小麦苗期耐热性全基因组关联分析

doi:10.3864/j.issn.0578-1752.2025.09.001

Abstract

Abstract:

【Objective】 Wheat is a cornerstone of global food security, with its production being pivotal in both China and the international community. With global climate change, the threat of high temperature has become increasingly prominent, posing a significant challenge to wheat cultivation. The strategic identification and selection of heat-tolerant germplasm, coupled with the exploration of genes associated with heat resistance, are crucial steps. These efforts are essential for broadening the genetic diversity of heat tolerance in wheat within China, providing prerequisites for breeding heat-tolerant wheat varieties and ultimately contributing to the safeguarding of our nation’s food security in the face of a warming climate. 【Method】 In this study, a natural population of 331 wheat accessions was utilized, and artificial climate chambers were employed to simulate high temperatures conditions. The heat tolerance of wheat seedlings was assessed by monitoring their survival rate under various durations of treatment, using heat resistance grade as the evaluative metric. Meanwhile, a genome-wide association study (GWAS) was conducted using the 55K SNP chip to identify genetic loci associated with heat tolerance. Expression data from multiple tissues, including roots, leaves under heat stress were analyzed, leading to the selection of genes related to heat tolerance. Subsequently, qPCR validation of candidate genes was performed using the extremely heat-tolerant accession Xinong 889 and the heat-sensitive accession Chinese Spring (CS) as materials. 【Result】 Under high-temperature stress, significant variations in survival rates were observed among different wheat accessions. The extremely heat-tolerant, moderately heat-tolerant, moderately heat-sensitive, and extremely heat-sensitive germplasm accounted for 110, 104, 110, and 7, respectively, representing 33.23%, 31.42%, 33.23%, and 2.12% of the total. Heat-tolerant germplasms, including Xinong 889, Zhengmai 7698, Zhongmai 895, Zhoumai 18, and Fengchan 3, were identified. Through GWAS, a total of 293 SNP loci significantly associated with the 12-hour survival rates (SR) and heat resistance grades (HRG) were detected, with the phenotypic variation explained ranging from 4.40% to 12.46%. Among these, 200 loci were related to the 12-hour survival rates, and 257 were related to the heat resistance grades, with 164 loci identified as the same heat-related loci. Based on significantly associated SNP markers, 313 heat-related genes were predicted. According to gene annotation information and expression data under heat stress, 23 heat tolerance candidates were selected, and after qPCR validation of differentially expressed candidate’s genes, 20 key heat tolerance candidate genes were identified. 【Conclusion】 At the seedling stage, 331 wheat germplasms were identified for heat tolerance. A rapid method was developed for determining the survival rate of wheat seedlings subjected to treatments of varying durations at 45 ℃ to assess their heat tolerance In total, 38 heat-tolerant germplasms and 293 loci significantly associated with seedling heat tolerance were screened. Also, TraesCS1A02G355900, TraesCS1A02G389500, TraesCS5A02G550700, TraesCS5D02G557100, TraesCS6D02G402500 and TraesCS7A02G232500 represented as candidate genes were filtered out.

Key words: wheat, heat stress, 55K SNP array, genome-wide association analysis, candidate genes

LI YunLi, DIAO DengChao, LIU YaRui, SUN YuChen, MENG XiangYu, WU ChenFang, WANG Yu, WU JianHui, LI ChunLian, ZENG QingDong, HAN DeJun, ZHENG WeiJun. Genome-Wide Association Study of Heat Tolerance at Seedling Stage in A Wheat Natural Population[J].Scientia Agricultura Sinica, 2025, 58(9): 1663-1683.

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Figures/Tables 10

Table 1

Table 2

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 3

SNP loci significantly associated with heat tolerance index at seedling stage and their phenotypic variation explained (PVE)"

模型 Model	性状 Character	标记 Marker	染色体 Chromosome	位置 Position (bp)	P值 P value	表型变异解释率 PVE (%)
GLM	SR/HRG	Affx-110203639	1	49968001	1.13E-05	5.67
GLM	SR/HRG	Affx-110259327	1	50496236	1.64E-05	5.46
GLM	HRG	Affx-109674237	1	538774197	9.91E-05	4.48
GLM	SR/HRG	Affx-110640791	1	557461051	1.16E-05	5.66
GLM	SR/HRG	Affx-88398227	1	557559230	8.36E-07	7.09
GLM/MLM	SR/HRG	Affx-109638477	1	558084863	9.74E-07	7.00
GLM/MLM	SR/HRG	Affx-109123802	1	568519872	1.27E-07	8.10
GLM	SR/HRG	Affx-109894023	1	568536246	2.11E-06	6.58
GLM	SR/HRG	Affx-110933596	2	363956701	4.45E-05	4.92
GLM	SR/HRG	Affx-109481111	2	364490098	3.89E-05	4.99
GLM/MLM	SR/HRG	Affx-109680038	2	415260451	5.56E-09	9.78
GLM	SR/HRG	Affx-109296086	2	687299508	5.20E-06	6.09
GLM	SR/HRG	Affx-109074941	2	687414153	9.70E-07	7.00
GLM	HRG	Affx-111756085	2	687563841	8.81E-05	4.55
MLM	SR/HRG	Affx-92851507	3	478121127	5.26E-05	4.81
GLM	HRG	Affx-110533812	4	30823301	5.25E-05	4.83
GLM	HRG	Affx-110656171	4	30873784	7.33E-05	4.65
GLM	HRG	Affx-111407436	7	669182809	8.96E-06	5.80
GLM	HRG	Affx-88482618	7	669567157	2.17E-05	5.31
GLM	SR/HRG	Affx-108908406	7	715655099	1.92E-07	7.88
GLM	HRG	Affx-110877304	9	596092037	3.82E-06	6.26
GLM	HRG	Affx-109610822	9	596160889	1.86E-05	5.40
GLM	HRG	Affx-92882408	9	596667885	9.79E-05	4.49
GLM	HRG	Affx-109992803	9	596719240	4.31E-05	4.94
GLM	HRG	Affx-109248342	9	596783243	1.37E-05	5.56
GLM	HRG	Affx-110040862	9	596918477	8.43E-05	4.57
GLM	HRG	Affx-111157176	9	596981313	6.53E-05	4.71
GLM	HRG	Affx-109233700	9	596997315	9.40E-05	4.51
MLM	SR/HRG	Affx-109675350	10	177137946	3.69E-06	6.21
MLM	SR/HRG	Affx-109262328	10	350961409	1.17E-06	6.83
GLM	SR/HRG	Affx-108903932	13	70663254	3.60E-05	5.04
GLM	SR/HRG	Affx-111642655	13	71232276	2.26E-05	5.29
GLM	HRG	Affx-109362879	13	704336151	6.75E-05	4.69
GLM	SR/HRG	Affx-111121454	13	706549941	1.22E-05	5.63
MLM	SR/HRG	Affx-111502569	14	557349764	3.77E-05	5.00
GLM	HRG	Affx-109166219	15	542651449	3.77E-05	5.01
GLM	HRG	Affx-111824230	15	543266757	7.22E-05	4.66
GLM/MLM	HRG	Affx-88453586	15	543509336	1.76E-06	6.68
GLM	HRG	Affx-88405117	15	559746041	1.16E-04	4.40
MLM	SR/HRG	Affx-92741886	15	50782762	2.01E-05	5.34
MLM	SR/HRG	Affx-110196154	15	547839798	1.25E-05	5.57
MLM	SR/HRG	Affx-108863028	17	140466504	2.53E-05	5.19
GLM	HRG	Affx-88610450	18	466894251	3.25E-06	6.35
GLM	SR/HRG	Affx-88552720	18	472303256	6.75E-06	5.95
GLM	HRG	Affx-111744400	18	472304296	3.50E-05	5.05
GLM	SR/HRG	Affx-110231695	19	92790790	1.21E-05	5.63
GLM	SR/HRG	Affx-109123340	19	93120026	2.63E-05	5.21
GLM	SR/HRG	Affx-109154771	19	136533979	2.07E-05	5.34
GLM	SR/HRG	Affx-110241168	19	136761050	6.22E-06	5.99
GLM	SR/HRG	Affx-111653438	19	155162964	3.76E-05	5.01
GLM	SR/HRG	Affx-109191237	19	156264119	1.36E-05	5.57
GLM	SR/HRG	Affx-111167533	19	168994686	3.15E-05	5.11
GLM	SR/HRG	Affx-88778846	19	171435266	1.72E-05	5.44
GLM/MLM	SR/HRG	Affx-110244104	19	452295538	1.04E-10	11.87
GLM/MLM	SR/HRG	Affx-110433752	19	452307903	3.40E-11	12.46
MLM	SR/HRG	Affx-111880833	19	202738729	1.69E-05	5.41
GLM/MLM	SR/HRG	Affx-108977126	20	135773041	1.55E-07	8.00
GLM/MLM	SR/HRG	Affx-110431431	20	137367874	2.37E-07	7.77
GLM	SR/HRG	Affx-111742284	20	726432033	7.66E-07	7.13
GLM	SR/HRG	Affx-109626634	20	726567819	2.72E-07	7.69
GLM	HRG	Affx-111473128	21	57857093	9.77E-05	4.49
GLM	SR/HRG	Affx-108998170	21	89304658	2.30E-05	5.28
GLM	HRG	Affx-111304820	21	89471033	6.10E-05	4.75
GLM	HRG	Affx-111880319	21	89530482	9.05E-05	4.53
GLM	SR/HRG	Affx-110923201	21	89532556	2.19E-05	5.31
GLM	SR/HRG	Affx-109041698	21	89556144	1.76E-07	7.93
GLM	SR/HRG	Affx-111854248	21	89598649	8.63E-07	7.07
GLM	SR/HRG	Affx-111809041	21	90634443	3.72E-05	5.02

Table 3

Fig. 5

Table 4

Prediction and annotation of the candidate gene underlying heat tolerance"

候选基因 Candidate genes	染色体位置 Chromosomal location (bp)	基因注释或编码蛋白 Gene annotation or coding proteins
TraesCS1A02G355900	Chr.1A:539279131-539279556(-)	核转录因子Y组分C3 Nuclear transcription factor Y subunit C3
TraesCS1A02G356100	Chr.1A:539323095-539324401(+)	过氧化物酶1 Peroxidase 1
TraesCS1A02G387700	Chr.1A:556297389-556306081(-)	26S蛋白酶体非ATP酶调节亚基5 26S proteasome non-ATPase regulatory subunit 5
TraesCS1A02G389500	Chr.1A:557487151-557491334(+)	蛋白NINJA同源物1 Protein NINJA homolog 1
TraesCS1A02G391600	Chr.1A:558505998-558517659(-)	高尔基体候选蛋白5 Golgin candidate 5
TraesCS1A02G391900	Chr.1A:558550095-558553987(+)	类金属核蛋白PRN Pirin-like protein
TraesCS1B02G202800	Chr.1B:364418491-364420737(+)	UPF0496蛋白4 UPF0496 protein 4
TraesCS1D02G426000	Chr.1D:479494708-479499893(-)	糖转运蛋白ERDL6 Sugar transporter ERD6-like 6
TraesCS5A02G065400	Chr.5A:70676153-70676518(-)	乙烯响应转录因子ERF098 Ethylene-responsive transcription factor ERF098
TraesCS5A02G550700	Chr.5A:704338188-704339287(+)	热激转录因子HSF-C2a Heat stress transcription factor C-2a
TraesCS5A02G554100	Chr.5A:706235563-706237619(+)	重金属异戊二烯化植物蛋白39 Heavy metal-associated isoprenylated plant protein 39
TraesCS5B02G380400	Chr.5B:558341804-558347101(-)	丝氨酸/苏氨酸蛋白激酶STY13 Serine/threonine-protein kinase STY13
TraesCS5D02G055400	Chr.5D:52053749-52059633(+)	DnaJ同源超家族C成员14 DnaJ homolog subfamily C member 14
TraesCS5D02G557600	Chr.5D:559921945-559927074(-)	抗病蛋白RGA5 Disease resistance protein RGA5
TraesCS5D02G558500	Chr.5D:560226208-560228561(-)	泛素结合酶E2-23kDa Ubiquitin-conjugating enzyme E2-23 kDa
TraesCS5D02G557000	Chr.5D:559833743-559834390(+)	富含羟脯氨酸的糖蛋白Hydroxyproline-rich glycoprotein
TraesCS5D02G557100	Chr.5D:559856525-559861088(-)	核因子Y，推定的Nuclear factor Y, putative
TraesCS6D02G397000	Chr.6D:469205255-469207520(+)	转录因子TCP7 Transcription factor TCP7
TraesCS6D02G402500	Chr.6D:470902211-470908141(-)	热休克蛋白HSP70 Heat shock cognate 70 kDa protein
TraesCS7A02G232500	Chr.7A:203695192-203697934(+)	热休克蛋白26.2 kDa，线粒体26.2 kDa heat shock protein, mitochondrial
TraesCS7D02G139800	Chr.7D:89475764-89478415(-)	BSD结构域蛋白BSD domain containing protein
TraesCS7D02G140200	Chr.7D:89598936-89605640(-)	推定的网格组装蛋白Putative clathrin assembly protein
TraesCS7D02G142300	Chr.7D:90628658-90650108(+)	可待因O-甲基化酶Codeine O-demethylase

Table 4

Fig. 6

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处理时长 Heat treat time (h)	分级标准 Grade scale	耐热级数 HRG	热感类型 Thermal type
16	1.00≥SR≥0.75	1	极耐热Highly heat tolerance
	0.50≤SR<0.75	2	极耐热Highly heat tolerance
	0.25≤SR<0.50	3	极耐热Highly heat tolerance
	0.00≤SR<0.25	4	中等耐热Medium heat tolerance
12	1.00≥SR≥0.75	5	中等耐热Medium heat tolerance
	0.50≤SR<0.75	6	中等耐热Medium heat tolerance
	0.25≤SR<0.50	7	中等热敏感Medium heat sensitive
	0.00≤SR<0.25	8	中等热敏感Medium heat sensitive
8	1.00≥SR≥0.75	9	中等热敏感Medium heat sensitive
	0.50≤SR<0.75	10	极热敏感Highly heat sensitive
	0.25≤SR<0.50	11	极热敏感Highly heat sensitive
	0.00≤SR<0.25	12	极热敏感Highly heat sensitive

来源 Origin	名称 Name
中国China	鄂麦6号、丰产3号、藁城8901、黑宝-4、泾阳60、荆州47、陇黑838、宁春4号、糯麦1号、石家庄54、双大1号、苏麦3号、苏研麦0611、泰山4号、天民369、小白麦、艺麦1号、永良4号、豫圣黑麦1号、镇麦18、中原鼎紫1号、灰毛阿夫、毛颖阿夫 Emai 6 hao, Fengchan 3 hao, Gaocheng 8901, Heibao-4, Jingyang 60, Jingzhou 47, Longhei 838, Ningchun 4 hao, Nuomai 1 hao, Shijiazhuang 54, Shuangda 1 hao, Sumai 3 hao, Suyanmai 0611, Taishan 4 hao, Tianmin 369, Xiaobaimai, Yimai 1 hao, Yongliang 4 hao, Yushengmai 1 hao, Zhenmai 18, Zhongyuandingzi 1 hao, Huimao Funo, Maoying Funo
意大利Italy	阿勃、郑引1号 Abbondanza, St1472/506
智利Chile	欧柔Orofen
日本Japan	农林10号Norin 10
韩国Korea	水原86 Suwon 86
ICRADA	13W-25, 13W-40
其他Others	ARNEL、RUSSIA、捷克G377、小佛手、以色列小麦 ARNEL, RUSSIA, Czech G377, Xiaofoshou, Israel wheat

Genome-Wide Association Study of Heat Tolerance at Seedling Stage in A Wheat Natural Population

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