基于SNP标记的小麦籽粒性状全基因组关联分析

doi:10.3864/j.issn.0578-1752.2021.10.002

Abstract

Abstract:

【Objective】Grain traits are important factors affecting wheat yield. the significant locus of controlling wheat grain traits was explored by genome-wide association analysis of wheat grain traits, which provided a theoretical reference for the study of genetic improvement of wheat grain traits. 【Method】The genome-wide association analysis (GWAS) based on mixed linear model MLM (Q+K) was performed on 121 wheat grown in Xinjiang using wheat 50 K SNP chips for 6 traits which including grain length, grain width, grain length-width ratio, grain area, grain perimeter and 1000-grain weight.【Result】Six grain traits showed wide phenotypic variation in different environments, in which the maximum coefficient of variation of 1000-grain weight was 13.91-17.79 and the heritability of each grain trait was between 0.85-0.90. The polymorphism information content PIC value was 0.09-0.38, and the minimum allele frequency MAF value was 0.05-0.50. Group structure analysis shows that the natural groups used in the experiment can be divided into 4 subgroups. GWAS results showed that a total of 592 significant association sites (P<0.001) were detected in 6 traits, of which 29 SNPs were repeatedly detected in 2 or more environments, distributed in 1A(5), 1B(2), 1D, 2A(5), 3B, 5A, 5D, 6B(4), 6D, 7B and 7D(7) chromosomes, can explain 9.3% to 22.7% of the phenotypic variation. Six markers associated with stable grain length were detected, which distributed on 1A, 2A, and 7D chromosomes to explain the phenotypic variation of 9.9%-22.7%. Two markers associated with stable grain width were detected, which distributed on 3 B and 5 D chromosomes to explain the phenotypic variation of 9.6%-12.2%. Six markers associated with stable grain length-width ratio were detected, which distributed on 2A(2), 5A, 7B, and 7D(2) chromosomes to explain the phenotypic variation of 10.1%-19.4%. Three markers associated with stable grain area were detected, which distributed on 1A, 1B and 1D chromosome to explain the phenotypic variation of 9.9%-18.2%. Six markers with stable correlation with grain perimeter were detected, which distributed on 1A(2), 2A, 6D and 7D(2) chromosomes to explain the phenotypic variation of 9.3%-22.6%. Six markers associated with stable 1000-grain weight were detected, which distributed on 1B, 2A and 6B chromosomes to explain the phenotypic variation 9.7%-12.9%. Five dominant loci of pleiotropism with were found to control wheat grain traits, which distributed 1A, 2A(2) and 7D(2) chromosomes, explaining the phenotypic variation of 9.9%-22.7%.【Conclusion】In this study, the genetic diversity of the materials was abundant, a total of 29 multi-environment stability loci were found in natural population with 2 or more environmental associated with 6 grain traits.

Key words: wheat, SNP marker, GWAS, grain size-related traits

ZHANG Fang,REN Yi,CAO JunMei,LI FaJi,XIA XianChun,GENG HongWei. Genome-wide Association Analysis of Wheat Grain Size Related Traits Based on SNP Markers[J].Scientia Agricultura Sinica, 2021, 54(10): 2053-2063.

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Figures/Tables 7

Table 1

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Table 3

Supplemental table 1

Fig. 1

Fig. 2

Table 4

Loci for grain size related traits in the diversity panel identified by SNP-GWAS"

性状 Trait	标记 Marker	染色体 Chr.	位置 Position (Mb)	混合线性模型MLM		环境 Environment	前人报道 Previously reported
性状 Trait	标记 Marker	染色体 Chr.	位置 Position (Mb)	P值P value	贡献率R² (%)	环境 Environment	前人报道 Previously reported
千粒重 TKW	AX-111669426	1B	375.4	5.94E^-04-7.67E^-04	10.4—10.5	E1/E4	Xwmc269-Xwmc33^[27]
	AX-111531320	2A	204.5	5.88E^-04-8.98E^-04	10.3—11.3	E2/E4
	AX-109874065	6B	34.0	7.73E^-04-9.84E^-04	9.7—10.4	E1/E2	TKW-xgwm533^[28]
	AX-110446017	6B	486.1	3.98E^-04-7.98E^-04	10.3—12.9	E1/E2	QKWpur-6B^[24]AX_110368497^[25]
	AX-110936500	6B	569.4	4.97E^-04-6.86E^-04	10.5—10.6	E1/E2
	AX-109493716	6B	573.6	4.92E^-04-6.58E^-04	11.0—11.8	E1/E2
粒长 GL	AX-94757616	1A	64.6	3.56E^-04-7.55E^-04	10.7—11.9	E2/E4
	AX-111082947	1A	473.7	1.41E^-06-9.42E^-04	9.9—22.7	E1/E2/E3/E4
	AX-94497666	2A	748.4	3.30E^-04-7.90E^-04	10.3—11.8	E1/E2/E3/E4	TaFlo2^[25-26]
	AX-111614568	7D	13.7—13.9	1.96E^-05-2.03E^-04	12.9—17.3	E3/E4	TaGS-D1^[29]
	AX-95633409	7D	33.6	4.46E^-04-8.05E^-04	10.7—11.9	E3/E4	QKLpur-7D.1^[24]
	AX-111197303	7D	47.4—49.2	2.70E^-04-8.32E^-04	10.9—12.6	E1/E4	QKL.caas-7DS ^[30] QGw.ccsu-7D.1 ^[31]
粒宽 GW	AX-108948870	3B	24.6	5.20E^-04-9.21E^-04	10.6—12.2	E1/E4	Kukri_c14642_917^[23]
粒宽 GW	AX-179477405	5D	210.6	6.78E^-04-8.33E^-04	9.6—10.6	E2/E4
粒长宽比 LWR	AX-111722425	2A	131.7	1.38E^-05-9.53E^-04	10.1—18.3	E1/E2/E3/E4
	AX-111531320	2A	204.5	3.57E^-05-3.28E^-04	13.0—17.1	E2/E3
	AX-179560109	5A	141.9	1.02E^-04-1.08E^-04	14.7—15.2	E2/E3
	AX-112286258	7B	709.1	1.48E^-05-4.09E^-04	11.1—19.4	E1/E3	QGlwr.ccsu-7B.1^[32]
	AX-111614568	7D	13.7—13.9	4.98E^-05-5.51E^-05	10.9—15.9	E1/E4	TaGS-D1^[29]
	AX-158554015	7D	403.7	6.09E^-05-6.42E^-04	10.8—15.4	E1/E2
籽粒面积 GA	AX-95176275	1A	146.6	5.92E^-04-9.82E^-04	9.9—11.2	E1/E4
	AX-179476290	1B	377.4	1.21E^-05-8.31E^-04	10.0—18.2	E3/E4	qKA1B-1^[33]
	AX-179477117	1D	220.5	1.21E^-05-8.31E^-04	10.0—18.2	E3/E4
籽粒周长 GC	AX-111082947	1A	473.7	1.34E^-06-5.56E^-04	10.1—22.6	E1/E3/E4
	AX-109382284	1A	546.8	2.27E^-06-3.55E^-04	11.8—21.3	E3/E4
	AX-94497666	2A	748.4	7.62E^-04-8.68E^-04	9.3—10.3	E1/E4	TaFlo2^[25,26]
	AX-111583179	6D	242.7	2.11E^-04-5.00E^-04	12.0—13.2	E2/E3
	AX-111614568	7D	13.7—13.9	1.04E^-04-3.72E^-04	11.7—14.2	E3/E4	TaGS-D1^[29]
	AX-111197303	7D	47.4—49.2	7.15E^-04-8.05E^-04	10.0—10.4	E1/E4	QKL.caas-7DS ^[30]QGw.ccsu-7D.1 ^[31]

Table 4

References 42

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性状 Trait	环境 Environment	平均值 Mean	范围 Range	标准差 SD	变异系数 CV (%)	偏度 Ske.	峰度 Kur.
千粒重 TKW	2017	22.92	14.86—32.28	4.08	17.79	-0.18	-0.43
	2018	35.55	23.13—49.03	4.95	13.91	0.05	-0.02
	2019	37.84	19.15—54.15	5.62	14.85	-0.02	0.41
粒长 GL	2017	6.44	5.66—7.59	0.34	5.24	0.54	0.88
	2018	6.63	5.67—7.48	0.31	4.66	0.20	0.54
	2019	6.61	5.78—7.51	0.31	4.69	0.16	0.06
粒宽 GW	2017	3.14	2.61—3.61	0.24	7.52	-0.39	-0.28
	2018	3.15	2.61—3.65	0.22	6.95	-0.19	-0.65
	2019	3.27	2.69—3.64	0.18	5.50	-0.43	0.03
长宽比 LWR	2017	2.09	1.75—2.67	0.19	9.12	0.74	0.20
	2018	2.13	1.81—2.58	0.16	7.39	0.59	-0.06
	2019	2.03	1.75—2.41	0.13	6.40	0.68	0.43
籽粒面积 GA	2017	15.82	11.88—19.59	1.54	9.74	-0.11	0.16
	2018	16.24	12.55—21.34	1.59	9.76	0.23	0.02
	2019	16.67	12.65—20.84	1.38	8.28	-0.01	0.63
籽粒周长 GC	2017	16.61	14.52—18.62	0.76	4.56	0.07	0.67
	2018	16.78	14.61—19.11	0.72	4.30	0.22	0.58
	2019	17.27	15.73—19.80	0.72	4.17	0.25	0.44

性状 Trait	均方MS				F值F value			遗传力 h²
性状 Trait	基因型 Genotype	环境 Environment	基因型×环境 G×E	误差 Error	基因型 Genotype	环境 Environment	基因型×环境 G×E	遗传力 h²
千粒重TKW	157.46	17050.92	27.47	4.43	35.54***	3848.31***	6.20***	0.85
粒长GL	0.60	2.74	0.10	0.02	37.54***	170.47***	6.18***	0.86
粒宽GW	0.29	1.63	0.04	0.01	22.98***	131.03***	2.84***	0.89
长宽比LWR	0.16	0.96	0.02	0.00	40.15***	236.77***	4.53***	0.90
籽粒面积GA	14.19	52.10	1.96	0.53	26.59***	97.66***	3.68***	0.87
籽粒周长GC	3.28	36.25	0.52	0.14	23.40***	258.40***	3.71***	0.86

性状Trait	千粒重TKW	粒长GL	粒宽GW	长宽比LWR	籽粒面积GA
粒长GL	0.36***
粒宽GW	0.93***	0.22*
长宽比LWR	-0.64***	0.42***	-0.78***
籽粒面积GA	0.90***	0.64***	0.88***	-0.41***
籽粒周长GC	0.58***	0.94***	0.49***	0.15ns	0.83***

染色体 Chromosome	标记数量 No. of markers	物理长度 Physical distance (Mb)	标记密度Density of marker	遗传多样性Genetic diversity	最小等位基因频率MAF		多态信含量 PIC
染色体 Chromosome	标记数量 No. of markers	物理长度 Physical distance (Mb)	标记密度Density of marker	遗传多样性Genetic diversity	平均 Mean	范围 Range	平均 Mean	范围 Range
1A	2544	602.45	0.24	0.35	0.25	0.05—0.50	0.28	0.09—0.38
1B	1469	746.65	0.29	0.34	0.25	0.05—0.50	0.27	0.09—0.38
1D	1486	498.09	0.20	0.36	0.26	0.05—0.50	0.29	0.09—0.38
2A	2682	787.57	0.31	0.38	0.29	0.05—0.50	0.3	0.09—0.38
2B	2177	802.80	0.32	0.37	0.27	0.05—0.50	0.29	0.09—0.38
2D	1308	655.89	0.26	0.37	0.27	0.05—0.50	0.29	0.09—0.38
3A	2252	750.52	0.29	0.46	0.37	0.25—0.50	0.35	0.30—0.38
3B	2275	868.70	0.34	0.42	0.33	0.17—0.50	0.33	0.24—0.38
3D	1201	626.21	0.25	0.36	0.27	0.05—0.50	0.29	0.09—0.38
4A	2063	750.43	0.29	0.46	0.39	0.26—0.50	0.36	0.30—0.38
4B	1327	672.85	0.26	0.39	0.29	0.11—0.50	0.31	0.18—0.38
4D	817	521.81	0.20	0.39	0.29	0.05—0.50	0.31	0.09—0.38
5A	2251	709.53	0.28	0.49	0.43	0.35—0.50	0.37	0.35—0.38
5B	1605	713.57	0.28	0.46	0.38	0.26—0.50	0.35	0.29—0.38
5D	1373	573.30	0.22	0.41	0.31	0.16—0.50	0.32	0.23—0.38
6A	2315	625.50	0.24	0.49	0.43	0.34—0.50	0.37	0.35—0.38
6B	1305	725.17	0.28	0.45	0.37	0.21—0.50	0.35	0.28—0.38
6D	1330	498.56	0.19	0.45	0.36	0.20—0.50	0.34	0.27—0.38
7A	2407	745.91	0.29	0.48	0.41	0.31—0.50	0.36	0.34—0.38
7B	1332	750.19	0.29	0.45	0.37	0.22—0.50	0.35	0.28—0.38
7D	1354	643.15	0.25	0.44	0.32	0.19—0.50	0.33	0.26—0.38
A基因组A genome	16514	4971.91	0.30	0.44	0.37	0.05—0.50	0.34	0.09—0.38
B基因组 B genome	11490	5279.93	0.46	0.41	0.32	0.05—0.50	0.32	0.09—0.38
D基因组 D genome	8869	4017.01	0.45	0.40	0.30	0.05—0.50	0.31	0.09—0.38
总计Total	36873	14268.85	0.39	0.42	0.33	0.05—0.50	0.32	0.09—0.38

Genome-wide Association Analysis of Wheat Grain Size Related Traits Based on SNP Markers

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