-11	22.81	26.83	G/A
	11	4342720	8.80E-11	2.30E-10	24.01	25.40	A/T
	11	4342872	3.19E-10	1.38E-09	22.30	22.73	G/C
	11	4420462	1.43E-11	3.06E-10	21.97	21.28	A/G
	11	4835190	1.76E-09	1.30E-10	19.10	24.69	T/G
	11	4855046	1.86E-09	2.45E-10	18.67	22.55	G/A
	11	4902154	1.96E-09	2.16E-10	19.77	24.39	G/A
	11	5132979	4.75E-10	2.43E-09	16.23	16.08	G/A
	11	5164917	2.34E-09	1.70E-09	16.03	17.85	A/T
	11	5168340	4.44E-10	2.25E-10	16.72	19.05	A/G
	11	5169147	1.64E-09	2.72E-09	18.08	18.47	C/T
	16	14893081	1.17E-09	6.98E-10	17.83	18.70	G/A
	16	15790424	1.03E-09	1.96E-09	18.55	18.45	T/C
种子数目 Seed number	18	27835284	2.44E-09	8.72E-10	24.29	25.67	G/A
种子质量 Seed weight	18	26889437	4.90E-11	1.53E-13	40.11	48.29	C/A

基因ID Gene ID	基因组位置 Physical position	基因注释 NR annotation	参考文献 Reference
VIT_01s0150g00260	1: 22675690-22682439	E3泛素蛋白连接酶At3g02290 E3 ubiquitin-protein ligase At3g02290 [Vitis vinifera]	SONG等^[18]
VIT_05s0049g00460	5: 7500113-7506717	转录因子bHLH104异构体X2 Transcription factor bHLH104 isoform X2 [Vitis vinifera]	GU等^[19]
VIT_05s0049g00490	5:7542707-7543164	乙烯响应转录因子ERF095 Ethylene-responsive transcription factor ERF095 [Vitis vinifera]	YUSTE-LISBONA等^[20]
VIT_05s0049g00500	5: 7549843-7550323	乙烯响应转录因子ERF098 Ethylene-responsive transcription factor ERF098 [Vitis vinifera]	YUSTE-LISBONA等^[20]
VIT_05s0049g00510	5: 7567335-7580633	乙烯响应转录因子1B Ethylene-responsive transcription factor 1B [Vitis vinifera]	YUSTE-LISBONA等^[20]
VIT_11s0016g04630	11: 3959481-3961177	DELLA蛋白SLR1 DELLA protein SLR1 [Vitis vinifera]	UPADHYAY等^[21]
VIT_11s0016g05640	11:	生长素响应蛋白IAA9异构体X1 Auxin-responsive protein IAA9 isoform X1 [Vitis vinifera]	SU等^[22]
VIT_11s0016g05660	11: 5121267-5122148	转录因子MYB82 Transcription factor MYB82 [Vitis vinifera]	MORI等^[23]
VIT_16s0022g02310	16: 14861534-14863137	赤霉素-20-氧化酶 gibberellin 20-oxidase [Vitis vinifera]	WANG等^[24]
VIT_16s0022g02330	16: 14940190-14955349	MADS-box转录因子6异构体X1 MADS-box transcription factor 6 isoform X1 [Vitis vinifera]	IRELAND等^[25]
VIT_16s0100g00400	16: 15837953-15838931	乙烯响应转录因子ERF027 Ethylene-responsive transcription factor ERF027 [Vitis vinifera]	YUSTE-LISBONA等^[20]
VIT_18s0041g01880	18: 26888672-26896521	MADS-box蛋白5异构体X2 VviAGL11 MADS-box protein 5 isoform X2 VviAGL11 [Vitis vinifera]	ROYO等^[26]

Genome-Wide Association Studies for Grape Berry Weight Related Traits

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