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 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.
Highlights
Plants are fundamental to continued life on this planet as they are the basis of food production and an essential part of the global ecosystem
Given the documented lack of genetic diversity within the cultivars of sweet cherry, it is important to understand the pedigree information regarding the five genotypes used in this study namely, ‘Bing’, ‘Sweetheart’, ‘Staccato’, ‘Glory’ and ‘Kimberly’
Three of the known sweet cherry cultivars used for analysis in this study belong to different self-incompatibility S-allele genotypes [45]
Summary
Plants are fundamental to continued life on this planet as they are the basis of food production and an essential part of the global ecosystem. Sweet cherry (Prunus avium L.) is a member of the Rosaceae family, which represents many other important crop species, including apple, peach, plum, almond, strawberry, raspberry and rose [7]. Despite an estimated genome size of 225–330 Mb [8,9], sweet cherry is lacking in genomic information in comparison with other prominent Rosaceae members, including peach and apple [10,11]. Linkage maps and molecular markers have been developed for sweet cherry [12] as well as peach and almond, two other members of the sub-family Prunoideae [13,14,15], and a comprehensive and advanced draft of the peach genome serves as the foundation for several comparative studies [10]. To advance diversity and genetics-related studies, efforts were made to evaluate the transferability of the molecular markers from one member of Rosaceae family to other members with mixed success [17,18,19]
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