The transition to flowering in winter rapeseed during vernalization

Abstract

Flowering time is a major determinant of adaptation, fitness and yield in the allopolyploid species rapeseed (Brassica napus). Despite being a close relative to Arabidopsis thaliana, little is known about the timing of floral transition and the genes that govern this process. Winter, semi‐winter and spring type plants have important life history characteristics that differ in vernalization requirements for flowering and are important for growing rapeseed in different regions of the world. In this study, we investigated the timing of vernalization‐driven floral transition in winter rapeseed and the effect of photoperiod and developmental age on flowering time and vernalization responsiveness. Microscopy and whole transcriptome analyses at the shoot apical meristems of plants grown under controlled conditions showed that floral transition is initiated within few weeks of vernalization. Certain Bna.SOC1 and Bna.SPL5 homeologs were among the induced genes, suggesting that they are regulating the timing of cold‐induced floral transition. Moreover, the flowering response of plants with shorter pre‐vernalization period correlated with a delayed expression of Bna.SOC1 and Bna.SPL5 genes. In essence, this study presents a detailed analysis of vernalization‐driven floral transition and the aspects of juvenility and dormancy and their effect on flowering time in rapeseed.

A 598-bp InDel Variation in the Promoter Region of Bna.SOC1.A05 Is Predominantly Present in Winter Type Rapeseeds

“…A 598-bp PAV Upstream of Bna.SOC1.A05 Co-segregates With Crop Type in Rapeseed Previously, we identified certain flowering time genes that were upregulated in the shoot apical meristem in winter rapeseed upon the downregulation of Bna.FLC during vernalization. These genes included orthologs of the flowering time integrator and downstream target of FLC, SOC1, in addition to certain members of the SPL gene family (Matar et al, 2021). To study SVs between spring and winter rapeseed cultivars, within or upstream of the identified genes, we used the whole genome sequencing reads of 40 winter and 40 spring accessions, with an average sequencing depth ranging from 5 to 23.…”

“…To study SVs between spring and winter rapeseed cultivars, within or upstream of the identified genes, we used the whole genome sequencing reads of 40 winter and 40 spring accessions, with an average sequencing depth ranging from 5 to 23. The reads were aligned to our Darmor-bzh reference-based genome assembly of the winter rapeseed cultivar Express617 (Matar et al, 2021), using Bwa-mem (v.0.7.17). We first carried out a visual detection of read alignments using IGV with a mapping quality threshold of 5.…”

“…Interestingly, in winter types, Bna.SOC1.A05 was the only gene that was not detected before vernalization (Figure 5). In a transcriptome analysis of the winter accession during the course of vernalization, Bna.SOC1.A05 was the first gene to be induced during floral transition (Matar et al, 2021). This tight vernalization-controlled expression of Bna.SOC1.A05 further reinforces a pivotal role of this gene for the vernalizationdriven floral transition in winter rapeseed.…”

“…For RNA-Seq analyses, the raw RNA-Seq reads of 72 rapeseed accessions including 31 winter and 41 spring types from a previous transcriptomics study (Harper et al, 2012;Havlickova et al, 2018) were downloaded from SRA NCBI 1 using parallelfastq-dump. The reads were mapped to the Express617 genome (Matar et al, 2021) using STAR (Dobin et al, 2013;v.2.5.4). For transcriptome assembly, the RNA-Seq read alignments were used as an input file to run Cufflinks (v2.2.1;Trapnell et al, 2012).…”

“…Expression levels of six Bna.SOC1 genes were plotted in RStudio (Boston, Massachusetts), using the data visualization package ggplot2 (Wickham, 2011 Wu et al, 2019) using parallel-fastq-dump. Reads of each accession were mapped to the Darmor-bzh-based genome assembly of winter rapeseed Express617 (Matar et al, 2021) using Burrows-Wheeler Aligner mem (BWA-MEM v.0.7.17) software package (Li and Durbin, 2009). Visual detection of read alignments was performed using the Integrative Genome Viewer (IGV).…”