RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China

Wanwei Hou; Xiaojuan Zhang; Yuling Liu; Yujiao Liu; Bai Li Feng

doi:10.7717/peerj.14259

RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China

PeerJ. 2023 Jan 10:11:e14259. doi: 10.7717/peerj.14259. eCollection 2023.

Authors

Wanwei Hou^#^{1

2}, Xiaojuan Zhang^#³, Yuling Liu², Yujiao Liu², Bai Li Feng¹

Affiliations

¹ College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
² Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China.
³ College of Eco-Environmental Engineering, Qinghai Universit, Xining, Qinghai, China.

^# Contributed equally.

Abstract

Background: Faba bean (Vicia faba L) is one of the most important legumes in the world. However, there is relatively little genomic information available for this species owing to its large genome. The lack of data impedes the discovery of molecular markers and subsequent genetic research in faba bean. The objective of this study was to analyze the faba bean transcriptome, and to develop simple sequence repeat (SSR) markers to determine the genetic diversity of 226 faba bean varieties derived from different regions in China.

Methods: Faba bean varieties with different phenotype were used in transcriptome analysis. The functions of the unigenes were analyzed using various database. SSR markers were developed and the polymorphic markers were selected to conduct genetic diversity analysis.

Results: A total of 92.43 Gb of sequencing data was obtained in this study, and 133,487 unigene sequences with a total length of 178,152,541 bp were assembled. A total of 5,200 SSR markers were developed on the basis of RNA-Seq analysis. Then, 200 SSR markers were used to evaluate polymorphisms. In total, 103 (51.5%) SSR markers showed significant and repeatable bands between different faba bean varieties. Clustering analysis revealed that 226 faba bean materials were divided into five groups. Genetic diversity analysis revealed that the relationship between different faba beans in China was related, especially in the same region. These results provided a valuable data resource for annotating genes to different categories and developing SSR markers.

Keywords: Gene function analysis; RNA-Seq; Simple sequence repeats (SSR) markers; Vicia faba L.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling
Polymorphism, Genetic / genetics
RNA-Seq
Transcriptome / genetics
Vicia faba* / genetics

Grants and funding

This research was funded by Qinghai Applied Fundamental Research Program, grant number 2021-ZJ-744 and the China Agriculture Research System, grant number CARS-08. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.