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Journal of Integrative Agriculture
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Construction of SNP genetic map based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.)
LI Meng-wei1*, HE Yu-hua2*, LIU Rong1, LI Guan1, WANG Dong1, JI Yi-shan1, YAN Xin1, HUANG Shu-xian 1, WANG Chen-yu1, MA Yu3, LIU Bei4, YANG Tao1, ZONG Xu-xiao1

1 National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China

2 Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, P.R.China

3 Department of Horticulture, Washington State University, Pullman, WA 99164, USA

4 China Golden Marker (Beijing) Biotech Co., Ltd., Beijing 102200, P.R.China

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蚕豆(Vicia faba L.)基因组较大(约13 Gb),尚无参考基因组,与其他豆类相比,蚕豆遗传研究落后很多鉴于此,本研究选择三个蚕豆纯系(云豆8137H0003712H000572)作为亲本构建了两个F2群体,其中群体1云豆8137×H0003712)包含167个单群体2H000572×云豆8137)包含204个单株利用Targeted next-generation sequencingTNGS基因分型平台对两个F2群体进行基因分型,构建了两个高密度的蚕豆SNP遗传连锁图谱基于群体1构建的图谱包含5103SNP标记,长度1333.31 cM,平均标记密度0.26 cM基于群体2构建的图谱包含1904SNP标记覆盖长度1610.61 cM利用上述两个遗传连锁图谱及两个F2群体,挖掘了与蚕豆花、荚、株型和籽粒相关的14个农艺性状的98QTLs此外,本研究对上述两个遗传连锁图谱进行整合,构建了一张包含6895SNP标记,覆盖长度3324.48 cM的整合图谱。本研究不仅为蚕豆相关基因的图位克隆奠定了基础,有助于推动蚕豆分子标记辅助育种的发展


The reference genome for faba bean (Vicia faba L.) is lacking because of its large genome size (~13 Gb), and the genetic and gene mapping studies on faba bean are far behind compared with those for other legumes.  In this study, we selected three purified faba bean lines (Yundou 8137, H0003712, and H000572) as parents and constructed two F2 populations.  And two F2 populations, namely 167 F2 plants in Pop1 (Yundou 8137×H0003712) and 204 F2 plants in Pop2 (H000572×Yundou 8137), were genotyped using a targeted next-generation sequencing (TNGS) genotyping platform, and two high-density single nucleotide polymorphisms (SNP) genetic linkage maps of faba bean were constructed.  The map constructed from Pop1 contained 5103 SNPs with a length of 1333.31 cM and an average marker density of 0.26 cM.  The map constructed from Pop2 contained 1904 SNPs with a greater length of 1610.61 cM. In these two F2 populations, Quantitative trait locus (QTL) mapping identified 98 QTLs for 14 agronomic traits related to flowers, pods, plant types and grains.  Then, the two maps were merged into an integrated genetic linkage map containing 6895 SNPs, with a length of 3324.48 cM.  These results not only lay the foundation for fine mapping and map-based cloning of related genes, but also can accelerate molecular marker-assisted breeding of faba bean.

Keywords:  faba bean       targeted next-generation sequencing        single nucleotide polymorphisms        genetic linkage map        QTL mapping  
Online: 10 January 2023  

This study was supported by National Key R&D Program of China (2019YFD1001300, 2019YFD1001303), the Construction of Molecular Database of Faba Bean and Pea and Identification of Maize Germplasm Project (No.19200030), Yunnan Key R&D Program (202202AE090003) from Yunnan Province Science and Technology Department, China Agriculture Research System of MOF and MARA-Food Legumes (CARS-08), the Crop Germplasm Resources Protection (2130135) and the Major Agricultural Science and Technology Program of CAAS “Evaluation and Regulation of Nutritional Quality of Major Agricultural Products” (CAAS-XTCX20190025).

About author:  Correspondence YANG Tao, E-mail:; ZONG Xu-xiao, Tel: +86-10-62186651, Fax: +86-10-62186651, E-mail: * These authors contributed equally to this work.

Cite this article: 

LI Meng-wei, HE Yu-hua, LIU Rong, LI Guan, WANG Dong, JI Yi-shan, YAN Xin, HUANG Shu-xian, WANG Chen-yu, MA Yu, LIU Bei, YANG Tao, ZONG Xu-xiao. 2023. Construction of SNP genetic map based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.). Journal of Integrative Agriculture, Doi:10.1016/j.jia.2023.01.003

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