Genomics of Plant Genetic Resources pp 27-46
Mining the Genus Solanum for Increasing Disease Resistance
Plant Breeding is the art of selecting and discarding genetic material to achieve crop improvement. Favourable alleles resulting in quality improvement or disease resistance must be added, while unfavourable alleles must be removed. The source for novel alleles can be other varieties, landraces or crop wild relatives. The identification of allelic variation is referred to as allele mining. Before allelic variation can be used for breeding purposes several steps need to be taken. First of all an inventory is needed of the available genetic resources. Phenotypic screens are needed to uncover potential expected and even unanticipated alleles. Next, using genetic and molecular tools, the alleles responsible for the identified traits must be traced and distinguished in order to be introgressed into new varieties.
In this review we focus on the identification of novel disease resistance traits in the agronomically important genus Solanum. The fact that R genes are present in multigene clusters within the genome, which often include many paralogs necessitates thorough discussion on the distinction between alleles and paralogs. Often such a distinction cannot easily be made. An overview is given of how natural resources can be tapped, e.g. how germplasm can be most efficiently screened. Techniques are presented by which alleles and paralogs can be distinguished in functional and/or genetic screens, including also a specific tagging of alleles and paralogs. Several examples are given in which allele and paralog mining was successfully applied. Also examples are presented as to how allele mining supported our understanding about the evolution of R gene clusters. Finally an outlook is provided how the research field of allele mining might develop in the near future.