小麦穗发芽性状的全基因组关联分析

doi:10.3724/SP.J.1006.2021.01078

Abstract

Abstract:

To understand the genetic mechanism of wheat pre-harvest sprouting (PHS) in wheat breeding, it is significant to explore marker loci and candidate genes associated with PHS resistance using intact spikes. In this study, a total of 207 wheat varieties (lines) from China and 16,686 SNP markers were analyzed in wheat whole genome. The mixed liner model (Q + K) was used to analyze PHS phenotypic data in three environments. Genome-wide association study showed that there were abundant phenotypic variations in different environments and wheat varieties (lines). The coefficient of variation was 0.34 and 0.25, the polymorphic information content of value (PIC) was from 0.01 to 0.38, and the attenuation distance of whole genome LD was 3 Mb. The population structure and principal component analysis revealed that 207 wheat varieties (lines) could be divided into three subgroups. GWAS results indicated that 34 SNP markers were detected, which were significantly associated with pre-harvest sprouting at P < 0.001. They were located on chromosomes 3A, 3B, 4A, 4B, 5D, 6A, 6B, 6D, 7B, and 7D, and each explained 5.55%-11.63% of phenotypic variation. There were 16 markers loci detected in more than two environments, and the marker Np_Ex_c14101_22,012,676 on 6B chromosome detected in E1, E2, and average environment. Meanwhile, 13 candidate genes were screened out by mining association loci with large phenotypic effect value and stable inheritance. TraesCS3A01G589400LC, TraesCS6B01G138600/TraesCS6B01G516700LC/TraesCS6B01G548900LC, TraesCS6D01G103600, and TraesCS7B01G200100 could affect seed dormancy by regulating the sensitivity of endogenous ABA in plants. The F-box proteins were encoded by TraesCS3B01G415900LC, TraesCS6A01G144700LC, and TraesCS6B01G294800, which played major roles in plant hormone signal transduction, light signal transduction, and flower organ development. TraesCS6A01G108800, TraesCS6B01G138200/ TraesCS6B01G293700 encoded Myb transcription factor family. These candidate genes are important genes related to wheat sprouting.

Key words: wheat, pre-harvest sprouting, genome-wide association analysis, SNP, candidate gene

XIE Lei, REN Yi, ZHANG Xin-Zhong, WANG Ji-Qing, ZHANG Zhi-Hui, SHI Shu-Bing, GENG Hong-Wei. Genome-wide association study of pre-harvest sprouting traits in wheat[J].Acta Agronomica Sinica, 2021, 47(10): 1891-1902.

Figures/Tables 8

Fig. 1

Fig. 2

Table 1

Table 2

Fig. 3

Fig. 4

Table 3

Information of significant association sites for PHS"

标记 Marker	染色体 Chr.	位置 Position (Mb)	MLM		环境 Environment	已报道的QTL/标记/基因Known QTL/marker/gene
标记 Marker	染色体 Chr.	位置 Position (Mb)	P值 P-value	贡献率 R² (%)	环境 Environment	已报道的QTL/标记/基因Known QTL/marker/gene
Kukri_c8465_54	3A	684.04-685.36	2.35E-04-9.14E-04	5.55-8.75	E2/E3	TaVp-1^[32]
Kukri_c9259_421	4A	673.07	5.95E-04	6.34	E2	IWB23723^[23]
RAC875_rep_c107892_142	6A	77.78	2.56E-05-9.28E-05	8.04-9.25	E1/E3
Kukri_c5744_92	6A	483.90	2.78E-05-7.41E-04	8.34-9.25	E1/E3
RAC875_c43536_193	6A	490.50	3.03E-04	6.94	E1
IAAV8536	3B	422.52	6.78E-05	9.81	E1	TaDFR^[33]
Tdurum_contig60051_838	4B	644.68	7.10E-04	9.42	E2	Xwmc349^[34]
CAP11_c2542_147	6B	24.92	7.71E-05-3.83E-04	6.71-8.29	E1/E3	TaCYP707A1^[35]
Kukri_c33668_877	6B	119.53	4.55E-04-5.32E-04	6.05-6.16	E2/E3	AX-108844376^[24]
GENE-3171_203	6B	135.11-138.65	2.15E-05-5.50E-04	6.09-9.71	E1/E3
BS00069412_51	6B	143.20	9.03E-04	5.64	E1
Excalibur_c18382_760	6B	151.13	9.24E-04	5.60	E3
wsnp_Ku_c2614_4970880	6B	226.87	8.44E-04	5.59	E3
Tdurum_contig13698_141	6B	475.73	7.54E-04	5.70	E3
RFL_Contig6050_941	6B	481.47-481.86	3.10E-06-1.63E-04	8.83-11.63	E1/E3
wsnp_Ex_c3640_6644345	6B	485.54	2.36E-05-1.08E-04	8.21-11.04	E1/E3	IWB2831^[24]
wsnp_Ex_c14101_22012676	6B	492.02	2.26E-06-6.77E-04	5.86-11.61	E1/E2/E3
wsnp_Ex_c6143_10747643	6B	516.08-519.15	1.30E-05-1.65E-04	8.30-10.65	E1/E3
Kukri_c16568_287	6B	522.49	4.81E-05-1.69E-04	7.21-8.45	E1/E3
Excalibur_c7785_123	6B	526.48-528.92	1.19E-056.21E-04	5.94-10.02	E1/E3
Excalibur_c11245_880	6B	530.57	2.79E-04-5.34E-04	6.06-6.83	E1/E3
wsnp_Ex_c3990_7223090	6B	577.48	1.67E-05-6.19E-05	8.45-9.95	E1/E3	Qphs.ahau-6B^[36]
RAC875_c57261_265	6B	609.38	6.10E-04-6.34E-04	5.99-6.02	E1
标记 Marker	染色体 Chr.	位置 Position (Mb)	MLM		环境 Environment	已报道的QTL/标记/基因Known QTL/marker/gene
标记 Marker	染色体 Chr.	位置 Position (Mb)	P值 P-value	贡献率 R² (%)	环境 Environment	已报道的QTL/标记/基因Known QTL/marker/gene
RAC875_rep_c117796_352	6B	632.97	5.23E-04-5.35E-04	6.19-6.21	E3
wsnp_CV776265A_Ta_2_1	6B	651.01-652.00	1.21E-04-7.21E-04	5.78-7.51	E1/E3
BS00023032_51	6B	664.38	8.28E-04	5.90	E3
IAE36519	6B	701.98-704.04	7.44E-04-9.92E-04	5.87-6.09	E2
wsnp_Ku_c18780_28136150	7B	223.61	8.12E-05	10.12	E2
Excalibur_c25719_238	7B	363.24	3.92E-05-3.24E-04	6.64-8.89	E2/E3
RAC875_c4834_694	7B	613.38	7.14E-04	5.87	E2	Dorm-1^[37]
BobWhite_c8092_726	5D	246.30	4.94E-04	6.22	E3
wsnp_Ex_c1249_2399894	6D	67.39-68.10	8.81E-04-9.23E-04	5.72-5.78	E1
D_wsnpbe403818_Contig1_1	6D	389.70	6.71E-04	5.79	E3
D_contig10382_335	7D	23.50-55.42	7.24E-04-9.41E-04	5.70-6.15	E2	MST101^[37]

Table 3

Table 4

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变异来源 Source of variance	自由度 DF	平方和 SS	均方 MS	F值 F-value	P值 P-value	遗传力 h²
基因型Genotype (G)	206	95,102,272.00	312,836.40	540.38	0.00001	0.60
环境Environment (E)	1	756,525,632.00	378,262,816.00	653,396.18	0.00001
基因型×环境G×E	443	94,041,216.00	212,282.65	366.68	0.00001
误差Error	747	432,451.71	578.91
总变异Total	1397	946,109,312.00

染色体 Chromosome	标记数目 No. of markers	染色体长度 Chromosome length (Mb)	标记密度 Density of marker	多态信息量 PIC
染色体 Chromosome	标记数目 No. of markers	染色体长度 Chromosome length (Mb)	标记密度 Density of marker	平均值Mean	变异范围Range
1A	1263	592.38	0.47	0.27	0.01-0.38
2A	1145	780.46	0.68	0.24	0.01-0.38
3A	891	749.46	0.84	0.25	0.01-0.38
4A	708	741.73	1.05	0.25	0.01-0.38
5A	960	709.43	0.74	0.28	0.01-0.38
6A	1006	617.40	0.61	0.27	0.03-0.38
7A	1172	736.44	0.63	0.25	0.01-0.38
1B	1292	688.60	0.53	0.27	0.01-0.38
2B	1291	799.62	0.62	0.26	0.01-0.38
3B	1087	829.32	0.76	0.27	0.01-0.38
4B	571	672.56	1.18	0.26	0.01-0.38
5B	1156	712.82	0.62	0.28	0.01-0.38
6B	1085	720.82	0.66	0.25	0.01-0.38
7B	861	750.49	0.87	0.26	0.02-0.38
1D	568	495.14	0.87	0.13	0.01-0.38
2D	482	650.94	1.35	0.25	0.02-0.38
3D	232	613.92	2.65	0.24	0.01-0.38
4D	99	508.58	5.14	0.25	0.08-0.38
5D	240	563.41	2.35	0.26	0.02-0.38
6D	319	472.61	1.48	0.25	0.03-0.38
7D	260	637.17	2.45	0.23	0.01-0.38
A染色体组 Total genome A	7145	4927.30	0.72	0.26	0.01-0.38
B染色体组 Total genome B	7343	5174.23	0.75	0.27	0.01-0.38
D染色体组 Total genome D	2198	3941.77	2.33	0.23	0.01-0.38
总计Total	16686	14043.30	1.27	0.25	0.01-0.38

Genome-wide association study of pre-harvest sprouting traits in wheat

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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
Kukri_c8465_54	3A	684.76	TraesCS3A01G589400LC	Zinc finger MYM-type-like protein
IAAV8536	3B	421.53	TraesCS3B01G415900LC	F-box protein
RAC875_rep_c107892_142	6A	77.61	TraesCS6A01G144700LC	F-box family protein
	6A	77.54	TraesCS6A01G108800	Myb-like transcription factor family protein
GENE-3171_203	6B	135.71	TraesCS6B01G138200	Myb family transcription factor-like
	6B	135.94	TraesCS6B01G138600	RING/U-box superfamily protein
RFL_Contig6050_941	6B	481.79	TraesCS6B01G511400LC	Anaerobic nitric oxide reductase transcription regulator NorR
wsnp_Ex_c14101_22012676	6B	491.55	TraesCS6B01G516700LC	Zinc finger (C3HC4-type RING finger) family protein
Excalibur_c7785_123	6B	528.92	TraesCS6B01G294800	F-box protein
	6B	527.93	TraesCS6B01G293700	Myb family transcription factor-like
	6B	526.49	TraesCS6B01G548900LC	Zinc finger MYM-type-like protein
Excalibur_c25719_238	7B	363.00	TraesCS7B01G200100	Zinc finger C-x8-C-x5-C-x3-H type family protein
wsnp_Ex_c1249_2399894	6D	67.39	TraesCS6D01G103600	Zinc finger BED domain-containing protein DAYSLEEPER

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