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Article|01 May 2020|OPEN
Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species
Aliki Xanthopoulou1, Maria Manioudaki1, Christos Bazakos2, Christos Kissoudis3, Anna-Maria Farsakoglou4, Evangelos Karagiannis1, Michail Michailidis1, Chrysanthi Polychroniadou1, Antonios Zambounis5, Konstantinos Kazantzis5, Athanasios Tsaftaris3, Panagiotis Madesis6, Filippos Aravanopoulos4, Athanassios Molassiotis1 & Ioannis Ganopoulos2,
1Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki 570001, Greece
3Perrotis College, American Farm School, Thessaloniki GR-57001, Greece
4Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
5Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Department of Deciduous Fruit Growing, Naoussa 59035, Greece
6Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece

Horticulture Research 7,
Article number: 20060 (2020)
doi: 10.1038/hortres.2020.60
Views: 294

Received: 11 Nov 2019
Revised: 17 Jan 2020
Accepted: 18 Feb 2020
Published online: 01 May 2020

Abstract

Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of ‘Satonishiki’ cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.