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

Abstract

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

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

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

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