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
dou_TRINITY_DN57427_c0_g2:1905-2005dou_TRINITY_DN57427_c0_g2:1905-2005genetic_marker
hua_TRINITY_DN130603_c0_g4:304-404hua_TRINITY_DN130603_c0_g4:304-404genetic_marker
hua_TRINITY_DN130603_c0_g4:632-732hua_TRINITY_DN130603_c0_g4:632-732genetic_marker
dou_TRINITY_DN57145_c0_g2:406-506dou_TRINITY_DN57145_c0_g2:406-506genetic_marker
dou_TRINITY_DN58097_c0_g1:0-100dou_TRINITY_DN58097_c0_g1:0-100genetic_marker
ye_TRINITY_DN154205_c1_g1:243-343ye_TRINITY_DN154205_c1_g1:243-343genetic_marker
dou_TRINITY_DN10928_c0_g1:436-536dou_TRINITY_DN10928_c0_g1:436-536genetic_marker
hua_TRINITY_DN155615_c7_g6:57-157hua_TRINITY_DN155615_c7_g6:57-157genetic_marker
hua_TRINITY_DN155615_c7_g6:347-447hua_TRINITY_DN155615_c7_g6:347-447genetic_marker
ye_TRINITY_DN103236_c0_g2:67-167ye_TRINITY_DN103236_c0_g2:67-167genetic_marker
ye_TRINITY_DN103236_c0_g2:336-436ye_TRINITY_DN103236_c0_g2:336-436genetic_marker
hua_TRINITY_DN138663_c8_g5:179-279hua_TRINITY_DN138663_c8_g5:179-279genetic_marker
hua_TRINITY_DN138663_c8_g5:334-434hua_TRINITY_DN138663_c8_g5:334-434genetic_marker
hua_TRINITY_DN141876_c1_g4:431-531hua_TRINITY_DN141876_c1_g4:431-531genetic_marker
hua_TRINITY_DN147929_c1_g2:493-593hua_TRINITY_DN147929_c1_g2:493-593genetic_marker
ye_TRINITY_DN102823_c0_g3:131-231ye_TRINITY_DN102823_c0_g3:131-231genetic_marker
dou_TRINITY_DN52409_c3_g1:80-180dou_TRINITY_DN52409_c3_g1:80-180genetic_marker
dou_TRINITY_DN60493_c1_g2:701-801dou_TRINITY_DN60493_c1_g2:701-801genetic_marker
hua_TRINITY_DN134630_c2_g2:21-121hua_TRINITY_DN134630_c2_g2:21-121genetic_marker
hua_TRINITY_DN134630_c2_g2:171-271hua_TRINITY_DN134630_c2_g2:171-271genetic_marker
ye_TRINITY_DN132677_c3_g3:59-159ye_TRINITY_DN132677_c3_g3:59-159genetic_marker
ye_TRINITY_DN148425_c0_g1:175-275ye_TRINITY_DN148425_c0_g1:175-275genetic_marker
ye_TRINITY_DN148425_c0_g1:931-1031ye_TRINITY_DN148425_c0_g1:931-1031genetic_marker
ye_TRINITY_DN152633_c0_g1:56-156ye_TRINITY_DN152633_c0_g1:56-156genetic_marker
ye_TRINITY_DN152633_c0_g1:149-249ye_TRINITY_DN152633_c0_g1:149-249genetic_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