Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species

Aliki Xanthopoulou,Filippos Aravanopoulos,Chrysanthi Polychroniadou,Evangelos Karagiannis,Konstantinos Kazantzis,Antonios Zambounis,Panagiotis Madesis,Athanassios Molassiotis,Maria Manioudaki,Ioannis Ganopoulos,Christos Bazakos,Christos Kissoudis,Athanasios Tsaftaris,Anna-Maria Farsakoglou,Michail Michailidis

doi:10.1038/s41438-020-0281-9

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.

Highlights

Introduction Prunus aviumL. (Rosaceae), is a fruit crop with growing agronomic and economical importance
For crops or species that are propagated clonally, synonymous single nucleotide polymorphism (SNP) are outnumbered by non-synonymous SNPs, while the opposite is more commonly met in wild species[34]
Our results indicate that NLR genes are promising resources for breeding broad-spectrum resistance as it was previously mentioned[54,55]. This is the first report of whole genome genetic variation characterization between sweet cherry cultivars

Summary

Introduction

L. (Rosaceae), is a fruit crop with growing agronomic and economical importance. Sweet cherries exhibit important phenotypic variation in fruit size, shape, color, sugar content, flowering time and other agronomic traits such as defense reactions against pathogens[3]. The deeper study and characterization of sweet cherry genetic diversity as well as the identification of genes controlling traits of interest will be a key factor for sweet cherry breeding. Greece contains high rates of genetic diversity, many of local traditional landraces have been lost over years of evolution[2]. In Greece, various studies of molecular diversity, of modern cherry varieties, have been conducted using SSR markers, revealing their extensive genetic basis, a valuable finding that has been extensively used in breeding programs[2,5]. Whole Genome ReSequencing and other such techniques are the springboard for the discovery of allelic and genomic richness

Methods

Results

Conclusion