Genome assembly and genomic architecture of a prominent cold-resistant rapeseed germplasm

Abstract

Cold stress is one of the most limiting factors affecting crop production. Winter rapeseed, as an important oilseed crop, is often subjected to low temperature stress and consequent yield loss at high latitudes. Therefore, identification of highly cold-resistant winter type rapeseed and elucidation of the molecular mechanism of cold tolerance are crucial for genetic improvement of the trait. Here, we report a chromosome-level reference genome of a prominent cold-resistant winter rapeseed cultivar, NTS57. We elucidated the phylogeny of NTS57 with other public rapeseed cultivars and performed gene family and structure variation analysis at the pan-genome level. In addition, we profiled the DNA methylation and transcriptomic changes of NTS57 upon cold stress, and many cold response genes were identified. Furthermore, we surveyed the cold resistance of 290 rapeseed accessions and performed GWAS analysis to identify the potential gene loci controlling cold resistance, which discovered some important functional genes, includingMYB34andRLK1.Overall, this research provided a basis for genetic dissection and improvement of cold tolerance in rapeseed.