Genome-wide identification, and gene expression analysis of NBS-LRR domain containing R genes in Chenopodium quinoa for unveiling the dynamic contribution in plant immunity against Cercospora cf. chenopodii

• Published in: Physiology and molecular biology of plants Vol. 30; no. 7; pp. 1129 - 1144
• Main Authors: Ijaz, Siddra, Ul Haq, Imran, Habib, Zakia, Muti-Ullah, Afzal, Irfan, Khan, Nasir Ahmad, Abdullah
• Format: Journal Article
• Language: English
• Published: New Delhi Springer India 01-07-2024; Springer Nature B.V
• Subjects: Adenosine diphosphate; Binding sites; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Cell Biology; Cellular stress response; Cellular structure; Cercospora; Chenopodium quinoa; Defense mechanisms; Disease; Disease resistance; Gene expression; Gene regulation; Genes; Genomic analysis; Homology; Immune response; Immune system; Leucine; Life Sciences; NBS-LRR gene; Nucleotides; Pathogens; Pattern analysis; Plant diseases; Plant immunity; Plant Physiology; Plant Sciences; Polymerase chain reaction; Proteins; Quinoa; Research Article; Virulence; Plant-pathogen interaction; Biotic stress; NLRome; Evolutionary dynamics; NBS-LRR gene family; Plant immunity
• ISSN: 0971-5894; 0974-0430
• DOI: 10.1007/s12298-024-01475-0

The plant R genes encode the NLR proteins comprising nucleotide-binding sites (NBS) and variable-length C-terminal leucine-rich repeat domains. The proteins act as intracellular immune receptors and recognize effector proteins of phytopathogens, which convene virulence. Among stresses, diseases contribute majorly to yield loss in crop plants, and R genes confer disease resistance against phytopathogens. We investigated the NLRome of
Chenopodium quinoa
for intraspecific diversity, characterization, and contribution to immune response regulation against phytopathogens. One eighty-three NBS proteins were identified and grouped into four distinct classes. Exon–intron organization displayed discrimination in gene structure patterns among NLR proteins. Thirty-eight NBS proteins revealed ontology with defense response, ADP binding, and inter alia cellular components. These proteins had shown functional homology with disease-resistance proteins involved in the plant-pathogen interaction pathway. Likewise, expression analysis demonstrated that NLRs encoding genes showed differential expression patterns. However, most genes displayed high expression levels in plant defense response with varying magnitude compared to ADP binding and cellular components. Twenty-four NBS genes were selected based on Heatmap analysis for quantitative polymerase chain reaction under Cercospora disease stress, and their progressive expression pattern provides insights into their functional role under stress conditions. The protein–protein interaction analysis revealed functional enrichment of NLR proteins in regulating hypersensitive, immune, and stress responses. This study, the first to identify and characterize NBS genes in
C. quinoa
, reveals their contribution to disease response and divulges their dynamic involvement in inducing plant immunity against phytopathogens.