Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus

First author: Jia-Ming Song; Affiliations: Huazhong Agricultural University (华中农业大学): Wuhan, China

Corresponding author: Liang Guo

Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2–149.6  megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.

油菜是全球第二大的产油类作物，但其广泛表型变异潜在的遗传多样性还存在很多未知的地方。本文中，作者报道了8个油菜材料的全基因组测序和组装。利用泛基因组比较分析，作者鉴定到了数百万个小的变异以及77.2–149.6Mb的PAV变异。超过9.4%的基因存在大效应突变或者结构变异。作者利用以ZS11作为供体的嵌套联合作图，基于PAV的全基因组关联分析GWAS直接鉴定到了荚果长度、种子重量和开花时间相关的结构变异，这些是之前基于单核苷酸变异SNP进行的GWAS所没能鉴定出来的，充分说明了PAV-GWAS可以互补于SNP-GWAS用来鉴定特定性状相关的位点。进一步的分析显示三个FLC基因的PAV变异与开花时间及生态型分化密切相关。本文的研究为油菜的基因组结构解析和理解提供了新的遗产资源，同时也有利于未来油菜的遗传改良。

通讯：郭亮（http://cpst.hzau.edu.cn/info/1015/1656.htm）

个人简介：2001-2006年，四川大学，学士、硕士；2011年，美国密苏里大学，博士；2012-2014年，美国Donald Danforth Plant Science Center，博士后。

研究方向：油菜油脂合成和油菜抗逆性的遗传基础和分子机制。

doi: https://doi.org/10.1038/s41477-019-0577-7

Journal: Nature Plants

Published date: January 13, 2020