冬小麦千粒重的全基因组关联分析及候选基因预测

doi:10.3864/j.issn.0578-1752.2026.03.003

中国农业科学 ›› 2026, Vol. 59 ›› Issue (3): 499-514.doi: 10.3864/j.issn.0578-1752.2026.03.003

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

冬小麦千粒重的全基因组关联分析及候选基因预测

王勇胜¹^,²(), 牛丽¹^,², 王长杰¹^,², 马立花¹^,², 廉潇潇¹, 孟亚雄¹^,², 马小乐¹^,², 姚立蓉¹^,², 张宏¹^,², 杨轲¹^,², 李葆春²^,³, 王化俊¹^,², 司二静¹^,²(), 汪军成¹^,²()

¹ 甘肃农业大学农学院，兰州 730070
² 省部共建干旱生境作物学国家重点实验室，兰州 730070
³ 甘肃农业大学生命科学技术学院，兰州 730070

收稿日期:2025-07-31 接受日期:2025-09-15 出版日期:2026-02-01 发布日期:2026-01-31
通信作者:
司二静，E-mail：siej@gsau.edu.cn。
汪军成，E-mail：wangjc@gsau.edu.cn
联系方式: 王勇胜，E-mail：wangys1125@163.com。
基金资助:
甘肃省现代寒旱特色农业种业攻关项目(ZYGG-2025-3); 甘肃省现代寒旱特色农业种业攻关项目(ZYGG-2026-18); 甘肃省现代寒旱特色农业种业攻关项目(ZYGG-2025-12-3); 甘肃农业大学大学生创新训练项目(202501078); 甘肃省重点人才项目(2023RCXM70); 中央引导地方科技发展资金(25ZYJA002); 甘肃省现代寒旱特色农业麦类产业技术体系(GSARS-07); 甘肃省教育厅产业支撑计划(2021CYZC-12); 甘肃省自然科学基金重点项目(24JRRA637); 甘肃省农业农村厅种业攻关项目(GYGG-2024-2); 甘肃省科技计划(24CXNA038); 甘肃农业大学伏羲青年英才计划(Gaufx-03Y06); 甘肃农业大学伏羲青年英才计划(Gaufx-04Y011)

Genome-Wide Association Study and Candidate Gene Identification for Thousand Grain Weight in Winter Wheat

WANG YongSheng¹^,²(), NIU Li¹^,², WANG ChangJie¹^,², MA LiHua¹^,², LIAN XiaoXiao¹, MENG YaXiong¹^,², MA XiaoLe¹^,², YAO LiRong¹^,², ZHANG Hong¹^,², YANG Ke¹^,², LI BaoChun²^,³, WANG HuaJun¹^,², SI ErJing¹^,²(), WANG JunCheng¹^,²()

¹ College of Agronomy, Gansu Agricultural University, Lanzhou 730070
² State Key Laboratory of Aridland Crop Science, Lanzhou 730070
³ College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070

Received:2025-07-31 Accepted:2025-09-15 Published:2026-02-01 Online:2026-01-31

摘要/Abstract

摘要：

【目的】小麦千粒重作为直接影响最终产量的核心要素，其遗传解析至关重要。精准鉴定调控该性状的稳定显著关联位点及其关键候选基因，为分子标记辅助选育高千粒重、高产小麦新品种提供理论依据和遗传资源。【方法】通过对291份不同来源小麦种质资源进行100K SNP芯片基因型分型，并结合连续2年采集的千粒重表型数据及其最优无偏预测值（best linear unbiased prediction，BLUP），利用基于P+K模型的混合线性模型（mixed linear model，MLM）实施全基因组关联分析（genome-wide association study，GWAS）。最终，对定位到的显著关联位点进行单倍型分析。【结果】291份小麦千粒重在2年间及BLUP值下均呈广泛变异（均值38.24—38.82 g，变异系数17.62%—19.93%），2年间的千粒重相关系数为0.88（P<0.01），与BLUP值的相关系数均为0.97（P<0.01）达极显著水平。基于291份冬小麦种质资源的千粒重表型数据在不同环境条件下均呈现正态分布特征，符合全基因组关联分析对数量性状数据分布的基本要求，表明该数据集适用于后续关联分析。GWAS分析共检测到19个与千粒重显著相关的SNP位点，分布在3B、5A和7A染色体上，能够解释6.85%—9.68%的表型变异，其中，有16个标记在2个及以上的分析环境中出现，是比较稳定的SNP标记。通过对多环境下存在且表型贡献率高的多效应位点进行单倍型分析，位于7A染色体的7A_145980808位点发掘到与千粒重显著相关的Hap1、Hap2、Hap3和Hap4等4个不同单倍型，其中，Hap4是高千粒重单倍型（P<0.01），而Hap2为低千粒重单倍型（P<0.01）。4种单倍型分别占72.36%、14.55%、8.73%和4.36%。具有单倍型Hap1、Hap2、Hap3和Hap4的品种（系）的国内材料占比表现为Hap3（95.83%）>Hap4（83.33%）>Hap1（77.39%）>Hap2（65.00%）。通过分析高千粒重单倍型Hap4，发现其在分布上主要集中于西北冬麦区，尤其是甘肃来源的品种。基于关联分析结果，在3B、5A和7A染色体上筛选多环境显著性关联位点，并以其上下游3.6 Mb区域作为置信区间，共鉴定出95个候选基因。最终通过联合基因注释与基因表达情况，获得4个可能与小麦千粒重相关的候选基因。【结论】揭示了16个与千粒重显著关联的稳定位点，鉴定出4种不同单倍型，并筛选到4个关键候选基因。这些基因主要参与碳水化合物合成与转运、细胞壁多糖组装、蛋白质稳态维持，以及淀粉合成基因的转录调控等生理过程。

关键词: 小麦, 千粒重, SNP标记, 全基因组关联分析, 单倍型, 候选基因

Abstract:

【Objective】Thousand-grain weight (TGW), a key determinant of final wheat yield, is of great importance for genetic dissection. Precise identification of stable loci and key candidate genes controlling TGW provides theoretical foundations and genetic resources for marker-assisted breeding of high-TGW and high-yield wheat varieties. 【Method】A total of 291 wheat accessions from diverse origins were genotyped using a 100K SNP array. TGW phenotypic data collected over two consecutive years and their best linear unbiased predictions (BLUPs) were analyzed using a genome-wide association study (GWAS) based on a mixed linear model (MLM) incorporating both population structure (P) and kinship (K). Significant loci were further subjected to haplotype analysis. 【Result】TGW showed broad variation across years and BLUP values (mean: 38.24-38.82 g; coefficient of variation: 17.62%-19.93%). The correlation between years was 0.88 (P<0.01), and correlations with BLUP values reached 0.97 (P<0.01). Phenotypic data displayed normal distributions under different environments, meeting the basic requirements for GWAS. A total of 19 SNPs significantly associated with TGW were detected on chromosomes 3B, 5A, and 7A, explaining 6.85%-9.68% of the phenotypic variation; 16 of them were repeatedly detected across multiple environments, indicating stability. Haplotype analysis at locus 7A_145980808 revealed four haplotypes (Hap1-Hap4), of which Hap4 was associated with high TGW (P<0.01) and Hap2 with low TGW (P<0.01). The frequencies of Hap1-Hap4 were 72.36%, 14.55%, 8.73%, and 4.36%, respectively. Domestic accessions were enriched for Hap3 (95.83%) and Hap4 (83.33%), with Hap4 predominantly distributed in the Northwestern winter wheat region, especially in germplasm from Gansu. Candidate gene mining within 3.6 Mb regions flanking significant loci on chromosomes 3B, 5A, and 7A identified 95 genes, among which four were highlighted based on gene annotation and expression profiles. 【Conclusion】GWAS identified 16 stable SNP loci significantly associated with TGW, four distinct haplotypes, and four key candidate genes. These genes are mainly involved in carbohydrate synthesis and transport, cell wall polysaccharide assembly, protein homeostasis, and transcriptional regulation of starch biosynthesis, providing valuable targets for molecular breeding of high-yield wheat.

Key words: wheat, thousand-grain weight, SNP markers, GWAS, haplotype, candidate genes

王勇胜, 牛丽, 王长杰, 马立花, 廉潇潇, 孟亚雄, 马小乐, 姚立蓉, 张宏, 杨轲, 李葆春, 王化俊, 司二静, 汪军成. 冬小麦千粒重的全基因组关联分析及候选基因预测[J]. 中国农业科学, 2026, 59(3): 499-514.

WANG YongSheng, NIU Li, WANG ChangJie, MA LiHua, LIAN XiaoXiao, MENG YaXiong, MA XiaoLe, YAO LiRong, ZHANG Hong, YANG Ke, LI BaoChun, WANG HuaJun, SI ErJing, WANG JunCheng. Genome-Wide Association Study and Candidate Gene Identification for Thousand Grain Weight in Winter Wheat[J]. Scientia Agricultura Sinica, 2026, 59(3): 499-514.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2026.03.003

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小麦千粒重的重要候选基因的预测与注释"

候选基因 Candidate genes	染色体位置 Chromosome location (bp)	基因注释或编码蛋白 Gene annotation or coding proteins	拟南芥同源基因 Homologs in Arabidopsis thaliana
TraesCS3B03G0336700	3B: 128948207-128950128	赤霉素3-β-羟化酶2 Gibberellin 3-beta-hydroxylase 2	AT1G15550
TraesCS3B03G0338300	3B: 130257382-130258484	β-淀粉酶 Beta-amylase	AT4G36780
TraesCS3B03G0339200	3B: 130646139-130648627	F-box家族蛋白 F-box family protein	AT2G03560
TraesCS3B03G0343000	3B: 132089715-132091559	糖基转移酶 Glycosyltransferase	AT3G53150
TraesCS3B03G0343900	3B: 132904195-132906317	糖基转移酶 Glycosyltransferase	AT3G53150
TraesCS3B03G0344400	3B: 132999447-133000637	糖基转移酶 Glycosyltransferase	AT2G36750
TraesCS3B03G0345400	3B: 133381587-133383648	F-box家族蛋白 F-box family protein	AT4G00755
TraesCS3B03G0345500	3B: 133384475-133386349	糖基转移酶 Glycosyltransferase	AT2G36800
TraesCS3B03G0346600	3B: 133818631-133823762	硼转运蛋白 Boron transporter	AT1G15460
TraesCS5A03G0902700	5A: 574194918-574199874	bHLH转录因子 Basic helix-loop-helix transcription factor	AT2G20180
TraesCS5A03G0903300	5A: 574399521-574400834	F-box家族蛋白 F-box family protein	AT3G48880
TraesCS5A03G0903400	5A: 574482068-574485628	转运蛋白相关家族蛋白 Transporter-related family protein	AT3G13050
TraesCS5A03G0903600	5A: 574488360-574493061	转运蛋白相关家族蛋白 Transporter-related family protein	AT3G13050
TraesCS5A03G0904700	5A: 575322960-575329017	生长素管化蛋白 Auxin canalization protein	AT3G22810
TraesCS5A03G0912000	5A: 578061853-578067290	bHLH转录因子 Basic helix-loop-helix transcription factor	AT5G43650
TraesCS5A03G0912200	5A: 578446505-578449774	WRKY转录因子 WRKY transcription factor	AT2G30590
TraesCS7A03G0440800	7A: 146025353-146026920	NAC结构域蛋白 NAC domain protein	AT5G18270

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环境 Environment	最大值 Max (g)	最小值 Min (g)	平均值 Average (g)	标准差 SD (%)	峰度 Kurtosis	偏度 Skewness	变异系数 Coefficient of variation (%)	相关系数 Correlation coefficient
环境 Environment	最大值 Max (g)	最小值 Min (g)	平均值 Average (g)	标准差 SD (%)	峰度 Kurtosis	偏度 Skewness	变异系数 Coefficient of variation (%)	E1	E2
E1	57.44	20.26	38.39	7.25	-0.48	0.13	18.87
E2	57.10	19.12	38.82	7.70	-0.62	0.01	19.83	0.88**
E3	56.07	21.90	38.61	6.80	-0.55	0.09	17.62	0.97**	0.97**

染色体 Chromosome	染色体长度 Chromosome length (Mb)	标记数目 Number	标记密度 Density (markers/Mb)
1A	597.39	12892	21.58
1B	699.10	10645	15.23
1D	498.58	5626	11.28
2A	787.40	14438	18.34
2B	812.47	15453	19.02
2D	655.52	6628	10.11
3A	753.13	8471	11.25
3B	851.47	14238	16.72
3D	618.91	3861	6.24
4A	753.69	10308	13.68
4B	673.37	7616	11.31
4D	517.87	2190	4.23
5A	713.16	10341	14.50
5B	714.75	13228	18.51
5D	569.44	4150	7.29
6A	622.46	9200	14.78
6B	730.93	12594	17.23
6D	495.25	3986	8.05
7A	744.23	11698	15.72
7B	763.26	12149	15.92
7D	642.35	5546	8.63
A基因组A genome	4971.46	77348	15.56
B基因组B genome	5245.35	85923	16.38
D基因组D genome	3997.92	31987	8.00
总计Total	14214.73	195285	13.74

环境Environment	标记 Marker	染色体 Chr.	位置 Position (bp)	显著性阈值 -log₁₀(P)	贡献率 R²(%)
E1/E3	3B_143949526	3B	143949526	4.58-4.62	8.25-8.36
E2/E3	5A_579847898	5A	579847898	4.83-4.92	7.91-8.06
E2/E3	5A_579848522	5A	579848522	4.60-4.74	7.50-7.76
E2/E3	5A_579921639	5A	579921639	4.48-4.76	7.30-7.80
E2/E3	5A_579921681	5A	579921681	4.20-4.44	6.85-7.27
E2/E3	5A_579921718	5A	579921718	4.35-4.55	7.22-7.64
E2/E3	5A_579955478	5A	579955478	4.24-4.76	6.91-7.79
E2/E3	7A_148378633	7A	148378633	4.55-5.59	7.69-9.68

冬小麦千粒重的全基因组关联分析及候选基因预测

Genome-Wide Association Study and Candidate Gene Identification for Thousand Grain Weight in Winter Wheat

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