冬小麦淀粉糊化性状的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2024.18.001

Abstract

Abstract:

【Objective】 Starch is the main component of wheat kernel and plays an important role in processing. The gelatinization characteristic of starch is an important index to evaluate its quality. The genetic variation of starch gelatinization was studied to provide basis for improving wheat quality. 【Method】 Seven starch gelatinization traits, including gelatinization temperature, peak time, peak viscosity, trough viscosity, final viscosity, decay value and recovery value, were phenotypically determined in 205 winter wheat varieties. Genome-wide association analysis was performed using 90K chip, and haplotype analysis was performed on the stable and significant sites found. 【Result】 The seven characteristics, such as pasting temperature, showed abundant variation in different environments, and the coefficient of variation of attenuation value was the largest (29.31%-31.14%). There were significant differences among genotype, environment and genotype × environment, and the generalized heritability was 0.69-0.86. Through genome-wide association analysis, we found 198 loci that showed significant associations with seven traits. It was distributed in 20 other linked groups except 6D chromosome. There were 58 sites that were stable in 2 or more environments, involving all 7 traits, such as pasting temperature (10), peak time (5), peak viscosity (12), trough viscosity (10), final viscosity (7), break down (4) and set back (10), which could explain 5.54%-22.21% of genetic variation, twenty-one new sites were identified. By haplotype analysis of multiple effector sites that exist in multiple environments and have high phenotypic contribution, Four haplotypes, Hap1 (66.84%), Hap2 (16.84%), Hap3 (9.70%) and Hap4 (6.63%), were found at Kukri_c17417_407 on chromosome 4A, which were significantly related to peak viscosity and break down. Where Hap2 is the peak viscosity and high break down. (P<0.0001). The distribution frequency of varieties (lines) containing haplotype Hap2 in different ecological regions was from high to low as Huanghuai winter wheat region>foreign varieties>Southwest winter wheat region>Middle and lower reaches of Yangtze River winter wheat region>Northern winter wheat region. There were 11 single cause multieffect sites, among which there were 3 multiple effect sites associated with final viscosity, set back, peak time and trough viscosity. Jagger_c4026_328 and other 11 stable genetic loci located on 1B, 2A, 3A, 3B, 4A, 4B, 5B and 6B were mined, and 11 candidate genes that might be related to wheat starch gelatinization traits were screened. 【Conclusion】 In this study, RVA parameters had high heritability, and the RVA parameters of wheat starch were different in different environments. In this study, RVA parameters had high heritability, and the RVA parameters of wheat starch were different in different environments. 58 stable loci were detected that were significantly associated with starch gelatinization traits, and 4 different haplotypes were identified on chromosome 4A that were significantly associated with peak viscosity and break down, and 11 candidate genes related to starch gelatinization were screened, which could provide help for marker-assisted high-quality wheat breeding.

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

SHANG Hang, CHENG YuKun, REN Yi, GENG HongWei. Genome-Wide Association Analysis of Starch Gelatinization Traits in Winter Wheat[J].Scientia Agricultura Sinica, 2024, 57(18): 3507-3521.

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Figures/Tables 9

Table 1

Fig. 1

Fig. 2

Table 2

Stable sites significantly associated with wheat starch gelatinization traits"

性状 Trait	标记 Marker	染色体 Chr.	位置 Position	P值 P-value	表型贡献率 R²	环境 Environment
低谷黏度 TV (CP)	Excalibur_c47219_186	2A	711.64-718.22	4.31E^-04-9.81E^-04	5.65-6.95	E2/E3
	CAP8_c5161_541	2A	731.16	2.25E^-04-8.88E^-04	5.81-7.23	E1/E3
	Excalibur_rep_c70961_190	3A	154.03	3.05E^-04-4.54E^-04	6.30-6.69	E1-E2
	GENE-1205_484	6A	611.31	1.81E^-04-9.63E^-04	5.72-7.36	E2/E3
	RAC875_c13093_86	7A	675.40-678.58	1.76E^-04-9.07E^-04	5.78-7.44	E2/E3
	BS00067966_51	2B	725.96	2.25E^-04-7.05E^-04	6.29-8.18	E2/E3
	BS00106143_51	4B	604.2	3.72E^-04-8.25E^-04	5.70-6.58	E2/E3
	RAC875_c10859_229	4B	615.56	2.80E^-04-9.29E^-04	5.68-6.96	E2/E3
	wsnp_Ex_c4815_8597139	6B	24.92-30.89	1.23E^-04-9.93E^-04	5.68-9.55	E1/E2/E3
	BS00111247_51	7B	733.60-734.30	2.30E^-04-7.78E^-04	6.95-8.92	E1/E3
峰值时间 PT (min)	CAP8_c5161_541	2A	731.16	1.53E^-04-9.24E^-04	5.97-10.12	E1/E2/E3
	Ku_c12469_837	5A	596.47-596.52	2.18E^-04-9.79E^-04	5.56-7.60	E2/E3
	BS00067966_51	2B	725.96	2.06E^-04-5.35E^-04	6.02-9.32	E1/E2/E3
	BS00071042_51	3B	796.31	1.58E^-04-3.30E^-04	9.31-10.96	E2/E3
	wsnp_Ex_c4815_8597139	6B	24.92-30.15	1.50E^-04-9.87E^-04	5.62-11.55	E1/E2/E3
峰值黏度 PV (CP)	Kukri_c3289_932	3A	27.01	2.23E^-04-6.52E^-04	5.97-6.99	E1/E3
	Excalibur_rep_c70961_190	3A	154.03	5.65E^-04-6.41E^-04	5.95-6.07	E1/E3
	Kukri_c17417_407	4A	688.1	2.88E^-05-6.59E^-04	5.94-9.09	E1/E2/E3
	Excalibur_rep_c101560_1124	4A	726.45-734.00	4.75E^-04-5.62E^-04	8.30-9.49	E1/E2
	GENE-1205_484	6A	611.31-611.33	1.85E^-04-6.27E^-04	6.13-7.38	E2/E3
	RAC875_c13093_86	7A	675.40-678.58	3.12E^-04-8.96E^-04	5.73-6.84	E2/E3
	BS00067966_51	2B	725.96	5.81E^-04-7.88E^-04	5.71-6.05	E2/E3
	BS00014695_51	3B	636.45	5.53E^-04-5.89E^-04	6.10-8.63	E2/E3
	Tdurum_contig47622_234	4B	13.41	4.09E^-04-7.62E^-04	5.90-6.36	E1/E3
	BS00022525_51	5B	10.44	5.38E^-04-8.97E^-04	6.08-6.51	E2/E3
	Excalibur_c39830_862	6B	24.92-30.89	6.77E^-06-5.03E^-04	6.49-10.83	E1/E2/E3
	BS00111247_51	7B	734.3	5.97E^-04-8.61E^-04	5.97-6.50	E1/E2/E3
糊化温度 PTT (℃)	BobWhite_c2002_100	2A	535.72	2.85E^-04-7.02E^-04	5.88-6.81	E1/E3
	BS00084348_51	3A	9.85-9.86	1.66E^-04-5.46E^-04	6.15-7.29	E1/E3
	RAC875_c4454_1270	7A	127.77	8.94E^-04-9.26E^-04	5.58-5.62	E1/E3
	BS00064465_51	1B	2.33	1.72E^-04-1.84E^-04	10.05-13.10	E1/E3
	wsnp_Ku_c31_62657	2B	75.61	4.31E^-05-5.82E^-04	6.28-8.97	E1/E3
	BS00022512_51	3B	687.76-694.02	5.80E^-05-9.93E^-04	5.58-10.45	E1/E2/E3
	Kukri_c45876_157	6B	716.26	2.56E^-04-7.31E^-04	6.74-8.07	E2/E3
	CAP8_c3231_244	3D	2.80-3.99	6.84E^-04-7.81E^-04	6.00-8.01	E1/E2
	BobWhite_c21589_200	3D	526.05	1.79E^-04-2.18E^-04	7.02-7.27	E1/E3
	D_GDS7LZN01CWBG5_74	7D	516.03-517.22	2.80E^-04-7.53E^-04	5.94-7.03	E2/E3
回升值 SB (CP)	Jagger_c4026_328	2A	711.64-718.22	1.14E^-04-3.07E^-04	5.87-8.99	E1/E2/E3
	CAP8_c5161_541	2A	731.16	1.28E^-04-3.09E^-04	5.92-6.92	E2/E3
	Excalibur_rep_c70961_190	3A	154.03	3.86E^-04-4.48E^-04	6.75-7.29	E1/E3
	RFL_Contig6053_3082	6A	597.79	8.00E^-04-8.03E^-04	5.74-5.84	E1/E3
	BS00067966_51	2B	725.96	3.19E^-04-3.42E^-04	6.61-7.83	E1/E2/E3
	RAC875_c20041_976	3B	60.87	5.27E^-04-5.29E^-04	8.00-8.80	E1/E3
	BS00106143_51	4B	604.2	6.36E^-04-7.66E^-04	5.68-7.83	E2/E3
	RAC875_c10859_229	4B	615.56	6.19E^-04-6.78E^-04	7.21-8.00	E2/E3
	wsnp_Ex_c4815_8597139	6B	25.26-30.15	8.05E^-04-8.24E^-04	6.27-7.50	E2/E3
	BS00042112_51	7B	733.60-734.30	9.35E^-04-9.92E^-04	7.04-8.00	E1/E3
衰减值 BD (CP)	Kukri_c17417_407	4A	688.1	1.53E^-10-8.92E^-04	5.55-22.21	E1/E2/E3
	BS00044040_51	7A	175.69	5.92E^-04-8.45E^-04	5.70-6.04	E1/E3
	RAC875_c40444_84	1B	22.16	1.81E^-04-5.75E^-04	10.07-12.35	E2/E3
	BS00065936_51	5B	571.64	3.95E^-06-6.76E^-05	8.18-11.10	E1/E2/E3
最终黏度 FV (CP)	CAP8_c5161_541	2A	731.16	1.11E^-04-9.02E^-04	5.81-7.86	E2/E3
	Excalibur_rep_c70961_190	3A	154.03	1.33E^-04-9.54E^-04	5.54-7.51	E1/E2/E3
	BS00067966_51	2B	725.96	6.72E^-05-2.66E^-04	6.86-8.25	E1/E2/E3
	BS00106143_51	4B	604.2	2.00E^-04-6.16E^-04	5.99-7.22	E2/E3
	RAC875_c10859_229	4B	615.56	1.60E^-04-4.95E^-04	6.28-7.53	E2/E3
	wsnp_Ex_c4815_8597139	6B	24.92-30.15	7.39E^-05-9.45E^-04	5.64-8.64	E1/E2/E3
	BS00042112_51	7B	733.60-739.93	1.33E^-04-8.47E^-04	7.30-8.73	E1/E2/E3

Table 2

Table 3

Fig. 3

Table 4

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.	遗传力 h²
糊化温度PTT (℃)	E1	68.58-90.45	84.96±5.52	6.49	-1.71	1.89	0.69
糊化温度PTT (℃)	E2	68.90-90.05	84.69±5.95	7.03	-1.70	1.50	0.69
峰值时间 PT (min)	E1	5.03-5.90	5.58±0.17	3.05	-0.73	0.51	0.72
峰值时间 PT (min)	E2	4.87-6.13	5.74±0.22	3.91	-1.43	2.35	0.72
峰值黏度 PV (CP)	E1	506-2244	1411±311	22.01	-0.11	0.26	0.84
峰值黏度 PV (CP)	E2	603-2337	1529±334	21.84	-0.38	0.26	0.84
低谷黏度 TV (CP)	E1	188-1472	978±252	25.81	-0.62	0.28	0.84
低谷黏度 TV (CP)	E2	158-1537	1047±280	26.72	-1.06	0.68	0.84
最终黏度 FV (CP)	E1	406-2812	1961±453	23.10	-0.68	0.56	0.82
最终黏度 FV (CP)	E2	333-2738	2005±474	23.65	-1.25	1.32	0.82
衰减值 BD (CP)	E1	179-975	432.±127	29.31	1.30	2.52	0.86
衰减值 BD (CP)	E2	130-1031	483±150	31.14	0.97	1.14	0.86
回生值 SB (CP)	E1	216-1432	983±210	21.37	-0.61	0.72	0.80
回生值 SB (CP)	E2	175-1244	963±198	20.54	-1.53	2.54	0.80

Genome-Wide Association Analysis of Starch Gelatinization Traits in Winter Wheat

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性状 Trait	标记 Marker	染色体 Chr.	位置 Position	P值 P-value	表型贡献率 R²	环境 Environment
最终黏度、回生值FV、SB	BS00042112_51	7B	733.60-739.93	1.33E^-04-9.92E^-04	7.04-8.73	E1/E2/E3
最终黏度、回生值、峰值黏度、峰值时间、低谷黏度 FV、SB、PV、PT、TV	BS00067966_51	2B	725.96	6.72E^-05-7.88E^-04	5.71-9.32	E1/E2/E3
最终黏度、回生值、低谷黏度 FV、SB、TV	BS00106143_51	4B	604.20	2.00E^-04-8.25E^-04	5.70-8.00	E2/E3
峰值黏度、低谷黏度 PV、TV	BS00111247_51	7B	733.60-734.30	2.30E^-04-8.61E^-04	5.97-8.92	E1/E2/E3
最终黏度、回生值、峰值时间、低谷黏度 FV、SB、PT、TV	CAP8_c5161_541	2A	731.16	1.11E^-04-9.24E^-04	5.81-10.12	E1/E2/E3
最终黏度、回生值、峰值时间、低谷黏度 FV、SB、PT、TV	wsnp_Ex_c4815_8597139	6B	24.92-30.89	6.77E^-06-8.24E^-04	5.62-11.55	E1/E2/E3
最终黏度、回生值、峰值黏度、低谷黏度 FV、SB、PV、TV	Excalibur_rep_c70961_190	3A	154.03	1.33E^-04-9.54E^-04	5.54-7.51	E1/E2/E3
峰值黏度、低谷黏度 PV、TV	GENE-1205_484	6A	611.31-611.33	1.81E^-04-9.63E^-04	5.72-7.38	E2/E3
衰减值、峰值黏度 BD、PV	Kukri_c17417_407	4A	688.10	1.53E^-10-8.92E^-04	5.55-22.21	E1/E2/E3
最终黏度、回生值、低谷黏度 FV、SB、TV	RAC875_c10859_229	4B	615.56	1.60E^-04-9.29E^-04	5.68-8.00	E2/E3
峰值黏度、低谷黏度 PV、TV	RAC875_c13093_86	7A	675.40-678.58	1.76E^-04-9.07E^-04	5.73-7.44	E2/E3

性状 Trait	标记 Marker	染色体 Chr.	位置 Position	基因 Gene	基因注释或编码蛋白 Gene annotation or coding prtein
回生值 SB	Jagger_c4026_328	2A	711.64-718.22	TraesCS2A01G478500	β-葡萄糖苷酶 Beta-glucosidase
最终黏度、回生值、峰值时间、低谷黏度 FV、SB、PT、TV	CAP8_c5161_541	2A	731.16	TraesCS2A01G502400	质膜ATP酶 Plasma membrane ATPase
最终黏度、回生值、峰值黏度、低谷黏度 FV、SB、PV、TV	Excalibur_rep_c70961_190	3A	154.03	TraesCS3A01G157200	泛素结合酶E2 Ubiquitin-conjugating enzyme E2
衰减值、峰值黏度 BD、PV	Kukri_c17417_407	4A	688.10	TraesCS4A01G418100	琥珀酸脱氢酶亚基5 Succinate dehydrogenase subunit 5
衰减值BD	CAP8_c5161_541	1B	22.16	TraesCS1B01G042600	Dirigent蛋白质 Dirigent protein
峰值黏度PV	BS00014695_51	3B	636.45	TraesCS3B03G1002600	PF00686：淀粉结合域 PF00686: Starch binding domain
最终黏度、回生值、低谷黏度 FV、SB、TV	BS00106143_51	4B	604.20	TraesCS4B01G314900	泛素结合酶E2 Ubiquitin-conjugating enzyme E2
最终黏度、回生值、低谷黏度 FV、SB、TV	RAC875_c40444_84	4B	615.56	TraesCS4B01G324500	钙结合EF-Hand蛋白 Calcium-binding EF hand-containing protein
衰减值 BD	BS00065936_51	5B	571.64	TraesCS5B03G0980400	PF00646：F-box域 PF00646: F-box domain
峰值黏度 PV	Excalibur_c39830_862	6B	24.92-30.89	TraesCS6B01G040800	F-box家族蛋白 F-box family protein
最终黏度、回生值、峰值时间、低谷黏度 FV、SB、PT、TV	wsnp_Ex_c4815_8597139	6B	24.92-30.89	TraesCS6B01G050700	羧肽酶 Carboxypeptidase

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单倍型 Haplotypes	等位基因 Alleles	份数 Numbers	频率 Frequency (%)
Hap1	CAA	131	66.84
Hap2	CCG	19	9.70
Hap3	TAA	33	16.84
Hap4	CAG	13	6.63