Angel Fernandez i Marti 1, B. Athanson2 , T. Koepke3, C. Font i Forcada4, Amit Dhingra3 and Nnadozie Oraguzie3

Genetic diversity and relatedness of sweet cherry (Prunus avium L.) cultivars based on

single nucleotide polymorphic (SNP) markers

A total of 110 and 103 sweet cherry cultivars were used for the SNP and SSR study, respectively. A hundred SNP primers were used initially to screen a panel of 30 sweet cherry

cultivars of which 40 SNP that showed polymorphism were chosen for screening all germplasm (110). Additionally, seven SSR were used in this experiment to screen 103

accessions of sweet cherry in order to be compared with the dendrogram generated using SNPs.

SNP-PCR amplifications were performed on a LightCycler® 480 Real-Time PCR and the polymorphism was scored based on the melting temperature (Tm) of each accession. SSR

were amplified through PCR and detected on an ABI PRISM 3130 .

There is about 75% similarity between the dendrogram from both SNPs and SSRs. We observed in both cases, that the cultivars were grouped into three main clusters, with the

second cluster sub-divided into additional subgroups. The observed heterozygosity obtained with SNPs and SSRs were similar; 0.40 vs. 0.44.

SNPs were able to distinguish sport mutants from their wild type germplasm. For example, ‘Stella’ was separated from ‘Compact Stella’. This demonstrates the greater power of

SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a

manner consistent with their pedigree relationships. We would recommend the use of SNPs for genetic fingerprinting, parentage verification, gene mapping and study of genetic

diversity in sweet cherry.

.

Most published genetic studies in cherry have typically been based on microsatellite (SSR) markers. However, one

major limitation of SSR markers is the high cost of the fluorescent labels which renders the assay costly and unaffordable for

small scale studies.

1Plant Beeding & Genomics Department, Parque Científico Tecnológico Aula Dei (PCTAD), Zaragoza, Spain * afernandez@pctad.com 2 Washington State University Irrigated Agriculture Research and Extension Centre, Prosser WA 99350, USA 3Deparment of Horticulture and Landscape Architecture, Washington State University, Pullman, USA 4Departamento de Pomología (CSIC), Zaragoza ,Spain

Single nucleotide polymorphism (SNP) markers are gaining popularity as valuable and efficient molecular markers due to their abundance in

plant genomes. They can be used as genetic markers in many applications such as cultivar identification, construction of genetic maps, assessment

of genetic diversity or marker-assisted breeding. Furthermore, the identification of SNPs and INDELs has been simplified by the recent

developments in sequencing technology.

The use of next-generation sequencing technologies for SNP discovery and characterization is being demonstrated in large-scale plant studies,

which are then used to generate genotyping tools for breeding applications. Such SNPs developed in sweet cherry through 3’ UTR sequencing on a

GS 454 platinum platform have been made available for analyzing genetic variation and relationships in sweet cherry and in the current study it will

be validated for use as consistent and reliable genetic marker for establishing genetic identity, parentage verification, study of genetic diversity and

gene mapping.

SNP SSR

vs