Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.)

Seanna Hewitt; Benjamin Kilian; Ramyya Hari; Tyson Koepke; Richard Sharpe; Amit Dhingra

doi:10.1016/j.csbj.2017.03.002

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Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.)

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Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.)

Seanna Hewitt, Benjamin Kilian, Ramyya Hari, Tyson Koepke, Richard Sharpe and Amit Dhingra

Computational and structural biotechnology journal, Vol.15, pp.290-298

2017

DOI: https://doi.org/10.1016/j.csbj.2017.03.002

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https://hdl.handle.net/2376/100946

PMCID: PMC5376269

PMID: 28392892

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https://doi.org/10.1016/j.csbj.2017.03.002View

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Abstract

Target region amplification polymorphism (TRAP)

Next-generation sequencing

SNParray

Prunus avium

Genetic diversity

Whole genome sequencing (WGS)

Polymorphisms

Reduced representation sequencing

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 avium L.) 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.

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Title: Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.)
Creators: Seanna Hewitt - Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States
Benjamin Kilian - Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States
Ramyya Hari - Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
Tyson Koepke - Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States
Richard Sharpe - Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States
Amit Dhingra - Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States
Publication Details: Computational and structural biotechnology journal, Vol.15, pp.290-298
Academic Unit: Crop and Soil Sciences, Department of; Horticulture, Department of
Publisher: Elsevier B.V
Identifiers: 99900546528201842
Language: English
Resource Type: Journal article