Roel Hoekstra

AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota

BackgroundThe secondary genepool of our modern cultivated potato (Solanum tuberosum L.) consists of a large number of tuber-bearing wild Solanum species under Solanum section Petota. One of the major taxonomic problems in section Petota is that the series classification (as put forward by Hawkes) is problematic and the boundaries of some series are unclear. In addition, the classification has received only partial cladistic support in all molecular studies carried out to date.The aim of the present study is to describe the structure present in section Petota. When possible, at least 5 accessions from each available species and 5 individual plants per accession (totally approx. 5000 plants) were genotyped using over 200 AFLP markers. This resulted in the largest dataset ever constructed for Solanum section Petota. The data obtained are used to evaluate the 21 series hypothesis put forward by Hawkes and the 4 clade hypothesis of Spooner and co-workers.ResultsWe constructed a NJ tree for 4929 genotypes. For the other analyses, due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. We show a NJ jackknife and a MP jackknife tree. A large part of both trees consists of a polytomy. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with >69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana.ConclusionMost of the series that Hawkes and his predecessors designated can not be accepted as natural groups, based on our study. Neither do we find proof for the 4 clades proposed by Spooner and co-workers. A few species groups have high support and their inner structure displays also supported subdivisions, while a large part of the species cannot be structured at all. We believe that the lack of structure is not due to any methodological problem but represents the real biological situation within section Petota.

Diversity, Distribution, and Evolution of Solanum bulbocastanum Late Blight Resistance Genes

Knowledge on the evolution and distribution of late blight resistance genes is important for a better understanding of the dynamics of these genes in nature. We analyzed the presence and allelic diversity of the late blight resistance genes Rpi-blb1, Rpi-blb2, and Rpi-blb3, originating from Solanum bulbocastanum, in a set of tuber-bearing Solanum species comprising 196 different taxa. The three genes were only present in some Mexican diploid as well as polyploid species closely related to S. bulbocastanum. Sequence analysis of the fragments obtained from the Rpi-blb1 and Rpi-blb3 genes suggests an evolution through recombinations and point mutations. For Rpi-blb2, only sequences identical to the cloned gene were found in S. bulbocastanum accessions, suggesting that it has emerged recently. The three resistance genes occurred in different combinations and frequencies in S. bulbocastanum accessions and their spread is confined to Central America. A selected set of genotypes was tested for their response to the avirulence effectors IPIO-2, Avr-blb2, and Pi-Avr2, which interact with Rpi-blb1, Rpi-blb2, and Rpi-blb3, respectively, as well as by disease assays with a diverse set of isolates. Using this approach, some accessions could be identified that contain novel, as yet unknown, late blight resistance factors in addition to the Rpi-blb1, Rpi-blb2, and Rpi-blb3 genes.

SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species

BackgroundThe cultivated potato (Solanum tuberosum L.) is an important food crop, but highly susceptible to many pathogens. The major threat to potato production is the Irish famine pathogen Phytophthora infestans, which causes the devastating late blight disease. Potato breeding makes use of germplasm from wild relatives (wild germplasm) to introduce resistances into cultivated potato. The Solanum section Petota comprises tuber-bearing species that are potential donors of new disease resistance genes. The aim of this study was to explore Solanum section Petota for resistance genes and generate a widely accessible resource that is useful for studying and implementing disease resistance in potato.DescriptionThe SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota. We have explored Solanum section Petota for resistance to late blight in high throughput disease tests under various laboratory conditions and in field trials. From resistant wild germplasm, segregating populations were generated and assessed for the presence of resistance genes. All these data have been entered into the SolRgene database. To facilitate genetic and resistance gene evolution studies, phylogenetic data of the entire SolRgene collection are included, as well as a tool for generating phylogenetic trees of selected groups of germplasm. Data from resistance gene allele-mining studies are incorporated, which enables detection of R gene homologs in related germplasm. Using these resources, various resistance genes have been detected and some of these have been cloned, whereas others are in the cloning pipeline. All this information is stored in the online SolRgene database, which allows users to query resistance data, sequences, passport data of the accessions, and phylogenic classifications.ConclusionSolanum section Petota forms the basis of the SolRgene database, which contains a collection of resistance data of an unprecedented size and precision. Complemented with R gene sequence data and phylogenetic tools, SolRgene can be considered the primary resource for information on R genes from potato and wild tuber-bearing relatives.

Exploring the Natural Biodiversity of Potato for Late Blight Resistance

This paper gives an overview of the activities in Sub-project 4 of the BIOEXPLOIT programme. The European genebank collections of potato need to be narrowed down into (customized) core collections by focusing on loci associated with disease resistance. Therefore, new and more efficient molecular methods are being developed to identify these loci, extensive genotyping of resistance to Phytophthora infestans and signalling loci is being performed, and genotyped selections of accessions are phenotypically analysed for their resistance specificities. The results of these activities are being assembled in an integrated database.

Solarium sectionPetota in Costa Rica: taxonomy and genetic resources

Prior to 1996, worldwide holdings of germplasm of wild potatoes from Costa Rica amounted to just two collections; this country therefore formed a priority for collecting. We mapped all localities of wild potatoes from herbarium specimen data from Costa Rica and collected throughout the country. We made 13 collections, 10 of these with botanical seeds. These collections considerably extend the numbers of accessions and geographic range of the germplasm available from Costa Rica. The taxonomic identity of the species of wild potatoes (Solanum sect. Petota) in Costa Rica was previously unresolved. Our fieldwork supports the concept that Costa Rican wild potatoes belong to a single species,S. longiconicum.ResumenAntes de 1996, las colecciones de germoplasma de papas silvestres de Costa Rica eran sólo dos en todo el mundo; este país, por lo tanto, estableció como una prioridad formar su colección. Con ese fin, asociamos todas las localidades de papas silvestres, tomándolas de una base de datos de muestras de herbarios de Costa Rica y las colectamos a lo largo y ancho del país. Formamos 13 colecciones, 10 de ellas con semilla botánica. Esas colecciones extendieron considerable-mente el número de accesiones y rangos geográficos del germoplasma disponible de Costa Rica. La identidad taxonómica de las especies de papa silvestre (Solatium sect.Petota) de Costa Rica no había sido resuelta previamente. Nuestros trabajos de campo apoyan el concepto de que las papas silvestres de Costa Rica pertenecen a la especie singularS. longiconicum.