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.
Highlights
Rapeseed (Brassica napus) is an allotetraploid crop formed by spontaneous interspecific hybridization of two diploid species; Brassica rapa and Brassica oleracea around 7,500 years ago (Chalhoub et al, 2014)
A 598-bp presence/absence variations (PAVs) Upstream of Bna.SOC1.A05 Co-segregates With Crop Type in Rapeseed
The sequence-depth analysis further confirmed the segregation of the Structural variations (SVs) between winter and spring types, where more than 87% of the spring accessions showed absence of the genomic sequence at the analyzed region, while 85% of the winter accessions showed the presence of the insertion (Figure 1C; Supplementary Table S2)
Summary
Rapeseed (Brassica napus) is an allotetraploid crop formed by spontaneous interspecific hybridization of two diploid species; Brassica rapa and Brassica oleracea around 7,500 years ago (Chalhoub et al, 2014). B. napus can be divided into three different growth types; winter, semi-winter, and spring rapeseed (Zou et al, 2019). Winter types are grown mainly in Europe; they have an obligate vernalization requirement, and are suggested to be the original type of rapeseed (Lu et al, 2019). Spring types are grown in Australia and North America and flower without any vernalization requirement. Semi-winter types were formed gradually after the introduction of winter types into China in the 20th century, where they were adapted to flower after a short period of vernalization (Qian et al, 2006).
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