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

Abstract

During rapeseed domestication and breeding, genetic diversity allowed to adapt it to different eco-geographical regions and to shape its useful traits. Structural variations (SVs), including presence/absence variations (PAVs), are thought to play a major role in the genetic diversity and phenotypic plasticity of rapeseed. In this study, we detected a 598-bp PAV within the promoter region of an Arabidopsis ortholog of a major flowering time gene and a downstream target of FLC, SOC1, which is one of the first genes that are upregulated in rapeseed during vernalization. Further analysis showed that the insertion is present predominantly in winter types while absent in spring types. The 589-bp sequence is present only in the A sub-genome indicating that it originated from Brassica rapa. Since the genomic region around Bna.SOC1.A05 showed a strong reduction in nucleotide diversity, the insertion might represent a larger selected sweep for rapeseed adaptation. Cis-element analysis showed that the insertion contains an ACGTG box, which is the strongest binding motif for the HY5 transcription factor in Arabidopsis. In addition, expression analyses showed that mRNA levels of Bna.SOC1.A05 were lower in accessions carrying the insertion compared to the ones that had no insertion.

A transcriptomic time-series reveals differing trajectories during pre-floral development in the apex and leaf in winter and spring varieties of Brassica napus

“…9 ). This supports other studies which have found SOC1 homologues in Brassica species to have different expression patterns, due to a partitioning of transcription factor binding sites between the different copies 48 , 86 , 87 . There are also between-variety differences between the copies, with the genes being consistently higher expressed in Westar relative to Tapidor (Fig.…”

“…In particular, the BnaFT.A2 gene is strongly associated with flowering time differences between two winter OSR varieties 44 . Within other flowering time integrators, a specific promoter variant of BnaSOC1.A5 is predominantly found in winter OSR varieties 48 . These findings point towards variation in known flowering time genes from Arabidopsis being responsible for flowering time diversity between OSR, particularly in terms of vernalisation requirement.…”

Development of Omni InDel and supporting database for maize

“…First, mining InDel loci of different lengths has traditionally relied on the examination of a single reference genome, which leads to genomic bias and the inevitable loss of some InDel loci. Furthermore, these mining strategies based on single reference genomes often use second-generation short reads for mapping, but many important InDels associated with agronomic traits are too large to be easily detected with Illumina short reads (Liu et al, 2020;Matar and Melzer, 2021). Therefore, the identification of medium (3-50 bp) and large (≥50 bp) InDels requires the use of a multigenome collinearity approach rather than a single-genome mining strategy.…”