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A genome-wide association study prioritizes VRN1-2 as a candidate gene associated with plant height in soybean

文献类型： 外文期刊

作者： Wang, Le 1 ; Xue, Hong 2 ; Hu, Zhenbin 3 ; Li, Yang 4 ; Siqin, Tuya 5 ; Zhang, Hengyou 1 ;

作者机构： 1.Chinese Acad Sci, Northeast Inst Geog & Agroecol, State Key Lab Black Soils Conservat & Utilizat, Key Lab Soybean Mol Design Breeding, Harbin 150081, Peoples R China

2.Heilongjiang Acad Agr Sci, Keshan Branch, Qiqihar 161100, Peoples R China

3.ARS, Anim Genom & Improvement Lab, USDA, USDA, Beltsville, MD 20705 USA

4.Beijing Univ Technol, Inst Operat Res & Informat Engn, Beijing 100124, Peoples R China

5.Heilongjiang Inst Atom Energy, Harbin 150086, Peoples R China

期刊名称：THEORETICAL AND APPLIED GENETICS （ 影响因子：4.2； 五年影响因子：4.9 ）

ISSN： 0040-5752

年卷期： 2025 年 138 卷 4 期

页码：

收录情况： SCI

摘要： Plant height is an important architectural trait that affects crop growth, yield, and stress resistance. Tremendous efforts have been dedicated to revealing the genetic basis or regulatory mechanism; however, the underlying molecular mechanism remains largely unknown primarily due to the lack of controlling genes. In this study, we conducted a single-nucleotide resolution genome-wide association study (GWAS) of plant height using a diverse soybean panel collected worldwide with 6.7 million genome-wide variants (SNPs and Indels). The GWAS of plant height identified three QTLs on chromosomes 10, 18, and 19, of which the one on chromosome 19 precisely co-localized with Dt1, known as a major stem growth habit-controlling gene. Other loci without reported genes for plant height were regarded to be new. A close investigation within QTL intervals proposed nine genes that were likely involved in the regulation of plant height according to the expression specificity in developing shoot tip meristems. VRN1-2 underlies the significant QTL on chromosome 10 was prioritized as the most promising candidate gene. VRN1-2 shows higher expression in Williams 82 with indeterminate growth habit than Dongnong50 with semi-determinate growth habit across vegetative (V2, V3) and reproductive (R1) growth stages. VRN1-2 carries non-synonymous variants in the coding region that were significantly associated with plant height variation. The GT allele conferring short plant height was likely subjected to artificial selection during domestication. These results provide a source of new loci and genes for further elaborating the regulatory mechanism of plant height and the key variants would facilitate soybean molecular breeding.

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