Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm
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Author
Micheletti, Diego
Dettori, Maria Teresa
Micali, Sabrina
Aramini, Valeria
Pacheco, Igor
Linge, Cassia Da Silva
Foschi, Stefano
Banchi, Elisa
Barreneche, Teresa
Quilot-Turion, Bénédicte
Lambert, Patrick
Pascal, Thierry
Wang, Li-rong
Ma, Rui-juan
Li, Xiong-wei
Gao, Zhong-shan
Nazzicari, Nelson
Troggio, Michela
Bassi, Daniele
Rossini, Laura
Verde, Ignazio
Laurens, François
Publication date
2015-09-09ISSN
1932-6203
Abstract
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European
and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern
breeding programs.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
19
Publisher
Public Library of Science
Is part of
PLoS ONE
Citation
Micheletti, Diego, Maria Teresa Dettori, Sabrina Micali, Valeria Aramini, Igor Pacheco, Cassia Da Silva Linge, and Stefano Foschi et al. 2015. "Whole-Genome Analysis Of Diversity And SNP-Major Gene Association In Peach Germplasm". PLOS ONE 10 (9): e0136803. doi:10.1371/journal.pone.0136803.
Grant agreement number
EC/FP7/265582/EU/Integrated approach for increasing breeding efficiency in fruit tree crops/FRUIT BREEDOMICS
MINECO/Programa Nacional de Proyectos de Investigación Fundamental/AGL2012-40228-C02-01/ES/Uso de la secuencia genomica para la caracterizacion de la variabilidad intraclonal e interespecifica en Melocotonero y almendro/
INIA/Programa Nacional de Proyectos de Investigación Fundamental/RF2012-00024-C04-04/ES/Conservación y caracterización de germoplasma de melocotonero introducido/
Program
Fructicultura
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2651]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/