NBS-Encoding Genes in Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci.

Genes containing nucleotide-binding sites (NBS) play an important role in pathogen resistance in plants. However, the evolutionary fate of NBS-encoding genes after formation of allotetraploid (AACC, 2n = 38) is still unknown. We performed a genome-wide comparison of putatively functional NBS-encoding genes in and its progenitor species (AA, 2n = 20) and (CC, 2n = 18), identifying 464, 202, and 146 putatively functional NBS-encoding genes respectively, with genes unevenly distributed in several clusters. The A-subgenome of possessed similar numbers of NBS-encoding genes (191 genes) to the A genome of (202 genes) and similar clustering patterns. However, the C genome of had many more genes (273) than the C genome (146), with different clustering trends. Only 97 NBS-encoding genes (66.4%) in were homologous with NBS-encoding genes in , while 176 NBS-encoding genes (87.1%) were homologous between and . These results suggest a greater diversification of NBS-encoding genes in the C genome may have occurred after formation of Although most NBS-encoding genes in appeared to derive from the progenitors, the birth and death of several NBS-encoding genes was also putatively mediated by non-homologous recombination. The Ka/Ks values of most homologous pairs between and the progenitor species were less than 1, suggesting purifying selection during evolution. The majority of NBS-encoding genes (60% in all species) showed higher expression levels in root tissue (out of root, leaf, stem, seed and flower tissue types). Comparative analysis of NBS-encoding genes with mapped resistance QTL against three major diseases of (blackleg, clubroot and stem rot) found 204 NBS-encoding genes in located within 71 resistance QTL intervals. The majority of NBS-encoding genes were co-located with resistance QTLs against a single disease, while 47 genes were co-located with QTLs against two diseases and 3 genes were co-located with QTLs against all three. Our results revealed significant variation as well as interesting evolutionary trajectories of NBS-encoding genes in the different subgenomes, while co-localization of NBS-encoding genes and resistance QTL may facilitate resistance breeding in oilseed rape.