Solanum R gene Indexing (SolaRIndex)

This project aims at (1) indexing the diversity of all major resistance genes (R genes) within the genepool of Solanum with emphasis on the common potato (S. tuberosum) and its close relatives and at (2) developing a method for fast development of markers for selection in plant breeding. This research project will shed new light on the evolution and diversification of R genes and disease resistance. R genes are the triggers of disease resistance, they comprise 1-2% of all plant genes, and their high rates of diversification reflect the dynamics of the co- evolution with virulence genes of the numerous specialized pathogens. Most R genes, and exclusively R genes, carry a nucleotide binding site (NBS) domain which has highly conserved sequence motifs. R genes confer resistance against all classes of pathogens including viruses, bacteria, fungi, and pests. The high allelic specificity that determines the interaction of a particular R protein with a discrete pathogenic strain is brought about by features within the highly variable sequence parts near the NBS. The high conservation within NBS motifs will be used to amplify via polymerase chain reaction (PCR) with a few primers the majority of all R genes within a large group of solanaceous cultivars and varieties that are representative of the entire R gene pool. A second PCR primer placed at the recognition sequence of restriction enzymes plus an adapter assures that the amplified R gene fragments contain informative portions of polymorphic, non-conserved sequence. The R gene fragments isolated by PCR will be sequenced via the genome sequencing technology with long-read GS FLX Titanium chemistry to obtain the DNA sequence of all R alleles (R haplotypes) present. The digitalized sequences will be indexed via bioinformatics procedures and R alleles that are confined to varieties/cultivars which share a specific resistance phenotype will be detected. The association of a specific R allele and an R phenotype will be subsequently verified by allele-specific PCR on small segregating populations or groups of cultivars. The outcome of this research will overcome the current obstacles to obtaining sufficient numbers of reliable molecular markers for resistance selection in breeding of the tetraploid, heterozygous, and inbreeding-intolerant potato.

The nearly complete diversity of the cultivated potato's R (resistance) genes and their allelic variants has been decoded for the first time. Potatoes are the world's most important food plant after the cereals. Diseases cause the greatest costs of potato production and storage, and natural resistance is the ecological antidote of choice. Now, the genetic code of the R genes has been deciphered from ninety representative, modern and historical cultivars using modern high-throughput technology and bioinformatics. The SolariX database at www.cibiv.at/SolariX/ makes this information publicly accessible.The R-Genepool of the species was previously imputed to 576 genetic loci (a locus is a placeholder of a gene's variants which are known as alleles or haplotypes) representing 2% of all potato genes. These 576 loci correspond to the NBS R genes (R genes carrying a specific, Nucleotide Binding Site, motif in their code) in the current standard potato model genome. For the tetraploid potato (this plant possesses four copies of its basic set of chromosomes instead of two like humans and most other higher organisms), maximally 4 alleles were expected, however, up to 12 alleles were best fitted to a single locus. This unexpected large quantity of alleles suggests that the common potato may possess a much greater number of R loci than detected until present. The additional loci may not be found by the current methodology due to their highly similar genetic code.The data in SolariX allow for an unprecedented efficiency when identifying specific R alleles that make the plant resistant to individual diseases. This facilitates the development of molecular markers to select for those resistances, as has been demonstrated in this project for one example. Such markers for selection are urgently needed in potato breeding.But also plant researchers benefit from SolariX. The database facilitates studies at the molecular level of the relationships between potato cultivars and even entire breeding programs and it supports the understanding of genealogy and evolution of disease resistance.