ICARDA引进-小麦苗期抗旱性的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2024.09.004

中国农业科学 ›› 2024, Vol. 57 ›› Issue (9): 1658-1673.doi: 10.3864/j.issn.0578-1752.2024.09.004

所属专题：专题——小麦抗旱性鉴定及基因资源挖掘

• 专题：小麦抗旱性鉴定及基因资源挖掘 • 上一篇下一篇

ICARDA引进-小麦苗期抗旱性的全基因组关联分析

张颖¹(), 石婷瑞¹, 曹瑞¹, 潘文秋¹, 宋卫宁¹, 王利²(), 聂小军¹()

¹ 西北农林科技大学农学院/作物抗逆与高效生产全国重点实验室，陕西杨凌712100
² 山东省农业科学院农业资源与环境研究所/养分资源高效利用全国重点实验室，济南250100

收稿日期:2023-07-12 接受日期:2023-09-18 出版日期:2024-05-01 发布日期:2024-05-09
通信作者:
王利，E-mail：wangli2630000@hotmail.com。
聂小军，E-mail：small@nwsuaf.edu.cn。
联系方式: 张颖，E-mail：yingz99040001@gmail.com。
基金资助:
国家自然科学基金(U22A20457); 国家重点研发计划(2021YFD1900190)

Genome-Wide Association Study of Drought Tolerance at Seedling Stage in ICARDA-Introduced Wheat

ZHANG Ying¹(), SHI TingRui¹, CAO Rui¹, PAN WenQiu¹, SONG WeiNing¹, WANG Li²(), NIE XiaoJun¹()

¹ College of Agronomy, Northwest A&F University/State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Yangling 712100, Shaanxi
² Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences/State Key Laboratory of Nutrient Use and Management, Ji’nan 250100

Received:2023-07-12 Accepted:2023-09-18 Published:2024-05-01 Online:2024-05-09

摘要/Abstract

摘要：

【目的】干旱是限制小麦生产最主要的逆境因子之一。挖掘、鉴定优异抗旱新种质、克隆抗旱新基因，以期丰富我国小麦抗旱遗传基础，为小麦抗旱遗传改良提供材料。【方法】以198份从国际干旱地区农业研究中心（ICARDA）引进的抗旱种质为材料，采用PEG-6000模拟干旱方法，通过调查苗期干旱和正常条件下的地上部鲜重、地下部鲜重、生物量和根冠比4个性状，鉴定、评价其抗旱性，结合660K SNP芯片对其抗旱性进行全基因组关联分析，发掘抗旱性相关染色体区间及关联位点，结合干旱胁迫下根等多组织的表达量数据，筛选抗旱性相关基因，最后以强抗旱性品系IR214和干旱敏感品系IR36为材料，利用qRT-PCR方法对候选基因进行验证，并分析关键候选基因的优异单倍型。【结果】干旱胁迫下，小麦的生长发育受到显著抑制，各性状表型均显著低于正常对照，不同小麦品系间也表现出显著差异，4个性状在2种处理下均呈现正态分布，变异系数为0.363—0.760，多样性指数为0.310—0.400；基于加权隶属函数值（D值）综合评价各个品种的抗旱性，发现品系IR214的D值最大，为0.851，其次为IR92、IR213、IR235和IR218等，它们可作为新的优异抗旱种质；在此基础上，通过全基因组关联分析（genome-wide association study，GWAS），共检测到102个与4个性状抗旱系数显著关联的SNP位点，表型变异解释率范围为1.07%—38.70%，其中，与地上部鲜重相关的位点60个、地下部鲜重相关位点1个、生物量相关位点36个以及根冠比相关位点5个；基于基因组注释信息，筛选到31个抗旱相关基因，结合根等不同组织的RNA-seq数据，筛选出4个抗旱候选基因，对差异表达的候选基因进行qRT-PCR验证，鉴定到2个关键抗旱候选基因；最后，分析候选基因的单倍型效应，发现TraesCS6A02G048600的AX-86174509位点，2种基因型在抗旱性状上具有显著差异，是潜在的功能位点。【结论】共检测到102个与苗期抗旱性显著关联的位点，筛选出TraesCS5B02G053500和TraesCS6A02G048600 2个关键候选基因，TraesCS6A02G048600的AX-86174509位点是潜在的抗旱性功能位点。

关键词: 小麦, 干旱胁迫, 660K SNP芯片, 全基因组关联分析, 候选基因

Abstract:

【Objective】Drought is one of the most destructive environmental stresses limiting wheat production. The novel germplasm with excellent drought tolerance as well as their candidate loci were identified and characterized to enrich the genetic basis of drought tolerance and lay a material foundation for wheat genetic improvement in China. 【Method】In this study, the drought tolerance of 198 wheat accessions introduced from International Dry Area Agriculture Research (ICARDA) were investigated at seedling stage through hydroponic method with PEG6000 simulating drought. Drought tolerance index (DTI) was calculated using the shoot fresh weight, root fresh weight, total biomass and root-shoot ratio, respectively. Genome-wide association analysis was performed using 660K SNP array genotyping to obtain the SNP loci and chromosome regions associating with drought tolerance index. Combined with the expression patterns in root and other tissues, the potential candidate genes were identified, and then they were further verified by qRT-PCR approach with the most drought-tolerant accession IR214 and the most drought-sensitive accession IR36 as materials. Finally, the excellent haplotypes of key candidate genes were analyzed. 【Result】Compared to normal control condition, the growth and development of wheat were significantly impaired under drought treatment. There were also significant phenotypic variations among different accessions with all of the four traits displayed normal distribution. The coefficient of variation ranged from 0.363 to 0.760 with genetic diversity from 0.310 to 0.400. Using the weighted membership function value (D value), the drought tolerance of these accessions was evaluated. Results showed that accession IR214 had the highest D value with 0.851, followed by IR92, IR213, IR235, and IR218, which could be considered as the novel excellent drought-tolerance germplasm. Furthermore, through genome-wide association study (GWAS) analysis, a total of 102 loci were significantly associated with the DTI values based on these four traits, with the phenotypic variation explained value (PVE) from 1.07% to 38.70%, of which 60 loci were associated with above-ground fresh weight, 1 locus associated with underground fresh weight, 36 loci associated with biomass and the remaining 5 loci associated with root-shoot ratio. Then, 31 candidate genes were predicated based on genomic annotation information and LD block. Combined with the expression patterns of them in roots and other tissues, 4 candidates displaying differential expression between CK and drought conditions were obtained. Finally, the expression levels of these 4 candidates were further verified by qRT-PCR method with the most drought- tolerant accession IR214 and the most drought-sensitive accession IR36 as materials to obtain two key candidates associating with drought tolerance. Additionally, their haplotype effects were investigated. It was found that the different genotypes of AX-86174509 locus in TraesCS6A02G048600 gene showed significant differences in drought tolerance, which might be considered as a causal locus.【Conclusion】Totally, 102 loci and 2 key candidate genes (TraesCS5B02G053500 and TraesCS6A02G048600) underlying drought tolerance at seedling stage were detected in ICARDA-introduced wheat, and AX-86174509 in TraesCS6A02G048600 was a potential functional locus.

Key words: wheat, drought stress, 660K SNP array, genome-wide association analysis, candidate genes

张颖, 石婷瑞, 曹瑞, 潘文秋, 宋卫宁, 王利, 聂小军. ICARDA引进-小麦苗期抗旱性的全基因组关联分析[J]. 中国农业科学, 2024, 57(9): 1658-1673.

ZHANG Ying, SHI TingRui, CAO Rui, PAN WenQiu, SONG WeiNing, WANG Li, NIE XiaoJun. Genome-Wide Association Study of Drought Tolerance at Seedling Stage in ICARDA-Introduced Wheat[J]. Scientia Agricultura Sinica, 2024, 57(9): 1658-1673.

图/表 9

图1

表1

图2

表2

苗期抗旱相关性状显著关联的SNP位点及其表型贡献率"

性状 Character	标记 Markers	染色体 Chr.	位置 Position (bp)	P值 P value	表型解释率 PVE (%)
地上部鲜重SFW	AX-108729035	Chr.5B	569808382	4.27E-09	3.93
地上部鲜重SFW	AX-108733337	Chr.5B	572139012	1.00E-08	11.84
地上部鲜重SFW	AX-108759766	Chr.4A	583701435	9.82E-09	7.02
生物量BIO	AX-108778026	Chr.4A	621846334	2.86E-08	17.18
生物量BIO	AX-108783190	Chr.3D	611110400	1.74E-08	11.36
地上部鲜重SFW	AX-108808371	Chr.5B	175234549	1.21E-10	11.17
生物量BIO	AX-108834910	Chr.7D	617295870	6.10E-13	1.07
生物量BIO	AX-108845700	Chr.5B	6647056	6.79E-09	2.57
生物量BIO	AX-108854943	Chr.1B	629035301	8.72E-09	13.20
地上部鲜重SFW	AX-108869016	Chr.3B	587178086	2.51E-08	14.18
地上部鲜重SFW	AX-108900105	Chr.6B	467267816	3.14E-09	8.40
生物量BIO	AX-108906545	Chr.3B	278404009	6.33E-10	11.21
地上部鲜重SFW	AX-108914639	Chr.4A	602892400	3.12E-08	2.78
生物量BIO	AX-108941515	Chr.3B	469534193	8.58E-09	2.66
地上部鲜重SFW	AX-108941538	Chr.6A	614489969	1.38E-08	3.54
根冠比RSR	AX-109084187	Chr.7A	690626229	1.51E-10	2.23
生物量BIO	AX-109102300	Chr.6B	198063929	4.59E-09	10.14
地上部鲜重SFW	AX-109284173	Chr.4A	613541932	2.93E-08	11.23
地上部鲜重SFW	AX-109317181	Chr.3B	764180952	8.90E-09	34.66
生物量BIO	AX-109350000	Chr.3B	415937806	6.22E-09	11.95
生物量BIO	AX-109370689	Chr.7B	607425328	6.10E-13	4.92
根冠比RSR	AX-109384491	Chr.7A	690193717	2.69E-10	2.43
生物量BIO	AX-109394823	Chr5A	570133660	1.95E-08	7.23
地上部鲜重SFW	AX-109395329	Chr.3B	350426152	1.34E-08	8.84
地上部鲜重SFW	AX-109406330	Chr.7B	66821933	7.39E-09	21.61
地上部鲜重SFW	AX-109442599	Chr.1A	574190347	5.57E-10	1.46
生物量BIO	AX-109464813	Chr.2B	178867730	1.49E-08	1.66
生物量BIO	AX-109483959	Chr.3A	597826146	8.32E-09	7.98
生物量BIO	AX-109489650	Chr.6B	146700467	8.58E-09	11.84
生物量BIO	AX-109495431	Chr.5B	593442274	4.01E-10	13.78
生物量BIO	AX-109533280	Chr.2B	756707494	2.16E-09	13.36
地上部鲜重SFW	AX-109549207	Chr.4A	569474177	6.19E-10	4.03
地上部鲜重SFW	AX-109569380	Chr.5B	593660955	4.21E-09	4.29
生物量BIO	AX-109926501	Chr.5B	611478805	6.31E-13	5.95
生物量BIO	AX-109932327	Chr.7A	590944141	1.95E-08	9.99
根冠比RSR	AX-109951696	Chr.5B	690361180	3.37E-10	4.98
地上部鲜重SFW	AX-110008321	Chr.1B	462797045	2.70E-09	24.66
地上部鲜重SFW	AX-110013665	Chr.3B	544902602	1.96E-08	1.89
生物量BIO	AX-110019023	Chr.5B	404539089	2.14E-08	3.31
生物量BIO	AX-110025532	Chr.7A	582132117	1.95E-08	2.13
地上部鲜重SFW	AX-110039998	Chr.5B	607474823	1.07E-08	6.17
地上部鲜重SFW	AX-110068305	Chr.2A	445576038	1.63E-08	8.21
地上部鲜重SFW	AX-110091667	Chr.6B	712350186	1.52E-09	11.71
地上部鲜重SFW	AX-110363991	Chr.5B	57981237	9.95E-11	17.72
生物量BIO	AX-110365890	Chr.7A	612378254	9.99E-10	4.61
地上部鲜重SFW	AX-110377479	Chr.5A	468466491	1.95E-12	1.89
地上部鲜重SFW	AX-110419650	Chr.7A	608395311	1.07E-08	5.21
地上部鲜重SFW	AX-110430526	Chr.3B	144807718	3.14E-09	4.75
地上部鲜重SFW	AX-110462825	Chr.1A	577478241	4.27E-09	13.33
地上部鲜重SFW	AX-110476280	Chr.3B	580060753	4.27E-09	8.75
地上部鲜重SFW	AX-110483678	Chr.7B	159513174	1.72E-09	31.58
地上部鲜重SFW	AX-110498186	Chr.4B	605731378	3.12E-08	13.40
地上部鲜重SFW	AX-110500421	Chr.7A	588877976	4.27E-09	28.18
地上部鲜重SFW	AX-110503277	Chr.4B	611433171	1.71E-10	9.61
地上部鲜重SFW	AX-110535744	Chr.7B	568487694	4.27E-09	18.48
地上部鲜重SFW	AX-110558355	Chr.2A	589689131	9.82E-09	1.36
生物量BIO	AX-110652899	Chr.5B	58567089	1.43E-10	5.45
生物量BIO	AX-110889119	Chr.3D	604125290	6.10E-13	5.87
地上部鲜重SFW	AX-110919290	Chr.3B	414371305	1.93E-10	6.58
地上部鲜重SFW	AX-110924463	Chr.1B	512424681	3.78E-09	38.70
地上部鲜重SFW	AX-110973125	Chr.4A	725499434	4.73E-12	13.76
地上部鲜重SFW	AX-110995410	Chr.2A	751057672	8.68E-11	4.21
生物量BIO	AX-110999606	Chr.5B	578826261	1.95E-08	6.86
地上部鲜重SFW	AX-111010056	Chr.7A	66985517	2.96E-08	3.028
生物量BIO	AX-111022500	Chr.7B	728831779	7.53E-10	17.96
生物量BIO	AX-111050362	Chr.7D	58626667	1.81E-09	36.01
生物量BIO	AX-111058445	Chr.6A	570916695	1.51E-10	10.25
生物量BIO	AX-111073918	Chr.7A	470125650	5.30E-09	27.74
生物量BIO	AX-111092822	Chr.2B	576053662	1.41E-08	4.79
生物量BIO	AX-111132848	Chr.5D	405255511	6.15E-10	13.92
地上部鲜重SFW	AX-111160674	Chr.7D	615485527	2.23E-09	21.86
地上部鲜重SFW	AX-111190021	Chr.3B	760130726	3.14E-09	6.19
地下部鲜重RFW	AX-111192688	Chr.4A	468154775	1.04E-08	15.83
生物量BIO	AX-111208168	Chr.5B	463995322	8.58E-09	9.026
地上部鲜重SFW	AX-111212815	Chr.5A	582970887	9.82E-09	4.34
地上部鲜重SFW	AX-111359770	Chr.7D	615445739	6.66E-09	4.61
生物量BIO	AX-111464456	Chr.1A	48980552	2.11E-08	1.41
地上部鲜重SFW	AX-111534081	Chr.4A	610334173	3.24E-08	22.12
地上部鲜重SFW	AX-111564049	Chr.7B	224728151	3.17E-08	3.42
根冠比RSR	AX-111590236	Chr.7A	690440732	1.39E-09	10.59
地上部鲜重SFW	AX-111598552	Chr.3B	116099069	1.35E-08	32.51
地上部鲜重SFW	AX-111629228	Chr.7A	572186228	2.62E-08	10.99
地上部鲜重SFW	AX-111638609	Chr.5B	275345486	4.47E-09	1.79
地上部鲜重SFW	AX-111652946	Chr.6A	615722618	3.12E-08	12.64
地上部鲜重SFW	AX-111694379	Chr.2A	580854646	1.35E-08	34.63
地上部鲜重SFW	AX-111730956	Chr.4A	664219507	6.37E-09	3.17
生物量BIO	AX-111831025	Chr.2B	781926736	4.61E-09	1.13
地上部鲜重SFW	AX-111903622	Chr.7D	58049133	3.86E-09	1.07
地上部鲜重SFW	AX-86174509	Chr.6A	24829724	2.82E-09	6.40
地上部鲜重SFW	AX-89491115	Chr.3B	564771130	8.34E-09	6.11
地上部鲜重SFW	AX-89706493	Chr.3A	25500453	4.62E-09	11.81
根冠比RSR	AX-94454511	Chr.5B	678515559	3.29E-08	4.01
地上部鲜重SFW	AX-94654260	Chr.1D	462487722	3.14E-09	7.86
生物量BIO	AX-94687724	Chr.2D	577152448	1.95E-08	13.82
地上部鲜重SFW	AX-94757082	Chr.7A	436070614	4.62E-10	3.80
地上部鲜重SFW	AX-94768083	Chr.5B	563121347	1.27E-08	23.89
地上部鲜重SFW	AX-94784142	Chr.2A	194538621	2.01E-09	5.28
生物量BIO	AX-94863274	Chr.2D	571058114	1.95E-08	6.86
地上部鲜重SFW	AX-95149581	Chr.2D	590410753	1.09E-08	1.17
生物量BIO	AX-108921937	Chr.1A	583127676	2.53E-08	7.37
地上部鲜重SFW	AX-95244677	Chr.7A	575268359	4.27E-09	1.39
地上部鲜重SFW	AX-95659704	Chr.6D	453012504	1.65E-08	7.25

表2

图3

表3

抗旱性相关候选基因的预测"

位点 Marker	物理位置 Position (bp)	基因 Gene	染色体 Chr.	性状 Trait	基因注释或编码蛋白 Gene annotation or coding proteins
AX-111464456	48980552	TraesCS1A02G066400	Chr.1A	生物量BIO	氧化还原酶Oxidoreductase activity
AX-94784142	194538621	TraesCS2A02G210600	Chr.2A	地上部鲜重SFW	锌离子结合蛋白Zinc ion binding
AX-111694379	580854646	TraesCS2A02G344200	Chr.2A	地上部鲜重SFW	果胶酯酶Pectinesterase activity
AX-110558355	589689131	TraesCS2A02G349800	Chr.2A	地上部鲜重SFW	跨膜转运蛋白Transmembrane transport
AX-109533280	756707494	TraesCS2B02G565400	Chr.2B	生物量BIO	DUF952
AX-95149581	590410753	TraesCS2D02G493000	Chr.2D	地上部鲜重SFW	质子跨膜转运蛋白Proton transmembrane transport
AX-94863274	571058114	TraesCS2D02G464900	Chr.2D	生物量BIO	Remorin_C
AX-94687724	577152448	TraesCS2D02G473700	Chr.2D	生物量BIO	转录调控酶Regulation of DNA-templated transcription
AX-89706493	25500453	TraesCS3A02G048000	Chr.3A	地上部鲜重SFW	含重金属转运/解毒蛋白结构域的蛋白Heavy metal transport/detoxification protein domain containing protein
AX-109395329	350426152	TraesCS3B02G231600	Chr.3B	地上部鲜重SFW	DUF632/DUF630
AX-89491115	564771130	TraesCS3B02G354300	Chr.3B	地上部鲜重SFW	果胶酯酶Pectinesterase activity
AX-111192688	468154775	TraesCS4A02G189100	Chr.4A	地下部鲜重RFW	水解酶Alpha/beta hydrolase fold
AX-108778026	621846334	TraesCS4A02G341700	Chr.4A	生物量BIO	蛋白激酶Protein kinase
AX-110377479	468466491	TraesCS5A02G252300	Chr.5A	地上部鲜重SFW	结合蛋白Nucleic acid binding
AX-110363991	57981237	TraesCS5B02G053200	Chr.5B	地上部鲜重SFW	分生组织发育相关Meristem maintenance
AX-94768083	563121347	TraesCS5B02G384300	Chr.5B	地上部鲜重SFW	防御响应Defense response
AX-109569380	593660955	TraesCS5B02G418100	Chr.5B	地上部鲜重SFW	翻译延长因子Translational elongation
AX-110039998	607474823	TraesCS5B02G432900	Chr.5B	地上部鲜重SFW	结合蛋白RNA binding
AX-94454511	678515559	TraesCS5B02G513600	Chr.5B	RSR	HAD家族Haloacid dehalogenase-like hydrolase
AX-109951696	690361180	TraesCS5B02G533900	Chr.5B	根冠比RSR	膜组成蛋白Integral component of membrane
AX-108845700	6647056	TraesCS5B02G005000	Chr.5B	生物量BIO	GTP结合蛋白GTP binding
AX-110652899	58567089	TraesCS5B02G053500	Chr.5B	生物量BIO	气孔运动调节Regulation of stomatal movement
AX-86174509	24829724	TraesCS6A02G048600	Chr.6A	地上部鲜重SFW	Crr6蛋白Crr6 protein
AX-110091667	712350186	TraesCS6B02G456000	Chr.6B	地上部鲜重SFW	ATP结合蛋白ATP hydrolysis activity
AX-95659704	453012504	TraesCS6D02G362600	Chr.6D	地上部鲜重SFW	AANH
AX-94757082	436070614	TraesCS7A02G308300	Chr.7A	地上部鲜重SFW	组蛋白甲基化修饰酶Histone methylation
AX-95244677	575268359	TraesCS7A02G396700	Chr.7A	地上部鲜重SFW	结合蛋白Protein binding
AX-110419650	608395311	TraesCS7A02G416300	Chr.7A	地上部鲜重SFW	GGATC
AX-110365890	612378254	TraesCS7A02G421300	Chr.7A	生物量BIO	结合蛋白Protein binding
AX-110483678	159513174	TraesCS7B02G131900	Chr.7B	地上部鲜重SFW	催化酶Catalytic activity
AX-111160674	615485527	TraesCS7D02G514700	Chr.7D	地上部鲜重SFW	锌指蛋白Zinc finger protein

表3

图4

图5

图6

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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	20417	594.02	0.03	0.54	0.35
2A	22864	780.77	0.03	0.68	0.40
3A	13916	750.73	0.02	0.59	0.37
4A	13577	744.65	0.02	0.62	0.38
5A	18446	709.76	0.03	0.64	0.39
6A	13496	617.99	0.02	0.59	0.37
7A	19497	736.69	0.03	0.54	0.35
1B	17527	689.38	0.03	0.57	0.37
2B	23450	801.26	0.03	0.59	0.37
3B	40010	830.70	0.05	0.51	0.34
4B	10870	673.44	0.02	0.62	0.38
5B	28406	713.02	0.04	0.63	0.39
6B	18994	720.95	0.03	0.59	0.37
7B	12898	750.61	0.02	0.57	0.36
1D	7703	495.61	0.02	0.56	0.36
2D	7149	651.81	0.01	0.64	0.39
3D	4834	651.53	0.01	0.45	0.31
4D	1954	509.91	0.00	0.56	0.36
5D	4873	565.98	0.01	0.56	0.36
6D	4698	720.95	0.01	0.57	0.36
7D	6617	638.46	0.01	0.52	0.34
A基因组A genome	122213	704.94	0.02	0.60	0.374428571
B基因组B genome	152155	739.91	0.03	0.58	0.368
D基因组D genome	37828	604.89	0.01	0.55	0.354
总计Total	312196	683.25	0.02	0.58	0.36547619

ICARDA引进-小麦苗期抗旱性的全基因组关联分析

Genome-Wide Association Study of Drought Tolerance at Seedling Stage in ICARDA-Introduced Wheat

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