The development of a high-throughput marker platform for genome-wide mapping of NB-LRR resistance genes in potato.

Potato is one of the world’s most important food crops and pathogens cause large losses annually. The use of resistant potato varieties is one of the most important means of controlling the impact of these pathogens. However, not all genes responsible for these resistances are known. The majority of known pathogen resistances in potato are conferred by single dominant R genes encoding nucleotide binding leucine-rich-repeat (NB-LRR) proteins. NB-LRR genes occur in clusters throughout the genome and with the aid of the reference potato genome these clusters could be identified. Our aim was to establish a strategy based on cluster specific markers for genome-wide identification of NB-LRR genes conferring disease resistance to various pathogens in potato. For each gene cluster a primer pair was developed to specifically amplify a pool of fragments from the NB-LRR genes present in a single cluster. These primers were combined in ten-plex PCR setups. These pools of amplicons were subsequently sequenced using the Illumina MiSeq sequencing platform. A bioinformatics pipeline was set up to identify all the read variants present in the set of gene clusters and to convert them into informative markers to find correlations with known and unknown resistance traits in a panel of potato varieties or mapping populations. One of the major pathogens on potato are potato cyst nematodes (PCN’s; Globodera rostochiensis and G. pallida). Known R genes, such as the Gpa2 gene conferring resistance to G. pallida, will be used to validate the approach, showing its potential as a genome-wide HTP marker platform to find novel NB-LRR genes linked to disease resistances in potato.