Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage

Abstract

As one of the most important resistance (R) gene families in plants, the NBS-LRR genes, encoding proteins with nucleotidebinding site (NBS) and leucine-rich repeat (LRR) domains, play significant roles in resisting pathogens. The published genomic data for cabbage (Brassica oleracea L.) provide valuable data to identify and characterize the genomic organization of cabbage NBS-LRR genes. Ultimately, we identified 105 TIR (N-terminal Toll/interleukin-1 receptor)-NBS-LRR (TNL) genes and 33 CC (coiled-coil)-NBS-LRR (CNL) genes. Further research indicated that 50.7% of the 138 NBS-LRR genes exist in 27 clusters and there are large differences among the gene structures and protein characteristics. Conserved motif and phylogenetic analysis showed that the structures of TNLs and CNLs were similar, with some differences. These NBS-LRRs are evolved under negative selection and mostly arose from whole-genome duplication events during evolution. Tissue-expression profiling of NBS-LRR genes revealed that 37.1% of the TNL genes are highly or specifically expressed in roots, especially the genes on chromosome 7 (76.5%). Digital gene expression and reverse transcription PCR analyses revealed the expression patterns of the NBS-LRR genes upon challenge by Fusarium oxysporum f.sp. conglutinans: nine genes were upregulated, and five were downregulated. The major resistance gene Foc1 probably works together with the other four genes in the same cluster to resist F. oxysporum infection.

Genome-Wide Identification and Characterization of NBS-encoding Genes in Raphanus Sativus L. And Their Roles Related to Fusarium Oxysporum Resistance

“…This difference between gene types may be due to the conservative nature of CNL gene replications, which involve many regulatory components. This result is also consistent with those reported for A. thaliana, B. rapa, and B. oleracea [17,20,35]. Although the TNL and CNL genes are related to signaling and resistance speci city during pathogen recognition, the genes in these two subfamilies vary regarding sequences and associated signaling pathways and they cluster separately according to phylogenetic analyses [44].…”

“…Additionally, with a focus on the NBS-LRR genes, we examined the encoded conserved domains as well as phylogenetic relationships and synteny with genes from A. thaliana, B. rapa, and B. oleracea. Furthermore, the pathogen-induced NBS-LRR gene expression pro les indicated that some R genes are highly expressed in various genetic backgrounds [35]. Our results provide crucial insights into the evolution of this gene family in the radish genome.…”

“…Although the TNL and CNL genes are related to signaling and resistance speci city during pathogen recognition, the genes in these two subfamilies vary regarding sequences and associated signaling pathways and they cluster separately according to phylogenetic analyses [44]. Previous studies proved that the TNL group forms four phylogenetic clades in B. rapa [18] and B. oleracea [35]. Our motif analysis with the MEME program uncovered diverse motif compositions in the different RsTNL subfamilies.…”

“…The NBS-LRR genes form a large family of stress resistance genes that are ubiquitous in all plant species. Genome-wide analyses of NBS-LRR gene families have been conducted for numerous species with sequenced genomes [17,20,35]. In the current study, we identi ed candidate NBS-LRR genes and studied their distribution, structure, clustering, duplication, synteny, and conservation.…”

“…Our RNA-seq and qRT-PCR data also indicated that RsTNL06 (Rs053740) was more highly expressed in 'YR18' than in 'YR4' after the FOR59 infection, suggesting that RsTNL06 negatively regulates Fusarium wilt resistance in radish. Interestingly, RsTNL06 was identi ed as an ortholog of the B. oleracea gene Bo7g106630, and may contribute to plant responses to Fusarium species [35]. The potential positive and negative regulators of Fusarium wilt resistance that were identi ed following the comprehensive analyses of RNA-seq and qRT-PCR data will need to be thoroughly functionally characterized to assess their utility for enhancing the Fusarium wilt resistance of radish.…”