title: Genomic architecture of potato resistance to Synchytrium endobioticum disentangled using SSR markers and the 8.3k SolCAP SNP genotyping array.
abstract: BACKGROUND
  The soil borne, obligate biotrophic fungus Synchytrium endobioticum causes tumor-like tissue proliferation (wart) in potato tubers and thereby considerable crop damage. Chemical control is not effective and unfriendly to the environment. S. endobioticum is therefore a quarantined pathogen. The emergence of new pathotypes of the fungus aggravate this agricultural problem. The best control of wart disease is the cultivation of resistant varieties. Phenotypic screening for resistant cultivars is however time, labor and material intensive. Breeding for resistance would therefore greatly benefit from diagnostic DNA markers that can be applied early in the breeding cycle. The prerequisite for the development of diagnostic DNA markers is the genetic dissection of the factors that control resistance to S. endobioticum in various genetic backgrounds of potato.
  
  
  RESULTS
  Progeny of a cross between a wart resistant and a susceptible tetraploid breeding clone was evaluated for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 most relevant in Europe. The same progeny was genotyped with 195 microsatellite and 8303 single nucleotide polymorphism (SNP) markers. Linkage analysis identified the multi-allelic locus Sen1/RSe-XIa on potato chromosome XI as major factor for resistance to all four S. endobioticum pathotypes. Six additional, independent modifier loci had smaller effects on wart resistance. Combinations of markers linked to Sen1/RSe-XIa resistance alleles with one to two additional markers were sufficient for obtaining high levels of resistance to S. endobioticum pathotypes 1, 2, 6 and 18 in the analyzed genetic background.
  
  
  CONCLUSIONS
  Potato resistance to S. endobioticum is oligogenic with one major and several minor resistance loci. It is composed of multiple alleles for resistance and susceptibility that originate from multiple sources. The genetics of resistance to S. endobioticum varies therefore between different genetic backgrounds. The DNA markers described in this paper are the starting point for pedigree based selection of cultivars with high levels of resistance to S. endobioticum pathotypes 1, 2, 6 and 18.
authors.affiliation: Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany. Jude.Obidiegwu@hutton.ac.uk.|National Root Crops Research Institute Umudike, PMB 7006, Umuahia, Abia State, Nigeria. Jude.Obidiegwu@hutton.ac.uk.
authors.forename: Jude Eijkeme
authors.initials: JE
authors.lastname: Obidiegwu
authors.affiliation: Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany. sanetomo@obihiro.ac.jp.|Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan. sanetomo@obihiro.ac.jp.
authors.forename: Rena
authors.initials: R
authors.lastname: Sanetomo
authors.affiliation: Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Kleinmachnow, Germany. Kerstin.Flath@jki.bund.de.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Flath
authors.affiliation: Bioplant GmbH, Ebstorf, Germany. Tacke@bioplant.de.
authors.forename: Eckhard
authors.initials: E
authors.lastname: Tacke
authors.affiliation: Böhm-Nordkartoffel Agrarproduktion GbR, Ebstorf, Germany. HRHofferbert@bna-kartoffel.de.
authors.forename: Hans-Reinhard
authors.initials: HR
authors.lastname: Hofferbert
authors.affiliation: Department of Genomics, Life & Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany. andrea.hofmann@uni-bonn.de.
authors.forename: Andrea
authors.initials: A
authors.lastname: Hofmann
authors.affiliation: Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany. walkemei@mpipz.mpg.de.
authors.forename: Birgit
authors.initials: B
authors.lastname: Walkemeier
authors.affiliation: Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany. gebhardt@mpipz.mpg.de.
authors.forename: Christiane
authors.initials: C
authors.lastname: Gebhardt
mesh_terms: D008411:Chytridiomycota; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study / Q000379:methods; D060005:Genotyping Techniques; D006239:Haplotypes; D018895:Microsatellite Repeats; D008957:Models, Genetic; D005810:Multigene Family; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D011198:Solanum tuberosum / Q000235:genetics* / Q000382:microbiology*