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Rosaceae conserved orthologous sequences marker polymorphism in sweet cherry germplasm and construction of a SNP-based map

Affiliation
Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA
Cabrera, Antonio;
Affiliation
Department of Crop and Soil Science, Michigan State University, East Lansing, MI, USA
Rosyara , Umesh R.;
Affiliation
Department of Fruit Tree and Woody Plant Sciences, University of Bologna, Bologna, Italy
Franceschi, Paolo De;
Affiliation
Department of Horticulture, Michigan State University, East Lansing, MI, USA
Sebolt, Audrey;
Affiliation
Department of Horticulture, Michigan State University, East Lansing, MI, USA
Sooriyapathirana, Suneth S.;
Affiliation
INRA-UR419, Unité de Recherches sur les Espèces Fruitières, Centre de Bordeaux, Villenave d’Ornon, France
Dirlewanger, Elisabeth;
Affiliation
INRA-UR419, Unité de Recherches sur les Espèces Fruitières, Centre de Bordeaux, Villenave d’Ornon, France
Quero-Garcia, Jose;
GND
1059103494
Affiliation
Julius Kühn-Institute (JKI), Institute for Breeding Research on Horticultural and Fruit Crops, Germany
Schuster, Mirko;
Affiliation
Department of Horticulture, Michigan State University, East Lansing, MI, USA
Iezzoni, Amy F.;
Affiliation
Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA
van der Knaap, Esther

The Rosaceae Conserved Orthologous Set (RosCOS) provides a gene-based genome-wide set of markers that have been used in comparative analyses of peach (Prunus persica), apple (Malus × domestica), and strawberry (Fragaria spp.). In order to extend the use of these RosCOS to sweet cherry (Prunus avium L.), we identified markers that are polymorphic in breeding germplasm. Ninety-five percent (595/627) of previously designed RosCOS primer pairs amplified a product in six sweet cherry cultivars predicted to represent the range of genetic diversity in breeding germplasm. A total of 45% (282/627) RosCOS were polymorphic among the six cultivars, and allele number ranged from 2 to 6, with a genome-wide mean of 2.35. A subset of 92 genome-wide single nucleotide polymorphisms (SNPs) corresponding to 76 RosCOS was analyzed in 36 founder accessions and progeny. The expected and observed heterozygosity suggested that 83% of the RosCOS were in Hardy–Weinberg equilibrium, implying that most RosCOS behave as neutral markers. Principal coordinate analysis (PCO) identified one wild accession and two Spanish landraces that clustered differently from the other accessions. The relatively high number of unique alleles found in the three differentially clustered selections suggested that their use as parents has potential to increase the genetic diversity in future US-bred cultivars. Of the 92 RosCOS SNPs, 81 SNPs that represented 68 genome-wide RosCOS segregated in four mapping populations. These RosCOS were mapped in four F1 populations, thereby greatly improving the genetic linkage map of sweet cherry.

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