Genetic diversity of disease resistance genes in foxtail millet (Setaria italica L.)

Foxtail millet (Setaria italica L.) is a potential biofuel plant species, which is also one of the most commonly cultivated millet species for food and fodder. In this study we aimed to conduct a genome-wide identification of Coiled-coil, Nucleotide-binding site, Leucine-rice repeat (CNL) disease resistance genes (R-genes) in foxtail millet and study their evolutionary relationships. We identified 242 CNL genes with domains for NBS-LRR receptor function, with the addition of a few genes that contained transmembrane or zinc finger domains. Of the identified CNL genes, more than half formed gene clusters within the foxtail millet genome, with the majority showing evidence of tandem duplications. Syntenic analysis displayed chromosomal similarities among foxtail millet, rice, and barley, identifying strong syntenic relationships between foxtail millet and rice. Approximately 30% of the foxtail millet CNL gene clusters were found on chromosome Si08, exhibiting strong synteny with chromosome Os11 of rice. Selection pressure analysis showed a prevalence of purifying selection among all phylogenetic clades. We also identified the foxtail millet homologs of several well-studied R-genes in other species. The results from this study will have implications in research on CNL gene signaling pathways and development of durable resistance in foxtail millet and other crop species in general.