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

Abstract

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.