Development and application of Faba_bean_130K Targeted Next-Generation Sequencing SNP genotyping platform based on transcriptome sequencing

Faba bean (Vicia faba L., 2n = 12) is an important food legume crop and
widely grown for multiple uses in the world. However, no reference genome
is currently available due to its giant genome (approximately 13 Gb) and
limited single nucleotide polymorphism (SNP) markers as well as high
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. 243,120 unigenes
were de novo assembled and functionally annotated. Moreover, a total of
1,579,411 SNPs were identified and were further filtered according to a
selection pipeline to develop a high-throughput, flexible and low-cost
Faba_bean_130K Targeted Next-Generation Sequencing (TNGS) genotyping
platform. A set of 69 Chinese faba bean accessions was genotyped with the
TNGS genotyping platform, and the average mapped 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 was up to 93.6%. Comprehensive
population genetic analyze was performed to the 69 Chinese faba bean
germplasm and identified four genetic subgroups correlated with geographic
distribution. This study provides valuable genomic resources and a
reliable genotyping tool, which could be implemented in genetic and
molecular breeding studies to accelerate the faba bean new cultivar
development and improvement.