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Journal of Integrative Agriculture  2022, Vol. 21 Issue (4): 933-946    DOI: 10.1016/S2095-3119(21)63693-6
Special Issue: 油料作物合辑Oil Crops
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean
TIAN Yu1, YANG Lei1, LU Hong-feng2, ZHANG Bo3, LI Yan-fei1, LIU Chen1, 4, GE Tian-li1, LIU Yu-lin5, HAN Jia-nan1, LI Ying-hui1, QIU Li-juan1
1 National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture and Rural Affairs/Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, P.R.China 
2 Novogene Bioinformatics Institute, Beijing 100015, P.R.China 
3 School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA 
4 School of Life Sciences, Liaoning Normal University, Dalian 116081, P.R.China 
5 College of Forestry, Northwest A&F University, Yangling 712100, P.R.China
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大豆株高是由主效或微效基因控制的重要农艺性状。在已报道的株高QTL中,绝大部分定位区间较大,限制了大豆株高分子调控机制的解析。增加遗传图谱的标记密度会显著地提高QTL定位的效率和准确性。本研究利用双亲中黄13和中品03-5373及其衍生的241个重组自交系(RILs)全基因组重测序数据,构建一个包含4011个重组bin标记、总遗传距离为3139.15 cM的高密度遗传图谱,相邻bin标记间的平均距离为0.78 cM。比较基因组分析表明,所构建的遗传图谱与大豆参考基因组具有较高的共线性。基于此图谱,在6个环境中共检测到9个株高QTL,包括3个新位点(qPH-b_11qPH-b_17qPH-b_18)。其中,两个环境稳定主效QTL qPH-b_13qPH-b_19-1可解释10.56%~32.7%的表型变异。qPH-b_13qPH-b_19-1被精细定位到440.12 kb和237.06 kb的基因组区间,分别包含54和28个注释基因。进一步的拟南芥同源基因功能和候选基因表达分析表明,基因Glyma.13G292600Glyma.19G194100分别为qPH-b_13qPH-b_19-1的候选功能基因

Abstract  Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects.  Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height.  Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping.  This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines (RILs) and their bi-parents, Zhonghuang 13 (ZH) and Zhongpin 03-5373 (ZP).  The total genetic distance of this bin map was 3 139.15 cM, with an average interval of 0.78 cM between adjacent bin markers.  Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome.  Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci (qPH-b_11, qPH-b_17 and qPH-b_18).  Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56–32.7% of the phenotypic variance.  They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively.  Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.
Keywords:  soybean       plant height        whole genome re-sequencing        bin map        QTL  
Received: 06 July 2020   Accepted: 25 March 2021
Fund: This research was supported by the National Key R&D Program of China (2016YFD0100201) and the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences.   
About author:  TIAN Yu, E-mail:; Correspondence LI Ying-hui Tel: +86-10-82105843, Fax: +86-10-82105840, E-mail:; QIU Li-juan, E-mail:

Cite this article: 

TIAN Yu, YANG Lei, LU Hong-feng, ZHANG Bo, LI Yan-fei, LIU Chen, GE Tian-li, LIU Yu-lin, HAN Jia-nan, LI Ying-hui, QIU Li-juan. 2022. QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean. Journal of Integrative Agriculture, 21(4): 933-946.

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