Rosaceae conserved orthologous sequences marker polymorphism in sweet cherry germplasm and construction of a SNP-based map |
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Authors: | Antonio Cabrera Umesh R Rosyara Paolo De Franceschi Audrey Sebolt Suneth S Sooriyapathirana Elisabeth Dirlewanger Jose Quero-Garcia Mirko Schuster Amy F Iezzoni and Esther van der Knaap |
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Institution: | (1) Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA;(2) Department of Crop and Soil Science, Michigan State University, East Lansing, MI 48824, USA;(3) Department of Fruit Tree and Woody Plant Sciences, University of Bologna, Bologna, Italy;(4) Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA;(5) INRA-UR419, Unit? de Recherches sur les Esp?ces Fruiti?res, Centre de Bordeaux, 33140 Villenave d’Ornon, France;(6) Julius K?hn-Institut, Federal Centre for Cultivated Plants, PillnitzerPlatz 3a, 01326 Dresden, Germany |
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Abstract: | 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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