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

摘要/Abstract

摘要：

【目的】随着工业化的推进,重金属尤其是铅对耕地的污染已成为世界性问题。小麦作为主要粮食作物,其健康生产对保障粮食安全意义重大,筛选铅耐受性强和铅低积累小麦品种、挖掘相关调控基因或QTL区间,为耐铅种质创新和揭示小麦铅耐受性遗传机制奠定基础。【方法】采用140 mg·kg^-1的硝酸铅溶液对102份小麦品种（系）进行苗期胁迫试验,以3个重复下的最大根长、根生物量和生长速率的耐铅系数的加权隶属函数值（D值）来评价小麦对铅的耐受性。结合小麦660K SNP芯片的335 438个高质量SNP标记对小麦铅耐受性进行全基因组关联分析（genome-wide association study,GWAS）,挖掘铅耐受性候选基因。【结果】小麦品种（系）之间的铅耐受性表现出丰富的变异,变异系数为44.8%—46.2%,相关系数介于0.87—0.97（P<0.001）;铅耐受性强的品种呈现出铅低积累特性。基因分型结果显示SNP多态性信息含量（polymorphic information content,PIC）为0.28—0.32,群体结构分析将供试材料分为7个亚群;2种GWAS分析方法共检测到20个与小麦铅耐受性显著关联的SNP（P≤0.001）和8个候选区间,分别分布在1B、2A、2D、3A、3B、5A和7A染色体上,单个位点可解释15.33%—19.75%的表型变异,其中10个位点和8个候选区间在2个及以上环境被检测到。分析稳定检测的显著关联位点及区间的候选基因,发现其功能主要与跨膜运输、蛋白修饰以及氧化应激反应有关,包括7个与转运蛋白相关基因（TraesCS1B02G433800、TraesCS7A02G118800、TraesCS7A02G117900等）、2个与泛素化与去泛素化相关的候选基因（TraesCS2A02G550900和TraesCS7A02G477300）、3个跨膜蛋白基因（TraesCS2D02G570500、TraesCS3B02G039900和TraesCS3B02G466000）和1个过氧化物酶相关的候选基因（TraesCS7A02G474200）。【结论】筛选出铅耐受性强的种质材料7份,检测到与小麦铅耐受性显著关联的20个SNP位点及8个候选区间,筛选出13个与小麦铅耐受性相关的候选基因。

关键词: 小麦, 铅耐受性, 全基因组关联分析, 候选基因分析

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

职蕾,者理,孙楠楠,杨阳,Dauren Serikbay,贾汉忠,胡银岗,陈亮. 小麦苗期铅耐受性的全基因组关联分析[J]. 中国农业科学, 2022, 55(6): 1064-1081.

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