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

摘要/Abstract

摘要：

【目的】果粒大小是葡萄外观和产量的重要构成因子之一，为受多基因调控的复杂数量性状，挖掘葡萄果粒大小相关性状的关键遗传调控位点和基因，将有助于葡萄产量的提高。【方法】本研究以150份葡萄品种资源为材料，分别于2019年和2020年对葡萄果实单粒重、种子数目和种子质量等进行测定，并结合重测序获得的高密度基因型数据进行全基因组关联分析（genome-wide association study，GWAS），挖掘调控各性状的遗传位点和基因。【结果】各性状在关联群体中呈现广泛的连续变异，变异系数为39.55%—68.89%；在不同年份均服从正态分布，符合数量性状遗传特征；相关性分析表明葡萄果实单粒重、种子数目和种子质量呈显著正相关。全基因组关联分析共检测到150个与果实单粒重显著关联的SNP，在2019年检测到99个SNP，解释表型变异的14.48%—25.59%；在2020年检测到73个SNP，解释表型变异的16.08%—26.83%；其中24个SNP位点在两个年份均检测到，主要位于1号、5号、11号和16号染色体。相较于果实单粒重，检测到的与种子数目显著关联的SNP较少，2019年检测到1个显著性SNP，表型解释率为24.29%；2020年检测到17个显著性SNP，均位于18号染色体。两个年份检测到与种子质量显著关联的SNP分别有1个和2个，位于18号染色体，解释表型变异的23.59%—48.29%。在两年重复检测到SNP位点基因组区域内，根据基因功能注释筛选出11个可能与果实单粒重相关的候选基因，其中包括乙烯信号通路基因（基因ID：VIT_05s0049g00490、VIT_05s0049g00500、VIT_05s0049g00510和VIT_16s0100g00400）、赤霉素信号途径基因（基因ID：VIT_11s0016g04630和VIT_16s0022g02310）、生长素响应蛋白基因（基因ID：VIT_11s0016g05640）和一些重要的转录因子基因（基因ID：VIT_05s0049g00460、VIT_11s0016g05660和VIT_16s0022g02330）。在18号染色体鉴定到与种子含量相关的候选基因（基因ID：VIT_18s0041g01880，编码MADS-box蛋白VviAGL11），位于该基因上的SNP基因型变化显著影响葡萄果实种子数目和质量。【结论】结合两个年份的表型数据，共检测到150个与果实单粒重显著关联的SNP，主要定位于1号、5号、11号和16号等染色体；检测到19个与种子含量关联的SNP，主要定位于18号染色体。基于基因注释和基因型分析结果，确定了包含VIT_11s0016g04630和VIT_16s0022g02310等在内的11个候选基因可能参与调控葡萄果实单粒重，确定候选基因（基因ID：VIT_18s0041g01880）与种子含量显著相关。

关键词: 葡萄, 果粒大小, 全基因组关联分析, 候选基因

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

王慧玲, 闫爱玲, 王晓玥, 刘振华, 任建成, 徐海英, 孙磊. 葡萄果粒质量相关性状全基因组关联分析[J]. 中国农业科学, 2023, 56(8): 1561-1573.

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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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]