Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars.

Elisabeth Dirlewanger,Nabil Girollet,José Antonio Campoy,Rémi Beauvieux,José Quero-García,Teresa Barreneche,Hélène Christmann,Emilie Lerigoleur-Balsemin

doi:10.1186/s12870-016-0712-9

Abstract

BackgroundDepiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a ‘core collection’ suitable for association genetic studies in sweet cherry.ResultsA total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A ‘core collection’ containing 156 accessions was selected using the maximum length sub tree method.ConclusionThe present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA’s Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0712-9) contains supplementary material, which is available to authorized users.

Highlights

Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources
Single Nucleotide Polymorphism (SNP) markers were LD pruned before performing Principal Coordinate Analysis (PCoA) and STRUCTURE analysis to avoid bias using PLINK [30]
We provide estimations of linkage disequilibrium, genetic structure using different approaches and the definition of a first French National Institute for Agricultural Research (INRA)’s Sweet Cherry core collection

Summary

Introduction

Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. In Europe, sweet cherry, the cultivated form of P. avium, is grown in large areas. Sweet cherry was probably domesticated in the Prunus avium area of origin but the hypothesis of several different domestication events from different wild populations cannot be discarded [4]. First cultivated in Greece [5], sweet cherry was later spread all over Europe. The economic and social status of cherries has changed in European societies between classical and medieval times [8]. These fruits played an important social role in the medieval elite diet regime [9] before becoming a more common fruit during the later centuries [8, 10]

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