小麦苗期铅耐受性的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2022.06.002

Abstract

Abstract:

【Objective】With the advancement of industrialization, the pollution of arable land by heavy metals, especially lead, has become a worldwide problem. Wheat is an important food crop, and its safe cultivation is critical to maintaining food security. Screening wheat varieties with strong tolerance to lead, low lead accumulation and mining relevant regulatory genes or QTL regions would lay foundation for further elucidating the genetic mechanism of lead tolerance in wheat. 【Method】The tolerance to lead of 102 wheat varieties (advanced lines) were evaluated with a 140 mg·kg^-1 lead nitrate solution at the seedling stage, by the weighted membership function value (D Value) of the lead tolerance coefficients of maximum root length, root biomass and growth rate under three replicates, combining with the 335 438 high-quality SNPs (single nucleotide polymorphism)markers by wheat 660K SNP chip, a genome-wide association study (GWAS) for lead tolerance in wheat was conducted, to mine the candidate genes for lead tolerance in wheat. 【Result】The lead among between wheat varieties (advanced lines) under different replicates showed rich variation, with the coefficient of variation of 44.8%-46.2%, and the correlation coefficient was between 0.87-0.97 (P<0.001). It was found that varieties with strong lead tolerance showed low lead accumulation characteristics. The genotyping results showed that the SNP polymorphic information content (PIC) was 0.28-0.32, the population structure analysis showed that these wheat materials could be divided into 7 subgroups; a total of 20 SNPs and 8 key chromosomal segments that were significantly associated with lead tolerance in wheat (P≤0.001) were detected by two GWAS methods respectively distributed on chromosomes 1B, 2A, 2D, 3A, 3B, 5A, and 7A. A single locus explains 15.33%-19.75% of the phenotypic variation, and 10 and 8 key chromosomal segments were detected in two and more environments. Analysis of candidate genes for significant and stable association sites and intervals revealed that the functions of the candidate genes were mainly related to transmembrane transport, protein modification and oxidative stress response, including 7 genes related to transporters, including TraesCS1B02G433800, TraesCS7A02G118800, TraesCS7A02G117900 etc. Two genes involved in ubiquitination and deubiquitination (TraesCS2A02G550900 and TraesCS7A02G477300), three genes encoding transmembrane proteins (TraesCS2D02G570500, TraesCS3B02G039900 and TraesCS3B02G466000), one gene related to peroxidase (TraesCS7A02G474200). 【Conclusion】Seven wheat materials with strong lead tolerance were screened, 20 SNPs in 8 candidate regions significantly related to lead tolerance in wheat were detected, and 13 candidate genes related to lead tolerance in wheat were finally screened.

Key words: wheat, lead tolerance, genome-wide association analysis, candidate gene analysis

ZHI Lei,ZHE Li,SUN NanNan,YANG Yang,Dauren Serikbay,JIA HanZhong,HU YinGang,CHEN Liang. Genome-Wide Association Analysis of Lead Tolerance in Wheat at Seedling Stage[J].Scientia Agricultura Sinica, 2022, 55(6): 1064-1081.

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重复 Repeat	均值±标准差 Mean±SD	变幅 Range	变异系数 CV	相关系数 Correlation coefficient				遗传力 H² (%)
重复 Repeat	均值±标准差 Mean±SD	变幅 Range	变异系数 CV	D1	D2	D3	D_Mean	遗传力 H² (%)
D1	0.157±0.072	0.034—0.331	45.64	1	0.92***	0.87***	0.96***	88.9
D2	0.162±0.073	0.022—0.303	44.80		1	0.90***	0.97***
D3	0.185±0.085	0.415—0.185	46.20			1	0.96***
D_Mean	0.168±0.075	0.029—0.342	44.85				1

名称 Name	最大根长耐铅系数 Relative maximum root length	根生物量耐铅系数 Relative root biomass	生长速率耐铅系数 Relative growth rate	D值 D value
西农794 Xinong 794	0.654	1.190	1.115	0.34
子麦603 Zimai 603	0.775	1.324	0.804	0.34
旱优98 Hanyou 98	0.406	1.280	1.464	0.33
洛旱7号Luohan 7	0.593	1.500	0.961	0.33
山农24号Shannong 24	0.499	1.809	0.861	0.32
中新78 Zhongxin 78	0.536	1.546	0.941	0.32
长6878 Chang 6878	0.648	1.676	0.541	0.30

染色体 Chromosome	SNP数目 No. of markers	长度 Length (Mb)	SNP标记密度 Density of SNP	遗传多样性 Genetic diversity	多态信息含量 PIC
1A	17217	594.02	0.03	0.38	0.30
1B	21487	689.81	0.03	0.40	0.31
1D	8098	495.31	0.06	0.38	0.30
2A	25429	780.77	0.03	0.38	0.30
2B	24508	801.26	0.03	0.41	0.32
2D	8441	651.82	0.08	0.40	0.31
3A	14081	750.73	0.05	0.41	0.32
3B	43683	830.65	0.02	0.38	0.30
3D	5548	651.49	0.12	0.36	0.30
4A	14465	744.54	0.05	0.39	0.31
4B	12101	673.47	0.06	0.34	0.28
4D	2563	509.85	0.20	0.39	0.31
5A	19762	709.76	0.04	0.39	0.31
5B	30304	713.02	0.02	0.40	0.32
5D	5799	565.72	0.10	0.39	0.31
6A	15159	618.00	0.04	0.40	0.31
6B	21651	720.95	0.03	0.39	0.31
6D	5253	473.56	0.09	0.38	0.30
7A	18154	736.69	0.01	0.40	0.31
7B	14434	750.61	0.05	0.40	0.32
7D	7304	638.55	0.09	0.39	0.31
A基因组A genome	124264	4934.69	0.02	0.39	0.31
B基因组B genome	168168	5179.77	0.03	0.39	0.31
D基因组D genome	43006	3986.30	0.09	0.38	0.30
总计Total	335438	14100.76	0.05	0.39	0.31

标记 Marker	染色体 Chromosome	物理位置 Position (bp)	环境 Environment	P值 P value	贡献率 R² (%)
AX-110941745	2A	756492456	D3	6.42E-04	19.39
AX-109277543	2A	757112239	D1/D2/BLUE	8.07E-04-8.22E-04	15.61—18.62
AX173574354	2D	635801642	D2/BLUE	9.63E-04	15.33
AX-110445716	2D	637991458	D1/D2/BLUE	5.55E-04-7.79E-04	18.76
AX-110075544	2D	638134169	D1/BLUE	7.88E-04	15.89
AX-109814994	2D	638145007	D1	9.92E-04	18.22
AX-108894641	2D	638369283	D1/D2/BLUE	3.56E-04-7.98E-04	18.69—18.75
AX-109811534	2D	639095540	D2/BLUE	8.24E-04	15.78
AX-108776369	2D	639356626	D1/D2/BLUE	3.93E-04-6.26E-04	16.36—17.57
AX-109916952	3A	516295407	D1	9.76E-04	18.26
AX-110613628	3A	516540778	D1/D2	6.61E-04-1.00E-03	18.11—19.27
AX-110631665	3B	20320827	D1/D2/D3	4.09E-04-7.54E-04	17.24—16.03
AX-174247868	3B	31796612	D1/D2	5.50E-04-8.29E-04	18.59—19.75
AX-109552715	3B	31814415	D1/D3	8.86E-04-9.51E-04	15.47—15.61
AX-109352323	3B	31815501	D1/D3	8.86E-04-9.51E-04	15.47—15.61
AX-109857484	5A	20357196	D3	2.22E-04	19.02
AX-111777618	5A	553255290	D3	7.80E-04	18.89
AX-110426494	5B	678333807	D1	8.95E-04	18.48
AX-109372076	7A	670816415	D1/D2/BLUE	3.70E-04-5.41E-04	16.71—17.72
AX-110625465	7A	671418037	D2/BLUE	8.55E-04	15.62

区间 Region	染色体 Chr.	物理位置 Position (Mb)	环境 Environment	标记数目 No. of markers	P值 P value	效应值 Effect
Pb_nwafu-1	1B	658.54—660.72	D1/D2/BLUP	5	4.32E-04—6.47E-04	-0.03—0.30
Pb_nwafu-2	2A	756.11—757.95	D1/D2/D3/BLUP	77	2.36E-05—9.88E-04	-0.04—0.04
Pb_nwafu-3	2D	637.99—639.36	D1/D2/D3/BLUP	29	2.36E-05—9.88E-04	-0.06—0.06
Pb_nwafu-4	3B	17.80—21.96	D1/D2/D3/BLUP	27	5.40E-05—9.40E-04	-0.06—0.06
Pb_nwafu-5	3B	708.94—717.31	D1/D2/D3/BLUP	38	2.65E-04—9.94E-04	-0.05—0.03
Pb_nwafu-6	5B	677.71—678.33	D1/D2/D3/BLUP	5	1.45E-04—8.92E-04	-0.03—0.04
Pb_nwafu-7	7A	669.73—671.42	D1/D2/D3/BLUP	15	5.81E-05—9.95E-04	-0.04—0.03
Pb_nwafu-8	7D	75.08—76.94	D1/D2/D3/BLUP	5	2.72E-04—9.09E-04	-0.04—0.04

Genome-Wide Association Analysis of Lead Tolerance in Wheat at Seedling Stage

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位点&区间 Marker & Region	染色体 Chr.	物理位置 Position (bp)	基因 Gene	基因注释或编码蛋白 Gene annotation or coding protein
Pb_nwafu-1	1B	658491409	TraesCS1B02G433800	多药耐药ABC转运蛋白家族蛋白 Multidrug resistance ABC transporter family protein
Pb_nwafu-2	2A	757947993	TraesCS2A02G550900	组蛋白H2A去泛素酶Histone H2A deubiquitylase
Pb_nwafu-3	2D	637522624	TraesCS2D02G570500	跨膜蛋白Transmembrane protein
Pb_nwafu-4	3B	19263438	TraesCS3B02G039900	跨膜蛋白Transmembrane protein
Pb_nwafu-4	3B	20348050	TraesCS3B02G040900	金属耐受蛋白Metal tolerance protein
Pb_nwafu-5	3B	708516550	TraesCS3B02G466000	跨膜蛋白Transmembrane protein
Pb_nwafu-6	7A	669727531	TraesCS7A02G474200	过氧化物酶Peroxidase
Pb_nwafu-7	7A	670959602	TraesCS7A02G477300	泛素结合因子E4 Ubiquitin conjugation factor E4
Pb_nwafu-8	7A	76192150	TraesCS7A02G117900	ABC转运蛋白C家族蛋白ABC transporter C family protein
Pb_nwafu-8	7A	76486026	TraesCS7A02G118800	ABC转运因子ABC transporter
Pb_nwafu-8	7A	76498276	TraesCS7A02G118900	ABC转运因子ABC transporter
Pb_nwafu-8	7A	76938327	TraesCS7A02G119300	ABC转运因子ABC transporter
AX-108894641	2D	638143208	TraesCS2D02G572000	转运蛋白Transport protein

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