冬小麦籽粒主要品质性状的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2023.11.002

Abstract

Abstract:

【Objective】The quality of wheat grain was an important factor affecting the processing quality and nutritional. Mining loci and candidate genes significantly associated with wheat grain quality traits provided a basis for broadening the understanding of the genetic mechanism of quality traits and molecular marker-assisted quality. 【Method】By measuring five quality traits, including protein content (GPC), wet gluten content (WGC), starch content (GSC), settling value (SV) and grain hardness (GH), in 259 winter wheat varieties (lines) from domestic and abroad, and conducting genome-wide association analysis in combination with 90K SNP chip, the significant association loci located were subjected to haplotype analysis. 【Result】All five traits conformed to normal distribution and showed rich variation among different environments, and the coefficient of variation of sedimentation value was the largest (20.11%-24.42%). All traits have shown highly significant differences (P<0.001) among genotype, environment, and genotype×environment, with a broad-sense heritability of 0.77-0.84. A total of 44 loci significantly associated (P<0.001) with five traits were detected by genome-wide association analysis, distributed in 19 linkage groups other than chromosomes 1D and 3D. Eighteen loci were stable in two or more environments, involving all five traits including protein content (12), wet gluten content (9), starch content (11), sedimentation value (12) and grain hardness (7), explaining 4.27%-10.98% of the genetic variation. Thirteen of them were multi-effect loci, with the largest number of multi-effect loci (7) associated with traits such as protein content, wet gluten content, settling value and starch content. The GENE-0762_631, IAAV7742 and RAC875_c66845_466 loci located on 2B, 2D and 3A chromosomes were detected simultaneously at two environmental and BLUP values with a range of 4.32%-7.07% phenotypic contribution. Through haplotype analysis of multi-effect loci present in multiple environments with high phenotypic contribution, four different haplotypes, Hap1, Hap2, Hap3 and Hap4, which were significantly associated with traits such as protein content, sedimentation value and starch content, were uncovered at the D_GDS7LZN02F4FP5_176 locus of chromosome 5D, among them Hap1 was a high starch content haplotype (P<0.001), while Hap2 and Hap3 were both haplotypes with high protein content and sedimentation value (P<0.05), and the four haplotypes accounted for 74.22%, 16.21%, 6.92% and 2.65%, respectively. The distribution frequencies of haplotypes from different sources of winter wheat were analyzed, in which the distribution frequencies of haplotype Hap2 with high protein content and sedimentation value were from high to low in the Huanghuai winter wheat regions>northern winter wheat region>abroad varieties>middle and lower reaches of the Yangtze River winter wheat region>southwest winter wheat region. Candidate genes were mined for stable genetic loci, and 10 candidate genes that might be related to wheat grain quality were screened. 【Conclusion】In the study, 18 stable loci significantly associated with grain quality traits were detected, 4 different haplotypes were identified, and 10 candidate genes related to grain quality were screened.

Key words: winter wheat, quality, SNP marker, GWAS, haplotype, candidate genes

DONG YiFan, REN Yi, CHENG YuKun, WANG Rui, ZHANG ZhiHui, SHI XiaoLei, GENG HongWei. Genome-Wide Association Study of Grain Main Quality Related Traits in Winter Wheat[J].Scientia Agricultura Sinica, 2023, 56(11): 2047-2063.

Figures/Tables 9

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Stable loci significantly associated with wheat grain quality traits"

性状 Trait	标记 Marker	染色体 Chr.	位置 Position (Mb)	P值 P-value	表型贡献率 R²	环境 Environment
蛋白质含量 GPC (%)	BobWhite_c1027_1127	1A	586.91—590.20	1.26E^-04-7.47E^-04	4.89—7.32	E2/E3
	wsnp_Ex_c5740_10081171	2B	733.71—742.81	4.60E^-04-8.98E^-04	4.63—5.14	E1/E3
	GENE-0762_631	2B	790.44—790.76	5.76E^-05-8.35E^-04	4.57—6.55	E1/E2/E3
	IAAV7742	2D	645.61	4.41E^-05-9.28E^-04	4.63—7.07	E2/E3
	RAC875_c66845_466	3A	54.46—61.31	1.47E^-04-9.65E^-04	4.32—5.78	E1/E2/E3
	wsnp_Ex_c8360_14085858	3B	5.67—5.95	6.13E^-04-8.42E^-04	4.55—7.67	E2/E3
	Excalibur_rep_c102020_253	4A	631.90—631.92	4.96E^-05-9.82E^-04	4.42—7.18	E1/E3
	Tdurum_contig33737_157	4B	37.69	3.04E^-04-7.19E^-04	4.59—5.02	E1/E3
	BS00077733_51	5B	693.87	3.25E^-04-9.88E^-04	4.27—5.82	E2/E3
	D_GDS7LZN02F4FP5_176	5D	559.92—562.12	2.12E^-04-8.58E^-04	4.53—6.26	E2/E3
	Kukri_c74599_85	7A	14.19—19.97	6.81E^-05-9.21E^-04	4.64—6.40	E1/E3
	RAC875_c80504_487	7A	30.09—35.60	8.05E^-04-9.89E^-04	5.61—8.55	E2/E3
湿面筋含量 WGC (%)	BobWhite_c1027_1127	1A	586.91	4.09E^-05-7.87E^-04	5.23—6.79	E2/E3
	wsnp_Ex_c5740_10081171	2B	742.81	5.86E^-04-9.77E^-04	4.46—5.02	E1/E3
	GENE-0762_631	2B	790.44—790.76	5.76E^-05-7.62E^-04	4.89—5.45	E1E3
	RAC875_c66845_466	3A	54.46	3.75E^-04-6.06E^-04	4.32—4.79	E1/E2/E3
	wsnp_Ex_c8360_14085858	3B	5.67—5.95	7.23E^-04-8.04E^-04	5.62—8.91	E2/E3
	Excalibur_rep_c102020_253	4A	631.90—631.92	3.35E^-04-7.28E^-04	4.69—6.36	E1/E3
	Tdurum_contig33737_157	4B	37.69	3.04E^-04-6.37E^-04	4.78—5.21	E1/E3
	BS00077733_51	5B	693.87	4.66E^-04-6.03E^-04	4.70—5.17	E2/E3
	Kukri_c74599_85	7A	14.19—19.97	4.02E^-04-6.23E^-04	4.74—5.08	E1/E3
沉降值 SV (mL)	BobWhite_c1027_1127	1A	586.91—593.30	5.25E^-04-5.79E^-04	4.66—7.36	E2/E3
	wsnp_Ex_c5740_10081171	2B	733.71—742.81	4.60E^-04-8.23E^-04	4.78—5.14	E1/E3
	GENE-0762_631	2B	790.44—790.76	6.26E^-04-7.09E^-04	5.02—6.19	E1/E2
	IAAV7742	2D	645.61	8.84E^-05-6.72E^-04	5.81—7.04	E1/E3
	RAC875_c66845_466	3A	54.46—61.31	4.03E^-04-9.58E^-04	4.25—5.02	E1/E3
	wsnp_Ex_c8360_14085858	3B	5.67—5.95	6.66E^-04-8.40E^-04	5.69—7.21	E2/E3
	Excalibur_rep_c102020_253	4A	631.90—631.92	5.30E^-04-6.78E^-04	4.66—5.19	E1/E3
	Tdurum_contig33737_157	4B	37.69	6.22E^-04-7.00E^-04	4.59—5.10	E1/E3
	BS00077733_51	5B	693.87	5.22E^-04-7.28E^-04	4.63—5.24	E2/E3
	D_GDS7LZN02F4FP5_176	5D	559.92—562.12	2.55E^-04-7.63E^-04	4.53—5.32	E2/E3
	Kukri_c67_1504	6A	73.72—75.02	2.86E^-04-9.14E^-04	4.44—5.44	E1/E3
	RAC875_c80504_487	7A	30.09—35.60	8.05E^-04-8.69E^-04	5.82—8.06	E2/E3
淀粉含量 GSC (%)	BobWhite_c1027_1127	1A	593.3	5.62E^-05-2.71E^-04	5.06—7.59	E2/E3
	wsnp_Ex_c5740_10081171	2B	733.71—742.81	4.60E^-04-7.67E^-04	4.46—5.11	E1/E3
	GENE-0762_631	2B	790.44—790.76	9.23E^-05-6.26E^-04	4.57—6.02	E2/E3
	IAAV7742	2D	645.61	7.78E^-05-4.36E^-04	5.03—6.58	E1/E2/E3
	RAC875_c66845_466	3A	54.46—61.31	2.06E^-04-7.26E^-04	4.65—5.28	E2/E3
	Excalibur_rep_c102020_253	4A	631.90—631.92	6.15E^-04-8.62E^-04	4.89—6.69	E1/E3
	Tdurum_contig33737_157	4B	37.69	5.32E^-04-5.98E^-04	4.63—5.63	E1/E3
	BS00077733_51	5B	693.87	4.24E^-04-6.06E^-04	4.27—5.82	E2/E3
	D_GDS7LZN02F4FP5_176	5D	559.92—562.12	4.62E^-04-7.31E^-04	5.26—7.08	E2/E3
	Kukri_c67_1504	6A	73.72—75.02	4.26E^-04-6.26E^-04	4.87—5.02	E1/E3
	RAC875_c80504_487	7A	35.6	8.05E^-04-9.08E^-04	6.23—7.03	E2/E3
籽粒硬度 GH (%)	GENE-1019_96	2A	2.48	1.51E^-04-4.90E^-04	4.96—5.83	E1/E2/E3
	BobWhite_c2002_100	2A	535.72	5.67E^-04-7.71E^-04	4.66—4.99	E1/E3
	BS00081871_51	2B	12.08—17.39	6.81E^-05-9.21E^-04	5.08—6.40	E1/E3
	wsnp_Ex_c8360_14085858	3B	5.67—5.95	6.18E^-04-6.41E^-04	5.60—7.99	E2/E3
	BS00000020_51	5D	3.61	4.06E^-07-1.82E^-05	7.75—10.98	E1/E2/E3
	Kukri_c74599_85	7A	14.19—19.97	5.22E^-05-7.26E^-04	5.02—6.21	E1/E3
	Kukri_c34147_152	7A	689.95—690.05	2.81E^-04-5.26E^-04	6.08—6.78	E2/E3

Table 3

Table 4

Stable loci significantly associated with two or more grain quality traits"

性状 Trait	标记 Marker	染色体 Chr.	位置 Position (Mb)	P值 P-value	表型贡献率 R²	环境 Environment
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	BobWhite_c1027_1127	1A	586.91—593.30	4.09E^-05-7.87E^-04	4.66—7.59	E2/E3
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	wsnp_Ex_c5740_10081171	2B	733.71—742.81	4.60E^-04-9.77E^-04	4.46—5.14	E1/E3
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	GENE-0762_631	2B	790.44—790.76	5.76E^-05-8.35E^-04	4.57—6.55	E1/E2/E3
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC	IAAV7742	2D	645.61	4.41E^-05-9.28E^-04	4.63—7.07	E1/E2/E3
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	RAC875_c66845_466	3A	54.46—61.31	1.47E^-04-9.65E^-04	4.32—5.78	E1/E2/E3
蛋白质含量、湿面筋含量、沉降值、籽粒硬度 GPC, WGC, SV, GH	wsnp_Ex_c8360_14085858	3B	5.67—5.95	6.13E^-04-8.42E^-04	4.55—8.91	E2/E3
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	Excalibur_rep_c102020_253	4A	631.90—631.92	4.96E^-05-9.82E^-04	4.42—7.18	E1/E3
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	Tdurum_contig33737_157	4B	37.69	3.04E^-04-7.19E^-04	4.60—5.21	E1/E3
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	BS00077733_51	5B	693.87	3.25E^-04-9.88E^-04	4.27—5.82	E2/E3
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC	D_GDS7LZN02F4FP5_176	5D	559.92—562.12	2.12E^-04-8.58E^-04	4.53—7.08	E2/E3
沉降值、淀粉含量SV, GSC	Kukri_c67_1504	6A	73.72—75.02	2.86E^-04-9.14E^-04	4.44—5.44	E1/E3
蛋白质含量、湿面筋含量、籽粒硬度 GPC, WGC, GH	Kukri_c74599_85	7A	14.19—19.97	6.81E^-05-9.21E^-04	4.64—6.40	E1/E3
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC	RAC875_c80504_487	7A	30.09—35.60	8.05E^-04-9.89E^-04	5.61—8.55	E2/E3

Table 4

Fig. 3

Fig. 4

Table 5

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性状 Traits	环境 Environment	范围 Range	平均值±标准差 Mean±SD	变异系数 CV (%)	偏度 Ske.	峰度 Kur.	F值F value			遗传力 h²
性状 Traits	环境 Environment	范围 Range	平均值±标准差 Mean±SD	变异系数 CV (%)	偏度 Ske.	峰度 Kur.	基因型 Genotype	环境 Environment	基因型×环境 G×E	遗传力 h²
蛋白质含量 GPC (%)	E1	13.52—19.22	16.38±1.15	7.01	-0.10	-0.70	16.96***	3101.12***	4.29***	0.79
蛋白质含量 GPC (%)	E2	12.77—18.67	15.55±1.21	7.77	0.40	-0.26	16.96***	3101.12***	4.29***	0.79
湿面筋含量 WGC (%)	E1	24.78—37.93	31.75±2.88	9.07	-0.03	-0.76	17.50***	2995.32***	4.38***	0.79
湿面筋含量 WGC (%)	E2	22.58—38.28	28.98±2.87	9.91	0.60	0.29	17.50***	2995.32***	4.38***	0.79
沉降值 SV (mL)	E1	24.05—68.55	48.18±9.69	20.11	-0.11	-0.80	13.10***	4212.30***	3.67***	0.77
沉降值 SV (mL)	E2	16.95—67.50	40.27±9.83	24.42	0.50	0.01	13.10***	4212.30***	3.67***	0.77
淀粉含量 GSC (%)	E1	57.89—62.94	60.88±0.79	1.29	-0.64	1.10	17.84***	2858.98***	4.39***	0.79
淀粉含量 GSC (%)	E2	59.94—64.14	62.40±0.75	1.20	-0.42	0.13	17.84***	2858.98***	4.39***	0.79
籽粒硬度 GH (%)	E1	41.22—77.87	65.21±7.28	11.17	-0.62	-0.18	17.10***	7352.58***	3.03***	0.84
籽粒硬度 GH (%)	E2	36.07—76.42	59.20±8.12	13.71	-0.16	-0.31	17.10***	7352.58***	3.03***	0.84

性状 Traits	统计参数 Statistical parameters	国内品种Domestic varieties				国外品种 Abroad varieties
性状 Traits	统计参数 Statistical parameters	黄淮冬麦区 Huanghuai winter wheat region	北部冬麦区 Northern winter wheat region	长江中下游冬麦区 Middle and lower reaches of the Yangtze River winter wheat region	西南冬麦区 Southwest winter wheat region	国外品种 Abroad varieties
蛋白质含量 GPC (%)	平均值±标准差 Mean±SD	16.17±0.78	16.06±0.95	15.87±0.77	15.54±0.65	15.69±0.93
	范围Range	13.94—18.15	14.46—17.98	14.32—17.10	14.62—16.89	13.61—17.6
	变异系数CV (%)	4.85	5.93	4.86	4.16	5.91
湿面筋含量 WGC (%)	平均值±标准差 Mean±SD	31.58±3.66	30.91±4.35	29.56±3.75	28.03±2.63	28.73±4.04
	范围Range	19.66—41.18	23.93—39.74	19.02—35.89	24.26—34.83	21.01—38.15
	变异系数CV (%)	11.60	14.09	12.69	9.37	14.05
沉降值 SV (mL)	平均值±标准差 Mean±SD	46.18±6.98	44.38±7.50	43.98±6.27	40.84±4.63	41.55±8.21
	范围Range	29.26—61.74	29.81—62.44	30.68—53.98	34.6—51.71	24.07—61.02
	变异系数CV (%)	15.11	16.91	14.26	11.33	19.76
淀粉含量 GSC (%)	平均值±标准差 Mean±SD	61.55±0.59	61.68±0.64	61.77±0.42	62.12±0.43	61.56±0.51
	范围Range	60.17—62.80	60.07—62.8	60.89—62.76	61.20—62.89	60.01—62.78
	变异系数CV (%)	0.95	1.04	0.67	0.69	0.83
籽粒硬度 GH (%)	平均值±标准差 Mean±SD	63.67±4.41	62.38±5.33	60.21±4.64	58.41±4.77	61.47±5.37
	范围Range	50.49—73.57	52.04—74.33	51.44—70.51	50.91—69.03	44.95—73.44
	变异系数CV (%)	6.92	8.55	7.71	8.17	8.74

Genome-Wide Association Study of Grain Main Quality Related Traits in Winter Wheat

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性状 Trait	位点 Marker	染色体 Chr.	物理位置 Position (Mb)	基因 Gene	基因注释或编码蛋白 Gene annotation or coding protein
籽粒硬度GH	BobWhite_c2002_100	2A	535.72	TraesCS2A02G312200	锌指蛋白 Zinc finger protein
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	GENE-0762_631	2B	790.44—790.76	TraesCS2B02G630000	激酶家族蛋白 Kinase family protein
籽粒硬度GH	BS00081871_51	2B	12.08—17.39	TraesCS2B02G027900	糖基转移酶 Glycosyltransferase
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC	IAAV7742	2D	645.61	TraesCS2D02G587400	LRR受体样激酶家族蛋白 LRR receptor-like kinase family protein
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	RAC875_c66845_466	3A	54.46—61.31	TraesCS3A02G084800	细胞色素P450家族蛋白 Cytochrome P450 family protein
蛋白质含量、湿面筋含量、沉降值、淀粉含量 GPC, WGC, SV, GSC	Excalibur_rep_c102020_253	4A	631.90—631.92	TraesCS4A02G360000	磷酸转运蛋白 Phosphate transporter protein
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC	D_GDS7LZN02F4FP5_176	5D	559.92—562.12	TraesCS5D02G558100	糖转运蛋白，推定 Sugar transporter, putative
籽粒硬度GH	BS00000020_51	5D	3.61	TraesCS5D02G004900	细胞色素P450家族蛋白 Cytochrome P450 family protein
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC	RAC875_c80504_487	7A	30.09—35.60	TraesCS7A02G061400	F-box家族蛋白 F-box protein
蛋白质含量、湿面筋含量、籽粒硬度 GPC, WGC, GH	Kukri_c74599_85	7A	14.19—19.97	TraesCSU02G168200	天冬氨酸蛋白酶 Aspartic proteinase

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