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Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp.

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Abstract

Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family’s classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein–protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas’ NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.

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Data availability

The datasets generated or analyzed during the current study are available from the corresponding author on reasonable request. All other data generated or analyzed during this study are included in this article supplementary information files.

Abbreviations

NBS:

Nucleotide-binding site

PTI:

Pathogen-triggered immunity

ETI:

Effector-triggered immunity

SAR:

Systemic acquired resistance

PAMPs:

Pathogen-associated molecular patterns

PRRs:

Pattern recognition receptors

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Funding

This study is financially supported by the Indian Council of Agricultural Research, New Delhi (Grant ID: IXX14668).

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  1. Anuradha Chelliah and Chandrasekar Arumugam contributed equally.

Authors and Affiliations

  1. ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India

    Anuradha Chelliah, Chandrasekar Arumugam, Backiyarani Suthanthiram, Thangavelu Raman & Uma Subbaraya

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  1. Anuradha Chelliah
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  2. Chandrasekar Arumugam
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  3. Backiyarani Suthanthiram
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  4. Thangavelu Raman
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  5. Uma Subbaraya
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Contributions

Anuradha Chelliah: project administration, conceptualization, work design, data curation, methodology, visualization, analyzed the data, writing—original draft, review and editing, formatting; Chandrasekar Arumugam: methodology, in silico analysis; Backiyarani Suthanthiram: validation; Thangavelu Raman: validation; Uma Subbaraya: validation.‬‬

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Correspondence to Anuradha Chelliah.

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Chelliah, A., Arumugam, C., Suthanthiram, B. et al. Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp.. Funct Integr Genomics 23, 7 (2023). https://doi.org/10.1007/s10142-022-00925-w

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  • DOI: https://doi.org/10.1007/s10142-022-00925-w

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