Abstract
As one of the most important resistance (R) gene families in plants, the NBS–LRR genes, encoding proteins with nucleotide-binding 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.
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Abbreviations
- DGE:
-
Digital gene expression
- R:
-
Resistance
- NBS:
-
Nucleotide-binding site
- LRR:
-
Leucine-rich repeat
- TIR:
-
N-terminal Toll/interleukin-1 receptor
- CC:
-
Coiled-coil
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Acknowledgements
This work was supported financially by grants from the National key research and development program (2016YFD0101804, 2016YFD0101702), the National Natural Science Foundation of China (31171958), and the Science & Technology Innovation Program of BAAFS (KJCX20180427, KJCX20170102, KJCX20170710).
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ZCL, JHY, JGK, JMX, and HPW designed the research. ZCL and HPW completed the experiments. JMX and HLL performed the data analysis and prepared the manuscript. ZCL, XHZ, JGK, and JX revised the manuscript. All authors had read and approved the final version of the manuscript.
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13205_2019_1714_MOESM1_ESM.tif
Exon-intron structures of CNLs. The green bars indicate the exons, and the black lines indicate the introns (TIFF 6142 kb)
13205_2019_1714_MOESM2_ESM.tif
Exon-intron structures of TNLs. The green bars indicate the exons, and the black lines indicate the introns (TIFF 7235 kb)
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Liu, Z., Xie, J., Wang, H. et al. Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage. 3 Biotech 9, 202 (2019). https://doi.org/10.1007/s13205-019-1714-8
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DOI: https://doi.org/10.1007/s13205-019-1714-8