基于全基因组关联分析解析小麦茎节间长度的遗传基础及其效应

doi:10.3864/j.issn.0578-1752.2026.12.002

中国农业科学 ›› 2026, Vol. 59 ›› Issue (12): 2551-2562.doi: 10.3864/j.issn.0578-1752.2026.12.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于全基因组关联分析解析小麦茎节间长度的遗传基础及其效应

叶美金¹^,⁷(), 王同著², 陈斌², LOHANI Md Nahibuzzaman², 陈家婷², 胡欣荣², 尹丽², 王超², 张昊芃², 杨夏², 王佳琳³, 姚琦馥⁴, 丁浦洋⁵, 王凤¹, 李小雨⁶(), 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 铜仁学院农林工程与规划学院/贵州省梵净山地区生物多样性保护与利用重点实验室，贵州铜仁 554300
⁵ 绵阳师范学院生物与制药学院，四川绵阳 621000
⁶ 南充市农业科学院，四川南充 637000
⁷ 特色园艺生物资源开发与利用重点实验室，成都 611130

收稿日期:2025-12-09 接受日期:2026-01-20 出版日期:2026-06-16 发布日期:2026-06-16
通信作者:
马建，E-mail：jianma@sicau.edu.cn。
李小雨，E-mail：l.xioayu@foxmail.com
联系方式: 叶美金，E-mail：091048@cdnu.edu.cn。
基金资助:
四川省自然科学基金项目面上项目(2024NSFSC0330); 大学生创新创业训练计划项目(202514389001); 特色园艺生物资源开发与利用重点实验室项目(TSYY202507)

Genetic Dissection of Stem Internode Length and Its Effects in Wheat Based on a Genome-Wide Association Study

YE MeiJin¹^,⁷(), WANG TongZhu², CHEN Bin², LOHANI Md Nahibuzzaman², CHEN JiaTing², HU XinRong², YIN Li², WANG Chao², ZHANG HaoPeng², YANG Xia², WANG JiaLin³, YAO QiFu⁴, DING PuYang⁵, WANG Feng¹, LI XiaoYu⁶(), MA Jian²()

¹ College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130
² Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130
³ College of Agronomy, Sichuan Agricultural University, Chengdu 611130
⁴ College of Agroforestry Engineering and Planning, Tongren University/Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren 554300, Guizhou
⁵ School of Biological and Pharmaceutical Sciences, Mianyang Teachers’ College, Mianyang 621000, Sichuan
⁶ Nanchong Academy of Agricultural Sciences, Nanchong 637000, Sichuan
⁷ Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu 611130

Received:2025-12-09 Accepted:2026-01-20 Published:2026-06-16 Online:2026-06-16

摘要/Abstract

摘要：

【目的】株高是影响小麦产量潜力和抗倒伏性的关键农艺性状，主要由茎秆节间的伸长决定。系统评估224份四川小麦品种的节间长度，解析其遗传基础，挖掘调控节间长度的稳定表达新位点，明确其遗传效应，并筛选相关候选基因，为高产小麦品种的定向选育提供重要基因资源和理论依据。【方法】在2个环境下分别测定小麦第一节间（IL1）、第二节间（IL2）和第三节间（IL3）的长度。利用小麦120K SNP芯片对供试群体进行基因型分析，通过全基因组关联分析（GWAS）鉴定调控节间长度的遗传位点，结合表型相关性分析解析主效位点的遗传效应，并基于公共数据库预测候选基因。【结果】表型分析显示，所有节间性状均呈连续变异，广义遗传力较高，估计值为75%—89%。相关性分析表明，3个节间长度均与最终株高呈正相关，其中，IL1的相关性最强。此外，IL2与IL3之间高度相关，提示下部茎节具有协调的遗传调控。GWAS检测到位于5A和4D染色体上的4个稳定位点，分别为调控第一节间的QIL1.sau.5A、调控第二节间的2个紧密连锁但独立的QTL QIL2.sau.5A.1和QIL2.sau.5A.2，以及调控第三节间的QIL3.sau.4D。多效性分析显示，QIL2.sau.5A.1显著增加株高和穗长，而QIL3.sau.4D主要促进节间伸长及整体株高。基于功能注释和时空表达数据，共鉴定出5个潜在候选基因，可能参与转录调控、激素信号传导和细胞生长过程。【结论】揭示了四川小麦节间伸长的遗传结构，鉴定出2个新QTL及多个具有多效性的遗传位点。

关键词: 小麦, 节间长度, SNP标记, 全基因组关联分析, 农艺性状, 候选基因

Abstract:

【Objective】Plant height is a key agronomic trait in wheat that influences both yield potential and lodging resistance. It is primarily determined by the elongation of stem internodes. This study aimed to systematically evaluate the internode lengths of 224 Sichuan wheat cultivars, identify stable quantitative trait loci (QTL) regulating internode length and clarify their effects on agronomic traits, and screen the underlying candidate genes, thus providing important genetic resources and a theoretical basis for the targeted breeding of high-yield wheat varieties. 【Method】The lengths of the first (IL1), the second (IL2), and the third (IL3) internodes were measured under two different environments. The panel was genotyped using the wheat 120K SNP array. A genome-wide association study (GWAS) was employed to identify QTL regulating internode length. The phenotyping data was used for correlation analysis and the interpretation of the genetic effects of major QTL. The candidate genes of the major QTL were predicted based on wheat omics data. 【Result】Phenotypic analysis revealed continuous variation for all internode traits, with high broad-sense heritability estimates ranging from 75% to 89%. Correlation analysis showed that lengths of all three internodes were positively correlated with final plant height, with IL1 exhibiting the strongest correlation. Furthermore, IL2 and IL3 were highly correlated with each other, suggesting coordinated genetic regulation of the lower stem internodes. GWAS detected four stable QTLs on chromosomes 5A and 4D, namely QIL1.sau.5A for IL1, two tightly linked but distinct QTL QIL2.sau.5A.1 and QIL2.sau.5A.2 for IL2, and QIL3.sau.4D for IL3, respectively. Pleiotropy analysis demonstrated that QIL2.sau.5A.1 significantly increased plant height and spike length, while QIL3.sau.4D primarily promoted internode elongation and overall plant height. Based on functional annotation and spatiotemporal expression data, five candidate genes potentially involved in transcriptional regulation, hormone signal transduction, and cell growth were identified. 【Conclusion】This study elucidated the genetic architecture of internode elongation in a panel of Sichuan wheat cultivars and identified two novel QTLs and several pleiotropic loci. These stable QTLs and the underlying candidate genes provided valuable resources for molecular marker-assisted selection aiming at optimizing plant height, improving lodging resistance, and enhancing yield potential in wheat.

Key words: Triticum aestivum L., internode lengths, SNP markers, GWAS, agronomic traits, candidate genes

叶美金, 王同著, 陈斌, LOHANI Md Nahibuzzaman, 陈家婷, 胡欣荣, 尹丽, 王超, 张昊芃, 杨夏, 王佳琳, 姚琦馥, 丁浦洋, 王凤, 李小雨, 马建. 基于全基因组关联分析解析小麦茎节间长度的遗传基础及其效应[J]. 中国农业科学, 2026, 59(12): 2551-2562.

YE MeiJin, WANG TongZhu, CHEN Bin, LOHANI Md Nahibuzzaman, CHEN JiaTing, HU XinRong, YIN Li, WANG Chao, ZHANG HaoPeng, YANG Xia, WANG JiaLin, YAO QiFu, DING PuYang, WANG Feng, LI XiaoYu, MA Jian. Genetic Dissection of Stem Internode Length and Its Effects in Wheat Based on a Genome-Wide Association Study[J]. Scientia Agricultura Sinica, 2026, 59(12): 2551-2562.

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性状 Trait	环境 Environment	最大值 Max	最小值 Min	平均值 Mean	标准差 Standard deviation	变异系数 CV (%)	广义遗传力 H² (%)
第一节间长度 IL1 (cm)	WJ2025	49.16	23.14	31.20	3.36	10.78	89
	CZ2025	42.84	22.16	29.61	3.30	11.14
	BLUP	41.94	25.33	30.41	2.20	7.22
第二节间长度 IL2 (cm)	WJ2025	25.34	12.02	18.89	2.11	11.19	85
	CZ2025	20.28	10.32	14.52	1.85	12.77
	BLUP	20.89	13.34	16.71	1.19	7.14
第三节间长度 IL3 (cm)	WJ2025	22.34	8.53	13.35	1.89	14.18	75
	CZ2025	15.14	5.88	10.03	1.60	15.97
	BLUP	15.22	9.79	11.69	0.78	6.67

性状 Trait	第一节间长度 IL1	第二节间长度 IL2	第三节间长度 IL3	株高 PH	有效分蘖数 ETN	穗长 SL	每穗小穗数 SNS
第二节间长度IL2	0.416**
第三节间长度IL3	0.311**	0.748**
株高PH	0.615**	0.556**	0.613**
有效分蘖数ETN	0.033	-0.009	-0.026	-0.098
穗长SL	0.095	-0.04	-0.117	0.283**	-0.021
每穗小穗数SNS	-0.024	-0.122	-0.042	0.109	-0.188**	0.380**
千粒重TKW	0.04	0.016	-0.031	0.11	0.105	0.198**	-0.245**

性状 Trait	位点 QTL	单核苷酸多态性 SNP	等位位点 Allele	染色体 Chromosome	物理位置 Position (bp)	显著性阈值 -log₁₀(P)	贡献率 R²(%)	环境 Environments
第一节间长度 IL1	QIL1.sau.5A	5A_501635166	T/C	5A	501635166	4.21-5.42	1.62-2.19	CZ2025, WJ2025, BLUP
第二节间长度 IL2	QIL2.sau.5A.1	5A_510913304	G/A	5A	510913304	4.23-5.58	5.90-8.18	CZ2025, WJ2025, BLUP
		5A_510913376	C/T	5A	510913376	4.21-5.68	5.82-8.30	CZ2025, WJ2025, BLUP
		5A_510913381	T/C	5A	510913381	4.21-5.68	5.82-8.30	CZ2025, WJ2025, BLUP
		5A_511296202	T/C	5A	511296202	4.02-5.54	5.88-8.59	CZ2025, WJ2025, BLUP
		5A_511296204	C/G	5A	511296204	4.02-5.54	5.88-8.59	CZ2025, WJ2025, BLUP
		5A_511991250	G/T	5A	511991250	4.01-5.76	5.98-9.16	CZ2025, WJ2025, BLUP
		5A_513013678	A/G	5A	513013678	4.02-5.69	5.88-8.88	CZ2025, WJ2025, BLUP
		5A_513255742	T/C	5A	513255742	4.04-6.08	5.95-9.65	CZ2025, WJ2025, BLUP
		5A_514724687	C/T	5A	514724687	4.14-5.41	8.06-11.04	CZ2025, WJ2025, BLUP
		5A_514884600	A/G	5A	514884600	4.04-6.08	5.95-9.65	CZ2025, WJ2025, BLUP
	QIL2.sau.5A.2	5A_517883089	G/A	5A	517883089	4.10-6.28	6.10-10.07	CZ2025, WJ2025, BLUP
		5A_518500826	T/C	5A	518500826	4.09-6.17	6.08-9.87	CZ2025, WJ2025, BLUP
		5A_518579568	A/G	5A	518579568	4.04-6.08	5.95-9.65	CZ2025, WJ2025, BLUP
		5A_519456501	C/T	5A	519456501	4.04-6.08	5.95-9.65	CZ2025, WJ2025, BLUP
		5A_519549809	G/A	5A	519549809	4.08-5.57	5.69-8.23	CZ2025, WJ2025, BLUP
		5A_519551494	C/T	5A	519551494	4.20-5.63	5.90-8.32	CZ2025, WJ2025, BLUP
		5A_519604654	T/C	5A	519604654	4.32-6.08	6.09-9.10	CZ2025, WJ2025, BLUP
		5A_521267698	G/A	5A	521267698	4.02-5.50	4.55-6.58	CZ2025, WJ2025, BLUP
第三节间长度 IL3	QIL3.sau.4D	4D_20705614	G/A	4D	20705614	4.04-5.03	7.76-10.07	CZ2025, WJ2025, BLUP
第三节间长度 IL3	QIL3.sau.4D	4D_21001512	G/T	4D	21001512	4.22-5.28	8.15-10.61	CZ2025, WJ2025, BLUP

位点 QTL	候选基因 Candidate genes	起始位置 Start position (Mb)	基因注释或编码蛋白 Gene annotation or coding proteins	同源基因 Homologs gene
QIL3.sau.4D	TraesCS4D02G041400	19.813161	ATP依赖性RNA解旋酶 ATP-dependent RNA helicase	OsRH21, OsRH52B, OsRH52C
QIL3.sau.4D	TraesCS4D02G042100	20.090627	碱性蓝蛋白 Basic blue protein	OsUCL8, OsUCL9, OsUCL12, ARPN, ENODL22
QIL1.sau.5A	TraesCS5A02G286200	494.413105	pfkB样碳水化合物激酶家族蛋白 pfkB-like carbohydrate kinase family protein	OsFKI, OsFKII
QIL2.sau.5A.2	TraesCS5A02G299500	509.602215	组蛋白H4 Histone H4	无Null
QIL2.sau.5A.2	TraesCS5A02G299800	509.669584	RNA聚合酶Ⅱ转录辅激活因子 RNA polymerase Ⅱ transcriptional coactivator	SI1, KIWI, KELP

基于全基因组关联分析解析小麦茎节间长度的遗传基础及其效应

Genetic Dissection of Stem Internode Length and Its Effects in Wheat Based on a Genome-Wide Association Study

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