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.

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
Faba_bean_130KFaba_bean_130KN/A N/A
Features
This publication contains information about 130,280 features:
Feature NameUniquenameType
hua_TRINITY_DN118913_c2_g1:680-780hua_TRINITY_DN118913_c2_g1:680-780genetic_marker
hua_TRINITY_DN149995_c1_g2:13-113hua_TRINITY_DN149995_c1_g2:13-113genetic_marker
hua_TRINITY_DN149995_c1_g2:330-430hua_TRINITY_DN149995_c1_g2:330-430genetic_marker
ye_TRINITY_DN141852_c2_g2:40-140ye_TRINITY_DN141852_c2_g2:40-140genetic_marker
ye_TRINITY_DN141852_c2_g2:254-354ye_TRINITY_DN141852_c2_g2:254-354genetic_marker
dou_TRINITY_DN52263_c2_g3:41-141dou_TRINITY_DN52263_c2_g3:41-141genetic_marker
dou_TRINITY_DN56182_c1_g1:255-355dou_TRINITY_DN56182_c1_g1:255-355genetic_marker
dou_TRINITY_DN56182_c1_g1:526-626dou_TRINITY_DN56182_c1_g1:526-626genetic_marker
dou_TRINITY_DN56182_c1_g1:965-1065dou_TRINITY_DN56182_c1_g1:965-1065genetic_marker
dou_TRINITY_DN56182_c1_g1:1359-1459dou_TRINITY_DN56182_c1_g1:1359-1459genetic_marker
dou_TRINITY_DN60365_c1_g1:1413-1513dou_TRINITY_DN60365_c1_g1:1413-1513genetic_marker
hua_TRINITY_DN144628_c0_g1:565-665hua_TRINITY_DN144628_c0_g1:565-665genetic_marker
ye_TRINITY_DN128681_c2_g4:272-372ye_TRINITY_DN128681_c2_g4:272-372genetic_marker
ye_TRINITY_DN128681_c2_g4:326-426ye_TRINITY_DN128681_c2_g4:326-426genetic_marker
ye_TRINITY_DN121885_c0_g3:370-470ye_TRINITY_DN121885_c0_g3:370-470genetic_marker
ye_TRINITY_DN121885_c0_g3:376-476ye_TRINITY_DN121885_c0_g3:376-476genetic_marker
ye_TRINITY_DN128426_c0_g1:82-182ye_TRINITY_DN128426_c0_g1:82-182genetic_marker
ye_TRINITY_DN128426_c0_g1:391-491ye_TRINITY_DN128426_c0_g1:391-491genetic_marker
ye_TRINITY_DN128426_c0_g1:409-509ye_TRINITY_DN128426_c0_g1:409-509genetic_marker
dou_TRINITY_DN46048_c0_g1:150-250dou_TRINITY_DN46048_c0_g1:150-250genetic_marker
dou_TRINITY_DN46048_c0_g1:455-555dou_TRINITY_DN46048_c0_g1:455-555genetic_marker
dou_TRINITY_DN56472_c2_g3:241-341dou_TRINITY_DN56472_c2_g3:241-341genetic_marker
dou_TRINITY_DN56472_c2_g3:821-921dou_TRINITY_DN56472_c2_g3:821-921genetic_marker
ye_TRINITY_DN119860_c0_g1:0-100ye_TRINITY_DN119860_c0_g1:0-100genetic_marker
ye_TRINITY_DN119860_c0_g1:1626-1726ye_TRINITY_DN119860_c0_g1:1626-1726genetic_marker

Pages

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
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:34117907