基于TNGS的蚕豆SNP遗传图谱构建及重要农艺性状基因定位

doi:10.1016/j.jia.2023.01.003

Journal of Integrative Agriculture ›› 2023, Vol. 22 ›› Issue (9): 2648-2659.DOI: 10.1016/j.jia.2023.01.003

基于TNGS的蚕豆SNP遗传图谱构建及重要农艺性状基因定位

收稿日期:2022-08-17 接受日期:2022-10-28 出版日期:2023-09-20 发布日期:2023-09-14

Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.)

LI Meng-wei^1*, HE Yu-hua^2*, LIU Rong¹, LI Guan¹, WANG Dong¹, JI Yi-shan¹, YAN Xin¹, HUANG Shu-xian¹, WANG Chen-yu¹, MA Yu³, LIU Bei⁴, YANG Tao^1#, ZONG Xu-xiao^1#

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

Received:2022-08-17 Accepted:2022-10-28 Online:2023-09-20 Published:2023-09-14
About author:#Correspondence YANG Tao, E-mail: yangtao02@caas.cn; ZONG Xu-xiao, Tel/Fax: +86-10-62186651, E-mail: zongxuxiao@caas.cn * These authors contributed equally to this study.
Supported by:
This study was supported by the National Key R&D Program of China (2019YFD1001300 and 2019YFD1001303), the Construction of Molecular Database of Faba Bean and Pea and Identification of Maize Germplasm Project, Ministry of Agriculture and Rural Affairs, China (19200030), the Yunnan Key R&D Program, China (202202AE090003), the earmarked fund for China Agriculture Research System (CARS-08), the Crop Germplasm Resources Protection (2130135) and the Major Agricultural Science and Technology Program of Chinese Academy of Agricultural Sciences (CAAS-XTCX20190025).

摘要/Abstract

摘要：

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8137、H0003712和H000572）作为亲本，构建了两个F₂群体，其中群体1（云豆8137×H0003712）包含167个单株，群体2（H000572×云豆8137）包含204个单株；利用Targeted next-generation sequencing（TNGS）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5103个SNP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1904个SNP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98个QTLs。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6895个SNP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，还有助于推动蚕豆分子标记辅助育种的发展。

Abstract: Owing to the limitation of a large genome size (~13 Gb), the genetic and gene mapping studies on faba bean (Vicia faba L.) are lagging far behind 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. These 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 5 103 SNPs with a length of 1 333.31 cM and an average marker density of 0.26 cM. The map constructed from Pop2 contained 1 904 SNPs with a greater length of 1 610.61 cM. In these two F₂ populations, QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers, pods, plant types and grains. The two maps were then merged into an integrated genetic linkage map containing 6 895 SNPs, with a length of 3 324.48 cM. These results not only lay the foundation for fine mapping and map-based cloning of related genes, but can also accelerate the molecular marker-assisted breeding of faba bean.

Key words: faba bean , targeted next-generation sequencing , single nucleotide polymorphisms , genetic linkage map , QTL mapping

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. 基于TNGS的蚕豆SNP遗传图谱构建及重要农艺性状基因定位[J]. Journal of Integrative Agriculture, 2023, 22(9): 2648-2659.

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. Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.)[J]. Journal of Integrative Agriculture, 2023, 22(9): 2648-2659.

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基于TNGS的蚕豆SNP遗传图谱构建及重要农艺性状基因定位

Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.)

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