Development of Molecular Tools for Distinguishing Between the Highly Similar Rx1 and Rx2 PVX Extreme Resistance Genes in Tetraploid Potato

The Rx1 and Rx2 are extreme resistance genes, which have been introgressed from different species into potato cultivars and breeding lines. These two genes have a 98% and 96% sequence similarity at the nucleotide as well as at the amino acid level, respectively. Except one extra amino acid in the Rx2 gene, the high variations of the amino acid chain are due to single and double nucleotide variations, which are scattered throughout the coding regions. The high level of sequence similarity makes it complicated to identify these genes and to distinguish them from other highly similar genes, like the Gpa2 or from paralogous sequences by a single polymerase chain reaction (PCR). Here, we report the development of markers for the simple and rapid identification of the Rx1 as well as the Rx2 gene. Further, a multiplex PCR reaction is recommended for the simultaneous detection of both genes in a single reaction. Since these genes reside on different chromosomes, following their inheritance by the multiplex PCR method could help the easy incorporation of both genes into breeding lines. The detection method shown here could be routinely used in marker-assisted selection for Potato virus X extreme resistance and could enhance the effectiveness of potato breeding programs. Besides potato breeding, this method could also be effectively applied to mapping experiments as well as in research studies of resistance.