title: Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array.
abstract: Genotyping arrays are tools for high-throughput genotyping, which is beneficial in constructing saturated genetic maps and therefore high-resolution mapping of complex traits. Since the report of the first cucumber genome draft, genetic maps have been constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and sequence-related amplified polymorphism (SRAP). In this study, we developed the first cucumber genotyping array consisting of 32,864 single-nucleotide polymorphisms (SNPs). These markers cover the cucumber genome with a median interval of ~2 Kb and have expected genotype calls in parents/F1 hybridizations as a training set. The training set was validated with Fluidigm technology and showed 96% concordance with the genotype calls in the parents/F1 hybridizations. Application of the genotyping array was illustrated by constructing a 598.7 cM genetic map based on a '9930' × 'Gy14' recombinant inbred line (RIL) population comprised of 11,156 SNPs. Marker collinearity between the genetic map and reference genomes of the two parents was estimated at R2 = 0.97. We also used the array-derived genetic map to investigate chromosomal rearrangements, regional recombination rate, and specific regions with segregation distortions. Finally, 82% of the linkage-map bins were polymorphic in other cucumber variants, suggesting that the array can be applied for genotyping in other lines. The genotyping array presented here, together with the genotype calls of the parents/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs.
authors: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
authors: Mor
authors: M
authors: Rubinstein
authors: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
authors: Mark
authors: M
authors: Katzenellenbogen
authors: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
authors: Ravit
authors: R
authors: Eshed
authors: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
authors: Ada
authors: A
authors: Rozen
authors: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Newe-Yaar Center, Ramat Yishai, Israel.
authors: Nurit
authors: N
authors: Katzir
authors: Plant Breeding, Genetics, Genomics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America.
authors: Marivi
authors: M
authors: Colle
authors: Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America.
authors: Luming
authors: L
authors: Yang
authors: Plant Breeding, Genetics, Genomics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America.
authors: Rebecca
authors: R
authors: Grumet
authors: Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America; United States Department of Agriculture (USDA)-ARS, Vegetable Crops Research Unit, Madison, Wisconsin, United States of America.
authors: Yiqun
authors: Y
authors: Weng
authors: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
authors: Amir
authors: A
authors: Sherman
authors: Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
authors: Ron
authors: R
authors: Ophir
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics*; D018553:Cucumis sativus / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D008040:Genetic Linkage / Q000235:genetics*; D018745:Genome, Plant; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci
chemical_list: D018744:DNA, Plant