Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus).

Tianhua Hu,Wuhong Wang,Haijiao Hu,Qingzhen Wei,Chonglai Bao,Weihai Mao,Qinmei Zhu,Yong Pyo Lim

doi:10.1371/journal.pone.0204137

Abstract

Floral induction that initiates bolting and flowering is crucial for reproductive fitness in radishes. CONSTANS-like (CO-like, COL) genes play an important role in the circadian clock, which ensures regular development through complicated time-keeping mechanisms. However, the specific biological and functional roles of each COL transcription factor gene in the radish remain unknown. In this study, we performed a genome-wide identification of COL genes in the radish genome of three cultivars including ‘Aokubi’, ‘kazusa’ and ‘WK10039’, and we analyzed their exon-intron structure, gene phylogeny and synteny, and expression levels in different tissues. The bioinformatics analysis identified 20 COL transcription factors in the radish genome, which were divided into three subgroups (Group I to Group III). RsaCOL-09 and RsaCOL-12 might be tandem duplicated genes, whereas the others may have resulted from segmental duplication. The Ka/Ks ratio indicated that all the COL genes in radish, Arabidopsis, Brassica rapa, Brassica oleracea, Capsella rubella and rice were under purifying selection. We identified 6 orthologous and 19 co-orthologous COL gene pairs between the radish and Arabidopsis, and we constructed an interaction network among these gene pairs. The expression values for each COL gene during vegetable and flower development showed that the majority of Group I members had similar expression patterns. In general, the expression of radish COL genes in Groups I and III decreased during development, whereas the expression of radish COL genes in Group II first increased and then decreased. Substantial numbers of radish COL genes were differentially expressed after vernalization treatment. The expression levels of RsaCOL-02 and RsaCOL-04 were significantly increased during vernalization treatment, while the expression of RsaCOL-10 was significantly decreased. These outcomes provide insights for improving the genetic control of bolting and flowering in radish and other root vegetable crops, and they facilitate genetic improvements to radish yields and quality.

Highlights

The transition from vegetative development to bolting and flowering is critical for reproductive success in the plant life cycle
In Arabidopsis thaliana, approximately 180 genes participate in flowering-time control, and they are involved in six interactive regulatory pathways including the vernalization pathway, autonomous pathway, photoperiod pathway, gibberellin (GA) pathway, ambient temperature pathway, and age pathway [1,3,4]
The identification of RsaCOL genes in the present study provides additional knowledge about the gene family in radish and a foundation for further investigating the flowering regulatory networks in radish and other Brassicaceae vegetables

Summary

Introduction

The transition from vegetative development to bolting and flowering is critical for reproductive success in the plant life cycle. We identified the COL genes in the radish genome and classified them into three groups based on the analysis of their exon-intron structure, gene phylogeny and synteny, as well as their expression in specific tissues. OrthoMCL software (v2.0.3) [40] was employed in searching for orthologous, co-orthologous and paralogous genes in radish, Arabidopsis, Brassica rapa, Brassica oleracea, Capsella rubella and rice using entire COL protein sequences.

Results

Conclusion