Whole-genome resequencing of a world-wide collection of rapeseed accessions reveals genetic basis of their ecotype divergence

First author: Dezhi Wu; Affiliations: Zhejiang University (浙江大学): Hangzhou, China

Corresponding author: Lixi Jiang

Rapeseed ( Brassica napus L.), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winter, semi-winter and spring types. Genomic variations underlying these ecotypes are largely unknown. Here, we report the global pattern of genetic polymorphisms of rapeseed by resequencing a world-wide collection of 991 germplasm accessions. A total of 5.56 or 5.53 million single nucleotide polymorphisms (SNPs) and 1.86 or 1.92 million InDels were identified by mapping reads to the reference genomes of ‘Darmor -bzh’ or ‘Tapidor’, respectively. We generated allelic drifting paths that show splits and mixtures of the main populations. The genetic diversity and linkage disequilibrium parameters indicate an asymmetric evolution of the two subgenomes of B. napus. The selective-sweep analysis (选择性清除：由于某一位点受到强选择后,其周围的位点的多态性因受改位点牵连而发生多态性降低的现象。) revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses. Further genome-wide association study identified SNPs in promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs, which specifically corresponded to different rapeseed ecotypes. Our study provides important insights into genomic footprints of the evolution of rapeseed and the flowering time divergence among three ecotypes, and will facilitate screening of molecular markers for accelerating rapeseed breeding.

油菜是重要的油料种子作物，适应了不同的气候带和纬度的三种主要生态型，即冬性、半冬性和春性型。这三种生态型的基因组变异还不清楚。本文，作者通过对全球收集的991份油菜种质资源的重测序鉴定了这个群体的遗传多样性。作者将测序数据比对到‘Darmor -bzh’和‘Tapidor’参考基因组上分别鉴定到了5.56个和5.53百万个SNP以及1.86和1.92百万个InDel。作者分析了等位基因漂移来显示主要群体间的分开与混合。遗传多样性和连锁不平衡显示油菜两个亚基因组的不对称演化。选择性清除分析显示调控植物发育和胁迫响应相关基因上的遗传改变。进一步基因组范围的关联分析鉴定了不同的生态型在FLT和FLC基因启动子区具有特异性SNP。本文的研究揭示了油菜的演化以及不同生态型开花时间分化在基因组上的足迹，将有助于油菜加速育种过程中的分子标记选择。

通讯：蒋立希 (https://person.zju.edu.cn/JiangLixi)

个人简介：1982-1986年，浙江农业大学，遗传育种专业，学士；1996-1998年，德国哥廷根大学，作物生产，硕士；1998-2001年，德国哥廷根大学，植物遗传，博士。

研究方向：种子脂肪酸形成的分子生物学机制；油菜种质资源基因组研究；基于基因组重测序基础上杂种优势预测。

doi: https://doi.org/10.1016/j.molp.2018.11.007

Journal: Molecular Plant

Accepted date: 18 November, 2018