Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.

Publication Overview
TitleDevelopment and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.
AuthorsWang C, Liu R, Liu Y, Hou W, Wang X, Miao Y, He Y, Ma Y, Li G, Wang D, Ji Y, Zhang H, Li M, Yan X, Zong X, Yang T
TypeJournal Article
Journal NameTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Year2021
CitationWang C, Liu R, Liu Y, Hou W, Wang X, Miao Y, He Y, Ma Y, Li G, Wang D, Ji Y, Zhang H, Li M, Yan X, Zong X, Yang T. Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2021 Jun 12.

Abstract

KEY MESSAGE
Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.

Features
This publication contains information about 130,280 features:
Feature NameUniquenameType
hua_TRINITY_DN125662_c0_g2:467-567hua_TRINITY_DN125662_c0_g2:467-567genetic_marker
hua_TRINITY_DN135955_c1_g2:239-339hua_TRINITY_DN135955_c1_g2:239-339genetic_marker
ye_TRINITY_DN108403_c0_g1:63-163ye_TRINITY_DN108403_c0_g1:63-163genetic_marker
ye_TRINITY_DN119918_c0_g1:256-356ye_TRINITY_DN119918_c0_g1:256-356genetic_marker
ye_TRINITY_DN119918_c0_g1:474-574ye_TRINITY_DN119918_c0_g1:474-574genetic_marker
ye_TRINITY_DN119918_c0_g1:1338-1438ye_TRINITY_DN119918_c0_g1:1338-1438genetic_marker
ye_TRINITY_DN120591_c0_g1:49-149ye_TRINITY_DN120591_c0_g1:49-149genetic_marker
ye_TRINITY_DN132320_c1_g5:58-158ye_TRINITY_DN132320_c1_g5:58-158genetic_marker
dou_TRINITY_DN11815_c0_g1:39-139dou_TRINITY_DN11815_c0_g1:39-139genetic_marker
dou_TRINITY_DN20087_c0_g1:349-449dou_TRINITY_DN20087_c0_g1:349-449genetic_marker
hua_TRINITY_DN129906_c0_g1:920-1020hua_TRINITY_DN129906_c0_g1:920-1020genetic_marker
ye_TRINITY_DN146657_c1_g2:86-186ye_TRINITY_DN146657_c1_g2:86-186genetic_marker
hua_TRINITY_DN106354_c0_g1:535-635hua_TRINITY_DN106354_c0_g1:535-635genetic_marker
hua_TRINITY_DN124134_c3_g1:126-226hua_TRINITY_DN124134_c3_g1:126-226genetic_marker
hua_TRINITY_DN124134_c3_g1:566-666hua_TRINITY_DN124134_c3_g1:566-666genetic_marker
hua_TRINITY_DN124134_c3_g1:793-893hua_TRINITY_DN124134_c3_g1:793-893genetic_marker
hua_TRINITY_DN125938_c3_g1:11-111hua_TRINITY_DN125938_c3_g1:11-111genetic_marker
ye_TRINITY_DN145974_c0_g1:236-336ye_TRINITY_DN145974_c0_g1:236-336genetic_marker
ye_TRINITY_DN145974_c0_g1:355-455ye_TRINITY_DN145974_c0_g1:355-455genetic_marker
ye_TRINITY_DN145974_c0_g1:526-626ye_TRINITY_DN145974_c0_g1:526-626genetic_marker
ye_TRINITY_DN154916_c0_g2:255-355ye_TRINITY_DN154916_c0_g2:255-355genetic_marker
ye_TRINITY_DN154916_c0_g2:565-665ye_TRINITY_DN154916_c0_g2:565-665genetic_marker
ye_TRINITY_DN154916_c0_g2:726-826ye_TRINITY_DN154916_c0_g2:726-826genetic_marker
dou_TRINITY_DN51383_c1_g1:7-107dou_TRINITY_DN51383_c1_g1:7-107genetic_marker
dou_TRINITY_DN57412_c0_g3:9-109dou_TRINITY_DN57412_c0_g3:9-109genetic_marker

Pages

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
Faba_bean_130KFaba_bean_130KN/A N/A
Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1432-2242
eISSN1432-2242
Publication Date2021 Jun 12
Journal AbbreviationTheor Appl Genet
DOI10.1007/s00122-021-03885-0
Elocation10.1007/s00122-021-03885-0
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryGermany