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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 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.

SUBMITTER: Liu Z

PROVIDER: S-EPMC6500516 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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

Liu Zeci Z Xie Jianming J Wang Huiping H Zhong Xionghui X Li Hailong H Yu Jihua J Kang Jungen J

3 Biotech 20190504 5

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 ...[more]

PMID: 31065502

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Project description:Fusarium wilt caused by Fusarium oxysporum f. sp. conglutinans (FOC) is a destructive disease of Brassica crops, which results in severe yield losses. There is little information available about the mechanism of disease resistance. To obtain an overview of the transcriptome profiles in roots of R4P1, a Brassica oleracea variety that is highly resistant to fusarium wilt, we compared the transcriptomes of samples inoculated with FOC and samples inoculated with distilled water. RNA-seq analysis generated more than 136 million 100-bp clean reads, which were assembled into 62,506 unigenes (mean size = 741 bp). Among them, 49,959 (79.92%) genes were identified based on sequence similarity searches, including SwissProt (29,050, 46.47%), Gene Ontology (GO) (33,767, 54.02%), Clusters of Orthologous Groups (KOG) (14,721, 23.55%) and Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) (12,974, 20.76%) searches; digital gene expression analysis revealed 885 differentially expressed genes (DEGs) between infected and control samples at 4, 12, 24 and 48 hours after inoculation. The DEGs were assigned to 31 KEGG pathways. Early defense systems, including the MAPK signaling pathway, calcium signaling and salicylic acid-mediated hypersensitive response (SA-mediated HR) were activated after pathogen infection. SA-dependent systemic acquired resistance (SAR), ethylene (ET)- and jasmonic (JA)-mediated pathways and the lignin biosynthesis pathway play important roles in plant resistance. We also analyzed the expression of defense-related genes, such as genes encoding pathogenesis-related (PR) proteins, UDP-glycosyltransferase (UDPG), pleiotropic drug resistance, ATP-binding cassette transporters (PDR-ABC transporters), myrosinase, transcription factors and kinases, which were differentially expressed. The results of this study may contribute to efforts to identify and clone candidate genes associated with disease resistance and to uncover the molecular mechanism underlying FOC resistance in cabbage.

Dataset Information

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

Publications

Identification and expression profiling analysis of NBS-LRR genes involved in <i>Fusarium oxysporum</i> f.sp. <i>conglutinans</i> resistance in cabbage.

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