Integrated genomics, QTL mapping, and co-expression analyses identifying candidates of low-temperature tolerance in Brassica napus L

Low-temperature is a major environmental factor that limits agricultural productivity of over-wintering crops such as rapeseed (Brassica napus L.). Low-temperature tolerance is a complex quantitative trait that is susceptible to environmental conditions. To understand the genetic basis of low-temperature tolerance in rapeseed, we applied whole-genome sequencing, genetic mapping, and transcriptomic analyses. A total of twenty-eight quantitative trait loci for frost damage index were detected across the different environments using whole-genome sequencing in a recombinant inbred line population derived from GZ hui (cold-tolerant) and 10B (cold-sensitive). Compared to the genetic variants of the parentals and the quantitative trait loci scanned by simple sequence repeat markers among an F₂ population, one major interval, qFDI.C02.1 in the 0.5–5.9 Mb physical position on C02 was a co-detected locus which was related to low-temperature tolerance. Moreover, genome wide identification of the homoeologous exchange events showed that qFDI.C02.1 overlapped with a homoeologous exchange of the genome, suggesting that chromosome structure variation was important for the low-temperature responses. Present/absent variation (PAV) markers were developed to distinguish the A and C subgenomes, and narrowed qFDI.C02.1 to PAV11-PAV14 approximately 1.6 Mb physical region. Combining with the results from RNA-seq and co-expression network analyses, seven cold-inducing genes were proposed as candidate genes in the qFDI.C02.1, including BnaC02g03120D (E2F_TDP family), BnaC02g03470D (Pseudo ARR-B family), BnaC02g02380D (chalcone-flavonone isomerase 3), BnaC02g03620D (Phosphopantothenate-cysteine ligase 1), BnaC02g03190D (Membrane magnesium transporter), BnaC02g03680D (L-type lectin-domain containing receptor kinase), and BnaC02g03590D (Haloacid dehalogenase-like hydrolase). This study will lay a foundation for exploring low-temperature tolerance genes of GZ hui and breeding cold-tolerance rapeseed varieties.