Comparative analysis of late blight resistance R genes and their coding proteins in some potato genotypes

Late blight (LB) disease can cause potato yield losses in both Egypt and the world. Therefore, the structural analysis of resistance (R) genes responsible for LB resistance will help in understanding their functions. This work aimed to identify the variations between the dominant and recessive alleles of two genes, R3a and R8 at the nucleotide and amino acid levels in five potato genotypes. Two genes of R3a and R8 representing the broad-spectrum LB resistance were amplified by specific primers, which gave one amplicon of 194 and 220 bp of each gene, respectively. Two fragments were sequenced after purification using an ABI 3730xl System DNA Sequencer. The DNA sequence alignments of two genes, R3a and R8, were determined among five selected potato genotypes. The percentage of genetic similarity of the nucleotide sequences of the R3a and R8 genes ranged between (82–83%) and (86–87%), respectively, in comparison to the reference sequences in the nucleotide BLAST. We report on the existence of positional differences in the nucleotide sequences, and base-pair substitutions of two fragments, resulting in amino acid changes between the resistant and susceptible potato genotypes. On the other hand, the highest total number of base-pair substitutions was recorded as 16 in the recessive allele r8 of the varieties Bellini and Cara. However, the lowest number was recorded as four in the dominant allele R3a of the variety Cara. The dendrograms of the five potato genotypes were made up of phylogenetically different clusters, separate from all the other named potato accessions of the two genes. The results of this study will create a solid base for the further understanding of the mechanism of plant-pathogen interactions and supply a theoretical reference for durable resistance to late blight diseases in the potato.