title: Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus aviumL.).
abstract: Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus aviumL.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.
authors.affiliation: Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States.
authors.forename: Seanna
authors.initials: S
authors.lastname: Hewitt
authors.affiliation: Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kilian
authors.affiliation: Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States.
authors.forename: Ramyya
authors.initials: R
authors.lastname: Hari
authors.affiliation: Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States.
authors.forename: Tyson
authors.initials: T
authors.lastname: Koepke
authors.affiliation: Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States.
authors.forename: Richard
authors.initials: R
authors.lastname: Sharpe
authors.affiliation: Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States.
authors.forename: Amit
authors.initials: A
authors.lastname: Dhingra
keywords: Genetic diversity; Next-generation sequencing; Polymorphisms; Prunus avium; Reduced representation sequencing; SNParray; Target region amplification polymorphism (TRAP); Whole genome sequencing (WGS)