AUTHOR=Fu Ying , Zhang Yaofeng , Mason Annaliese S. , Lin Baogang , Zhang Dongqing , Yu Huasheng , Fu Donghui 

TITLE=NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci

JOURNAL=Frontiers in Plant Science

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.00026

DOI=10.3389/fpls.2019.00026

ISSN=1664-462X

ABSTRACT=<p>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 <italic>Brassica napus</italic> (A<sub>n</sub>A<sub>n</sub>C<sub>n</sub>C<sub>n</sub>, 2n = 38) is still unknown. We performed a genome-wide comparison of putatively functional NBS-encoding genes in <italic>B. napus</italic> and its progenitor species <italic>Brassica rapa</italic> (A<sub>r</sub>A<sub>r</sub>, 2n = 20) and <italic>Brassica oleracea</italic> (C<sub>o</sub>C<sub>o</sub>, 2n = 18), identifying 464, 202, and 146 putatively functional NBS-encoding genes respectively, with genes unevenly distributed in several clusters. The A<sub>n</sub>-subgenome of <italic>B. napus</italic> possessed similar numbers of NBS-encoding genes (191 genes) to the A<sub>r</sub> genome of <italic>B. rapa</italic> (202 genes) and similar clustering patterns. However, the C<sub>n</sub> genome of <italic>B. napus</italic> had many more genes (273) than the <italic>B. oleracea</italic> C<sub>o</sub> genome (146), with different clustering trends. Only 97 NBS-encoding genes (66.4%) in <italic>B. oleracea</italic> were homologous with NBS-encoding genes in <italic>B. napus</italic>, while 176 NBS-encoding genes (87.1%) were homologous between <italic>B. rapa</italic> and <italic>B. napus</italic>. These results suggest a greater diversification of NBS-encoding genes in the C genome may have occurred after formation of <italic>B. napus.</italic> Although most NBS-encoding genes in <italic>B. napus</italic> 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 <italic>B. napus</italic> and the progenitor species were less than 1, suggesting purifying selection during <italic>B. napus</italic> 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 <italic>B. napus</italic> (blackleg, clubroot and <italic>Sclerotinia</italic> stem rot) found 204 NBS-encoding genes in <italic>B. napus</italic> 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 <italic>Brassica</italic> subgenomes, while co-localization of NBS-encoding genes and resistance QTL may facilitate resistance breeding in oilseed rape.</p>