title: Graphical genotyping as a method to map Ny(o,n)stoand Gpa5 using a reference panel of tetraploid potato cultivars.
abstract: The method of graphical genotyping is applied to a panel of tetraploid potato cultivars to visualize haplotype sharing. The method allowed to map genes involved in virus and nematode resistance. The physical coordinates of the amount of linkage drag surrounding these genes are easily interpretable. Graphical genotyping is a visually attractive and easily interpretable method to represent genetic marker data. In this paper, the method is extended from diploids to a panel of tetraploid potato cultivars. Application of filters to select a subset of SNPs allows one to visualize haplotype sharing between individuals that also share a specific locus. The method is illustrated with cultivars resistant to Potato virus Y (PVY), while simultaneously selecting for the absence of the SNPs in susceptible clones. SNP data will then merge into an image which displays the coordinates of a distal genomic region on the northern arm of chromosome 11 where a specific haplotype is introgressed from the wild potato species S. stoloniferum (CPC 2093) carrying a gene (Ny(o,n)sto) conferring resistance to two PVY strains, PVYOand PVYNTN. Graphical genotyping was also successful in showing the haplotypes on chromosome 12 carrying Ry-fsto, another resistance gene derived from S. stoloniferum conferring broad-spectrum resistance to PVY, as well as chromosome 5 haplotypes from S. vernei, with the Gpa5 locus involved in resistance against Globodera pallida cyst nematodes. The image also shows shortening of linkage drag by meiotic recombination of the introgression segment in more recent breeding material. Identity-by-descent was found to be a requirement for using graphical genotyping, which is proposed as a non-statistical alternative method for gene discovery, as compared with genome-wide association studies. The potential and limitations of the method are discussed.
authors.affiliation: Plant Breeding, Wageningen University and Research, P.O.Box 386, 6700 AJ, Wageningen, The Netherlands. herman.vaneck@wur.nl.
authors.forename: Herman J
authors.initials: HJ
authors.lastname: van Eck
authors.affiliation: Plant Breeding, Wageningen University and Research, P.O.Box 386, 6700 AJ, Wageningen, The Netherlands.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Vos
authors.affiliation: Plant Pathology Laboratory, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Jari P T
authors.initials: JP
authors.lastname: Valkonen
authors.affiliation: Plant Breeding, Wageningen University and Research, P.O.Box 386, 6700 AJ, Wageningen, The Netherlands.
authors.forename: Jan G A M L
authors.initials: JG
authors.lastname: Uitdewilligen
authors.affiliation: Averis Seeds B.V., Valtherblokken Zuid 40, 7876 TC, Valthermond, The Netherlands.
authors.forename: Hellen
authors.initials: H
authors.lastname: Lensing
authors.affiliation: Averis Seeds B.V., Valtherblokken Zuid 40, 7876 TC, Valthermond, The Netherlands.
authors.forename: Nick
authors.initials: N
authors.lastname: de Vetten
authors.affiliation: Plant Breeding, Wageningen University and Research, P.O.Box 386, 6700 AJ, Wageningen, The Netherlands.
authors.forename: Richard G F
authors.initials: RG
authors.lastname: Visser
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics; D056726:Genetic Association Studies; D005819:Genetic Markers; D060005:Genotyping Techniques; D006239:Haplotypes; D010935:Plant Diseases / Q000235:genetics / Q000469:parasitology / Q000821:virology; D020641:Polymorphism, Single Nucleotide; D017800:Potyvirus; D011198:Solanum tuberosum / Q000235:genetics* / Q000469:parasitology / Q000821:virology; D057891:Tetraploidy; D014431:Tylenchoidea
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers