基于GWAS的中国地方小麦成熟胚大小位点的鉴定及其遗传效应解析

doi:10.3864/j.issn.0578-1752.2026.06.002

中国农业科学 ›› 2026, Vol. 59 ›› Issue (6): 1157-1171.doi: 10.3864/j.issn.0578-1752.2026.06.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于GWAS的中国地方小麦成熟胚大小位点的鉴定及其遗传效应解析

叶美金¹^,⁶(), 吴雷²(), Lohani Md Nahibuzzaman², 尹丽², 胡欣荣², 刘亚西², 蒋云峰², 陈国跃², 蒲至恩³, 李阳³, 李婷²^,⁴, 邹亚亚²^,⁵, 吴佳怡¹, 马建²()

¹ 成都师范学院化学与生命科学学院，成都 611130
² 四川农业大学小麦研究所，成都 611130
³ 四川农业大学农学院，成都 611130
⁴ 四川省广元市昭化区农业农村局特色产业发展中心，四川广元 628021
⁵ 延安市农业科学研究院，陕西延安 716000
⁶ 乐山市特色植物资源创新利用工程技术研究中心，四川乐山 614000

收稿日期:2025-08-17 接受日期:2025-10-02 出版日期:2026-03-16 发布日期:2026-03-24
通信作者:
马建，E-mail：jianma@sicau.edu.cn
联系方式: 叶美金，E-mail：091048@cdnu.edu.cn。吴雷，E-mail：2169068493@qq.com。叶美金和吴雷为同等贡献作者。
基金资助:
四川省自然科学基金项目面上项目(2024NSFSC0330); 四川省大学生创新创业训练计划(S202514389093); 乐山市特色植物资源创新利用工程技术研究中心开放课题(TSZW2025-12)

Genome-Wide Association Study-Based Identification of Loci Controlling Mature Embryo Size in Chinese Wheat Landraces and Their Genetic Effects Analysis

YE MeJin¹^,⁶(), WU Lei²(), MD NAHIBUZZAMAN Lohani², YIN Li², HU XinRong², LIU YaXi², JIANG YunFeng², CHEN GuoYue², PU ZhiEn³, LI Yang³, LI Ting²^,⁴, ZOU YaYa²^,⁵, WU JiaYi¹, MA Jian²()

¹ College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130
² Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130
³ Agronomy College, Sichuan Agricultural University, Chengdu 611130
⁴ Characteristic Industry Development Center, Bureau of Agriculture and Rural Affairs of Zhaohua District, Guangyuan 628021, Sichuan
⁵ Yan'an Academy of Agricultural Sciences, Yan'an 716000, Shaanxi
⁶ Leshan Engineering Technology Research Center for Innovative Utilization of Feature Plant Resources, Leshan 61400, Sichuan

Received:2025-08-17 Accepted:2025-10-02 Published:2026-03-16 Online:2026-03-24

摘要/Abstract

摘要：

【目的】小麦胚是籽粒的重要组成部分，与种子的营养价值、萌发和幼苗建成密切相关。从遗传变异丰富的中国地方小麦中挖掘胚大小位点，并解析其遗传效应，拓展对小麦胚大小遗传基础的认识，为未来育种计划提供有价值的分子靶点。【方法】利用小麦660K SNP芯片对240份不同来源的中国地方小麦进行基因型分析，并结合3个环境的胚大小表型数据，通过混合线性模型进行全基因组关联分析，对检测到的显著性关联位点进行遗传效应分析和候选基因预测。【结果】在3个环境及最佳线性无偏预测值（BLUP）下，胚长、胚宽、胚面积、胚长宽比的范围分别为1.64—3.43 mm、0.93—2.58 mm、1.10—5.71 mm²和1.06—2.08，其广义遗传力分别为0.76、0.47、0.54和0.60。胚长、胚宽、胚面积、胚长宽比、胚长粒长比和胚宽粒宽比之间存在显著的正相关性，相关系数为0.271—0.922。主要胚性状（胚长、胚宽、胚面积）与粒长、千粒重、根干重呈显著正相关。共鉴定到18个在2个环境及BLUP中稳定表达的、与胚长和胚面积显著关联的SNP位点，这些位点被分为4个QTL区段，其中，控制胚长的有3个、控制胚面积的有1个，且胚面积QTL（QEA. sicau.3B）与胚长QTL（QEL.sicau.3B.2）共定位。针对主效胚长位点QEL.sicau.1B，预测了9个候选基因。遗传效应分析表明，QEL.sicau.1B的增效应位点在提高胚长、粒长、粒宽、粒重和缩短开花期方面具有显著作用，对提高幼苗根干重和地上部苗子干重方面具有显著优势，而对分蘖数和小穗数具有一定负效应。比较分析表明，QEL.sicau.1B和QEL.sicau.3B.2可能为新位点。【结论】通过全基因组关联分析检测到4个与胚大小显著相关的稳定QTL，针对胚长位点QEL.sicau.1B，预测了9个可能的候选基因。证实胚大小与籽粒大小呈显著正相关，且与苗期根系活力有一定关联。

关键词: 小麦, 胚大小, SNP标记, 全基因组关联分析, 农艺性状, 根系性状, 候选基因

Abstract:

【Objective】As a critical component of wheat grains, the embryo is closely correlated to nutritional value, germination, and seedling establishment. Mining embryo size loci from genetically diverse Chinese wheat landraces and deciphering their genetic effects will enhance our understanding of the genetic basis of embryo size and provide molecular targets for future breeding programs. 【Method】We genotyped 240 Chinese wheat landraces using the 660K SNP array and performed genome-wide association studies (GWAS) via a mixed linear model, integrating embryo size phenotypic data across three environments. Significant loci were subjected to genetic effect analysis and candidate gene prediction. 【Result】Phenotypic variation ranges across environments and BLUP values were: embryo length (1.64-3.43 mm), width (0.93-2.58 mm), area (1.10-5.71 mm²), and length-to-width ratio (1.06-2.08), with broad-sense heritabilities of 0.76, 0.47, 0.54, and 0.60, respectively. Significant positive correlations (r=0.271-0.922) existed among embryo traits, and between major embryo traits (length, width, area) and grain length or thousand-kernel weight. A total of 18 stable SNP loci significantly associated with embryo length and area were identified across two environments and BLUP values, which were clustered into four quantitative trait locus (QTL) intervals. These included three QTLs for embryo length and one for embryo area, with colocalization observed between QEA.sicau.3B and QEL.sicau.3B.2. For the major QTL QEL.sicau.1B, we predicted nine candidate genes. Genetic effect analysis revealed that the increasing allele of QEL.sicau.1B significantly enhanced embryo length, grain length and width, thousand-kernel weight, and reduced flowering time, while demonstrating superior effects on seedling root dry weight and shoot biomass, albeit with minor negative impacts on tiller number and spikelet number. Comparative analysis suggested both QEL.sicau.1B and QEL.sicau.3B.2 represent novel loci. 【Conclusion】GWAS identified four stable loci significantly associated with embryo size, among which nine potential candidate genes were predicted for the major embryo-length QTL (QEL.sicau.1B). The study demonstrated significant positive correlations between embryo size and grain dimensions, and revealed a functional association with seedling root vigor.

Key words: Triticum aestivum L., embryo size, SNP markers, GWAS, agronomic traits, root traits, candidate genes

叶美金, 吴雷, Lohani Md Nahibuzzaman, 尹丽, 胡欣荣, 刘亚西, 蒋云峰, 陈国跃, 蒲至恩, 李阳, 李婷, 邹亚亚, 吴佳怡, 马建. 基于GWAS的中国地方小麦成熟胚大小位点的鉴定及其遗传效应解析[J]. 中国农业科学, 2026, 59(6): 1157-1171.

YE MeJin, WU Lei, MD NAHIBUZZAMAN Lohani, YIN Li, HU XinRong, LIU YaXi, JIANG YunFeng, CHEN GuoYue, PU ZhiEn, LI Yang, LI Ting, ZOU YaYa, WU JiaYi, MA Jian. Genome-Wide Association Study-Based Identification of Loci Controlling Mature Embryo Size in Chinese Wheat Landraces and Their Genetic Effects Analysis[J]. Scientia Agricultura Sinica, 2026, 59(6): 1157-1171.

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性状 Trait	环境Environment	最小值Min	最大值Max	平均值Mean	标准差 Standard deviation	广义遗传力 H²
胚长 EL (mm)	2020YA	1.94	3.43	2.63	0.23	0.76
	2021CZ	1.74	2.38	2.01	0.11
	2021PX	1.64	2.50	2.06	0.13
	BLUP	2.06	2.44	2.23	0.07
胚宽 EW (mm)	2020YA	1.61	2.58	2.07	0.19	0.47
	2021CZ	0.97	1.58	1.12	0.07
	2021PX	0.93	1.55	1.15	0.09
	BLUP	1.38	1.53	1.45	0.02
胚面积 EA (mm²)	2020YA	2.38	5.71	3.95	0.67	0.54
	2021CZ	1.25	2.20	1.63	0.17
	2021PX	1.10	2.79	1.71	0.21
	BLUP	2.18	2.76	2.43	0.09
胚长宽比 EL/EW	2020YA	1.06	1.71	1.27	0.09	0.60
	2021CZ	1.22	1.95	1.80	0.09
	2021PX	1.28	2.08	1.79	0.11
	BLUP	1.54	1.74	1.62	0.03

性状 Traits		胚长 EL	胚宽 EW	胚面积 EA	胚长宽比 EL/EW	胚长粒长比 EL/KL	胚宽粒宽比 EW/KW
胚相关性状 Embryo-related traits	胚宽 EW	0.703**
	胚面积 EA	0.896**	0.922**
	胚长宽比 EL/EW	0.366**	-0.357**	0.003
	胚长粒长比 EL/KL	0.362**	0.307**	0.371**	0.112
	胚宽粒宽比 EW/KW	0.271**	0.370**	0.369**	-0.091	0.190**
农艺性状 Agronomic traits	有效分蘖数 ETN	-0.168**	-0.241**	-0.203**	0.135*	0.128*	0.237**
	小穗数 SNS	-0.06	-0.123	-0.086	0.113	0.245**	0.160*
	粒长 KL	0.334**	0.179**	0.249**	0.144*	-0.756**	-0.007
	粒宽 KW	0.064	0.103	0.066	-0.079	-0.058	-0.885**
	千粒重 TKW	0.256**	0.243**	0.239**	-0.023	-0.378**	-0.522**
	株高 PH	-0.189**	-0.141*	-0.170**	-0.038	0.107	-0.428**
	开花期 AD	-0.134*	-0.236**	-0.172**	0.227**	0.187**	0.251**
根相关性状 Root-related traits	根平均直径 RAD	0.023	0.016	0.032	0.033	-0.016	-0.086
	最大根长 MRL	0.062	-0.001	0.022	0.099	0.027	0.018
	根干重 RDW	0.191**	0.165*	0.178**	0.007	-0.315**	-0.017
	根表面积 RSA	0.023	0.049	0.02	-0.092	-0.122	0.131*
	根尖数 RTN	0.052	0.099	0.053	-0.106	0.037	-0.028
	根体积 RV	0.123	0.096	0.11	0.02	-0.163*	0.006
	地上部干重 SDW	0.075	0.091	0.084	-0.041	-0.094	0.105
	总根长 TRL	0.044	0.022	0.024	0.043	-0.035	0.083

位点 QTL	单核苷酸多态性 SNP	染色体 Chromosome	物理位置 Position (bp)	位点 Allele	显著性阈值 -log₁₀(P)	贡献率 R²(%)	环境 Environments
QEL.sicau.1B	AX-111181581	1B	141343104	T/G	3.10-3.94	3.27-4.19	2021CZ, 2021PX, BLUP
QEL.sicau.3B.1	AX-111538915	3B	719495993	T/A	3.73-4.31	1.59-1.85	2021CZ, 2021PX, BLUP
QEL.sicau.3B.1	AX-109479189	3B	718925366	C/G	3.42-4.02	1.85-2.44	2021CZ, 2021PX, BLUP
QEL.sicau.3B.2	AX-110440810	3B	142585929	A/G	3.13-3.62	1.24-1.45	2021CZ, 2021PX, BLUP
	AX-109903451	3B	142577728	C/T	4.09-4.93	2.71-3.04	2021CZ, 2021PX, BLUP
	AX-108783107	3B	142558781	A/G	3.57-4.79	1.59-2.02	2021CZ, 2021PX, BLUP
	AX-111075885	3B	142547414	T/C	3.33-3.86	1.27-1.60	2021CZ, 2021PX, BLUP
	AX-110920483	3B	143376780	G/A	3.93-5.22	1.85-2.31	2021CZ, 2021PX, BLUP
	AX-109278255	3B	142586814	T/C	3.36-5.15	1.35-1.96	2021CZ, 2021PX, BLUP
	AX-111064212	3B	142532066	G/A	3.16-4.64	1.82-2.63	2021CZ, 2021PX, BLUP
	AX-111737137	3B	142590393	A/G	3.29-4.19	1.50-1.79	2021CZ, 2021PX, BLUP
	AX-109414729	3B	143379652	T/C	3.93-5.22	1.85-2.31	2021CZ, 2021PX, BLUP
	AX-109002351	3B	142585807	A/G	3.20-3.88	1.51-1.68	2021CZ, 2021PX, BLUP
QEA.sicau.3B	AX-111064212	3B	142532066	G/A	3.22-3.93	1.87-2.18	2021CZ, 2021PX, BLUP
	AX-108783107	3B	142558781	A/G	3.22-4.35	1.40-1.82	2021CZ, 2021PX, BLUP
	AX-109903451	3B	142577728	C/T	3.67-4.43	2.15-2.88	2021CZ, 2021PX, BLUP
	AX-110920483	3B	143376780	G/A	3.52-4.32	1.63-1.85	2021CZ, 2021PX, BLUP
	AX-109414729	3B	143379652	T/C	3.52-4.32	1.63-1.85	2021CZ, 2021PX, BLUP

候选基因 Candidate genes	基因注释或编码蛋白 Gene annotation or coding proteins	水稻同源基因 Homologs in rice
TraesCS1B02G114700	F-box家族蛋白F-box family protein	OsFbox375, OsFbox376, OsFbox253
TraesCS1B02G114800	F-box家族蛋白F-box family protein	OsFbox375, OsFbox376
TraesCS1B02G114900	F-box家族蛋白F-box family protein	OsFbox375
TraesCS1B02G115400	细胞凋亡相关蛋白2 Programmed cell death protein 2	Null
TraesCS1B02G115500	WD重复域蛋白 WD-repeat protein	OsWD40-68, OsWD40-45, WDR5a, MAC3B
TraesCS1B02G191700LC	逆转录病毒相关Pol多聚蛋白LINE-1 Retrovirus-related Pol polyprotein LINE-1	Null
TraesCS1B02G196100LC	酪氨酰-DNA磷酸二酯酶1 Tyrosyl-DNA phosphodiesterase 1	Null
TraesCS1B02G196200LC	甘油-3-磷酸脱氢酶[NAD(P)⁺] Glycerol-3-phosphate dehydrogenase [NAD(P)⁺]	Null
TraesCS1B02G196600LC	HAT家族二聚化域蛋白 HAT family dimerisation domain containing protein	DAYSLEEPER

基于GWAS的中国地方小麦成熟胚大小位点的鉴定及其遗传效应解析

Genome-Wide Association Study-Based Identification of Loci Controlling Mature Embryo Size in Chinese Wheat Landraces and Their Genetic Effects Analysis

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