Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

Abstract

Summary Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large‐scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double‐low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double‐low and double‐high), accompanied by an increase in genetic load in the double‐low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra‐ and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.

A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency

“…For example, the Chinese elite variety and reference genome Zs11 was obtained through this strategy [70]. The frequent use of B. rapa in Asian B. napus breeding programs may partially explain why Asian oilseed rape varieties appear as a specific group of oilseed rape varieties and why it is still possible to detect B. rapa introgression in this material [71]. Similarly, direct crosses between B. napus and B. rapa have been performed to introduce in B. napus major resistance genes to clubroot [72] or blackleg [73].…”

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

“…Its dynamic allopolyploid genome plays a prime role in its diversification and adaptation to different natural environments. According to vernalization requirement, 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).…”

Fine Mapping of a Locus Underlying the Ectopic Blade-Like Outgrowths on Leaf and Screening Its Candidate Genes in Rapeseed (Brassica napus L.)

“…When aligning these SNPs and InDels to reference genome, we chose the semi-winter rapeseed “ZS11” genome. In fact, there have been several rapeseed materials de novo sequenced, which provides and releases different reference genomes ( Chalhoub et al, 2014 ; Bayer et al, 2017 ; Sun et al, 2017 ; Zou et al, 2019 ; Song et al, 2020 ) so far. These genomes differ from each other in sequence and even size, and that is because (1) the materials are different.…”