Single-Molecule Real-Time and Illumina-Based RNA Sequencing Data Identified Vernalization-Responsive Candidate Genes in Faba Bean (Vicia faba L.).

Xiaoyan Zhang,Qiong Wang,Bin Yan,Jiong Zhang,Xin Chen,Wenbiao Shen,Chenchen Xue,Xingxing Yuan,Jingbin Chen,Yun Lin

doi:10.3389/fgene.2021.656137

Xiaoyan Zhang, Qiong Wang + Show 8 more

Open Access

https://doi.org/10.3389/fgene.2021.656137

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Abstract

Faba bean (Vicia faba L.) is one of the most widely grown cool season legume crops in the world. Winter faba bean normally has a vernalization requirement, which promotes an earlier flowering and pod setting than unvernalized plants. However, the molecular mechanisms of vernalization in faba bean are largely unknown. Discovering vernalization-related candidate genes is of great importance for faba bean breeding. In this study, the whole transcriptome of faba bean buds was profiled by using next-generation sequencing (NGS) and single-molecule, real-time (SMRT) full-length transcriptome sequencing technology. A total of 29,203 high-quality non-redundant transcripts, 21,098 complete coding sequences (CDS), 1,045 long non-coding RNAs (lncRNAs), and 12,939 simple sequence repeats (SSRs) were identified. Furthermore, 4,044 differentially expressed genes (DEGs) were identified through pairwise comparisons. By Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, these differentially expressed transcripts were found to be enriched in binding and transcription factor activity, electron carrier activity, rhythmic process, and receptor activity. Finally, 50 putative vernalization-related genes that played important roles in the vernalization of faba bean were identified; we also found that the levels of vernalization-responsive transcripts showed significantly higher expression levels in cold-treated buds. The expression of VfSOC1, one of the candidate genes, was sensitive to vernalization. Ectopic expression of VfSOC1 in Arabidopsis brought earlier flowering. In conclusion, the abundant vernalization-related transcripts identified in this study will provide a basis for future researches on the vernalization and faba bean breeding and established a reference full-length transcriptome for future studies on faba bean.

Highlights

Vicia faba (L.), commonly known as faba bean or broad bean, is an annual or biennial herb of the family Fabaceae
Of the total RNA, 5 μg was reverse transcribed into complementary DAN using a SMARTer PCR cDNA synthesis kit (TaKaRa, Shiga, Japan), messenger RNAs (mRNAs) was purified from total RNA using poly-T oligo-attached magnetic beads, and was reverse transcribed into first-strand cDNA using a random hexamer primer
A total of 233,493 highquality reads of insert (ROIs) were further generated from circular consensus sequencing (CCS) after filtering with full passes and accuracy

Summary

Introduction

Vicia faba (L.), commonly known as faba bean or broad bean, is an annual or biennial herb of the family Fabaceae. It is a cross-pollinating diploid plant species (2n = 12) (Fuchs et al, 1998) that has a “giant genome” with an estimated genome size of 13 Gb (Johnston et al, 1999). Winter faba bean comprised 85.5% of the total area and 78.2% of the total production of faba bean in China (Ye et al, 2003) It is the fourth most widely grown cool season legume after pea (P. sativum), chickpea (Cicer arietinum), and lentil (Lens culinaris) (Alharbi and Adhikari, 2020)

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