Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement

Abstract

Brassica napus (2n = 4x = 38, AACC) is an important allopolyploid crop derived from interspecific crosses between Brassica rapa (2n = 2x = 20, AA) and Brassica oleracea (2n = 2x = 18, CC). However, no truly wild B. napus populations are known; its origin and improvement processes remain unclear. Here, we resequence 588 B. napus accessions. We uncover that the A subgenome may evolve from the ancestor of European turnip and the C subgenome may evolve from the common ancestor of kohlrabi, cauliflower, broccoli, and Chinese kale. Additionally, winter oilseed may be the original form of B. napus. Subgenome-specific selection of defense-response genes has contributed to environmental adaptation after formation of the species, whereas asymmetrical subgenomic selection has led to ecotype change. By integrating genome-wide association studies, selection signals, and transcriptome analyses, we identify genes associated with improved stress tolerance, oil content, seed quality, and ecotype improvement. They are candidates for further functional characterization and genetic improvement of B. napus.

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

“…Comparison of subgenomic SV frequency revealed significantly higher numbers of small-to 123 mid-scale SV per megabase in the B. napus A subgenome than the C subgenome in all twelve 124 analysed genotypes ( Figure 6 A and B, Supplementary Table S4). This reflects a 125 corresponding subgenomic bias also observed for large-scale SV in B. napus (Samans et al 126 2017), this could also be attributable to repeated introgressions from the A genome of B. rapa 127 during the breeding history of B. napus (Lu et al, 2019). Samans et al (2017) ).…”

“…Express 617). According to (Lu et al, 2019), who used whole-genome resequencing 149 data to investigate the species origin and evolution of B. napus, spring and semi-winter types 6 arose only very recently (<500 years) from winter-types. Our data concur with this 151 assumption, with fewer genes carrying SV in winter-type accessions (1072) than in spring 152 (1170) or semi-winter (3663) ecotypes ( Figure 1C).…”

Nonspecific phospholipase C6 increases seed oil production in oilseed Brassicaceae plants

“…Using this natural population, we performed candidate‐gene association analysis for the impact of 13 BnNPCs with seed oil content (SOC). It was estimated that the oilseed rape genome linkage disequilibrium (LD) decay value was c. 0.45–0.50 Mb (Liu et al , 2016; Lu et al , 2019; Wu et al , 2019). We used the doubled LD decay value regions (i.e.…”

Genome‐wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.)

“…napus of the world. In comparison with previously described GWASs, such as Arifuzzaman, Oladzadabbasabadi, McClean, and Rahman (), He et al (), Lu et al (), Wang et al () and Wu et al () and, the current approach involves a much smaller population that is easily handled for GWAS, but a very high SNP number (2705480), which lends power to the analysis and allows identification of tightly associated genes. Brassicaceae plants have a large variation in trichome formation across wild and cultivated species (Beilstein, Al‐Shehbaz, & Kellogg, ).…”