Functional genomic regions associated with blast disease resistance in rice predicted syntenic orthologs and potential resistance gene candidates from diverse cereal genomes

• Published in: Physiological and molecular plant pathology 2024-09, Vol.133, p.102344, Article 102344
• Main Authors: Gajanayake, Shanika, Wakkumbura, Janani, Fernando, Menaka, Abeysundara, Sachith, Wijewardena, Indika, Ariyarathna, Chandima
• Format: Article
• Language: English
• Subjects: Comparative genomics; Crop synteny; Magnaporthe oryzae; NBS-LRR; Resistance gene analogs; Resistance genes
• ISSN: 0885-5765
• DOI: 10.1016/j.pmpp.2024.102344

Blast disease is a major production constraint in cereal crops worldwide. Genome regions associated with blast resistance in rice were used in homology-based prediction of resistance gene orthologs across cereals. Seventy-four Resistance Gene Analogs (RGAs) that were collocated with rice QTLs (Quantitative Trait Loci) associated with blast resistance, predicted 89 orthologs from cereals,including 61 from finger millet. The RGA orthologs found hits in cereal transcriptomes derived from blast-infected tissues. Over 92% of the putative RGAs encoded NBS-LRR (Nucleotide Binding Site -Leucine Rich Repeat) proteins. Despite conserved primary protein structures, NBS-LRRs were variable in the encoding genes. Primers designed on conserved NBS-LRRs motifs amplified multiple fragments in PCR indicating the presence of highly similar paralogs in genomes. Rice chromosomes 1, 2, 4, 6, and 11 dock clusters of RGAs and syntenic clusters of orthologous RGAs were predicted from other cereal genomes identifying genome hotspots for resistance gene cassettes. RGAs in such cassettes were tightly linked with 50 %–90 % within-cluster similarity. Local finger millet germplasm identified multi-modes of resistance, and lack of correlation between the resistance traits points to independent expression of resistance mechanisms and associated genes in different tissues and development stages. The significant diversity, genomic abundance, and potential functional redundancy complicate use of RGAs for resistance breeding in given host genetic backgrounds, pathogen pools and agro-climates; therefore, robust technology pipelines that enable system-level analysis of expression and effectiveness can increase the practical use of RGAs. •Seventy-four RGAs that were collocated with rice QTLs associated with blast disease resistance predicted 89 orthologs from related cereals.•Over 92% of RGAs encoded NBS-LRR proteins that were similar in primary protein structure, but the encoding genes expressed a degree of variability.•RGAs aggregate in syntenic clusters across cereal genomes identifying genome hotspots for resistance gene cassettes.•Leaf blast resistance is expressed independently from neck and finger blast resistance, indicating diverse associated genes and mechanisms.