Development of InDel markers and identify candidate flowering time genes in radish (Raphanus sativus L.)

Abstract

Abstract Background The transition from the vegetative to reproductive growth is an important stage in radish life cycle (Raphanus sativus L.). However, the molecular mechanism of radish bolting and flowering is still unclear. To obtain new insight into the genomic variation, population structure, genetic diversity and molecular regulation mechanism of flowering time, genome resequencing and transcriptome sequencing were conducted between two cultivars with extreme differences in flowering time. Results In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome sequences between ‘YZH’ and ‘XHT’. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 10,983 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. RT-qPCR displayed that the expression pattern of ten DEGs were consistent with the results obtained by RNA-Seq analysis. Conclusions The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The detected flowering time-related DGEs could provide fundamental insight into bolting and flowering regulatory networks and accelerate further investigating molecular mechanisms underlying the transition from vegetative to reproductive growth in radish.