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

Publication Overview
TitleGenetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars
AuthorsCampoy JA, Lerigoleur-Balsemin E, Christmann H, Beauvieux R, Girollet N, Quero-García J, Dirlewanger E, Barreneche T
TypeJournal Article
Journal NameBMC plant biology
Volume16
Issue1
Year2016
Page(s)49
CitationCampoy JA, Lerigoleur-Balsemin E, Christmann H, Beauvieux R, Girollet N, Quero-García J, Dirlewanger E, Barreneche T. Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars. BMC plant biology. 2016; 16(1):49.

Abstract

BACKGROUND
Depiction 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.

RESULTS
A 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.

CONCLUSION
The 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.

Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN1471-2229
eISSN1471-2229
Publication Date2016
Journal AbbreviationBMC Plant Biol.
DOI10.1186/s12870-016-0712-9
Elocation10.1186/s12870-016-0712-9
Journal CountryEngland
Language Abbreng
Publication TypeJournal Article
LanguageEnglish
Cross References
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DatabaseAccession
PMID: PubMedPMID:26912051