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Title: Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of fruit species
Authors: Xanthopoulou, Aliki
Manioudaki, Maria
Bazakos, Christos
Kissoudis, Christos
Farsakoglou, Anna-Maria
Karagiannis, Evangelos
Michailidis, Michail
Polychroniadou, Chrysanthi
Zambounis, Antonios
Kazantzis, Konstantinos
Tsaftaris, Athanasios
Madesis, Panagiotis
Aravanopoulos, Filippos
Molassiotis, Athanassios
Ganopoulos, Ioannis
Subjects LC: Genomics
Cherry - Varieties
Keywords: Prunus avium L.
Sweet cherry cultivars
Cherry genotypes
Issue Date: 1-May-2020
Publisher: Springer Nature
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.
Length: 14 pages
Type: Journal Article
Relation (Part Of): Horticulture Research journal
Publication Status: Published
Citation: Xanthopoulou, A, Manioudaki, M, Bazakos, C, Kissoudis, C, Farsakoglou, A-M, Karagiannis, E, Michailidis, M, Polychroniadou, C, Zambounis, A, Kazantzis, K, Tsaftaris, A, Madesis, P, Aravanopoulos, F, Molassiotis, A, & Ganopoulos, I 2020, 'Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species', Horticulture Research, vol. 7, no.60, pp. 1-14.
Restrictions: Attribution 4.0 International
Language: en_US
Appears in Collections:Journal Articles

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