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

Jun Zou,Ruiyuan Li,Enhui Shen,Graham J King,Ian Bancroft,Kai Wang,Lei Shi,Yongji Huang,Jinling Meng,Dandan Hu,Dongya Wu,Yifei Shen,Meng Wang,Meihong Chen,Jie Qiu,Zhesi He,Qian Zhu ,Limin Mao ,Jia Lu ,Chu-Yu Ye

doi:10.1111/pbi.13115

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.

Highlights

Brassica napus L. (AnAnCnCn, 2n = 38) is the third largest source of vegetable oil globally and plays an important role in increasing the productivity of wheat–rapeseed intercropping systems (Ebrahimi et al, 2017)
B. napus is a young allopolyploid species derived from an interspecific cross between the two diploid progenitors, B. rapa (ArAr, 2n = 20) and B. oleracea (CoCo, 2n = 18)
In the 1970s, Asian rapeseed was further significantly improved by introgression of the double-low traits, which had first been discovered in Canada and introduced into European rapeseed

Summary

Introduction

A genome-based estimation has suggested a short history of post-Neolithic speciation (~7500 years) and domestication (~700 years) of the species (Chalhoub et al, 2014). According to their geographic origin and seasonal crop type, B. napus oilseed cultivars were classified into several distinct genetic groups, including European winter, Asian semi-winter, Canadian, Australian and European spring. Many distinct cultivars (e.g. Ningyou 7) were bred based on SL by introgression of traits from B. rapa, which has been frequently adopted to broaden the genetic diversity and improve the local adaptation of semi-winter B. napus in Asia (Zhang et al, 2014). In the 1970s, Asian rapeseed was further significantly improved by introgression of the double-low traits (low seed glucosinolate and low erucic acid), which had first been discovered in Canada and introduced into European rapeseed

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Conclusion