Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm

• Published in: PloS one 2015-09, Vol.10 (9), p.e0136803-e0136803
• Main Authors: Micheletti, Diego, Dettori, Maria Teresa, Micali, Sabrina, Aramini, Valeria, Pacheco, Igor, Da Silva Linge, Cassia, Foschi, Stefano, Banchi, Elisa, Barreneche, Teresa, Quilot-Turion, Bénédicte, Lambert, Patrick, Pascal, Thierry, Iglesias, Ignasi, Carbó, Joaquim, Wang, Li-Rong, Ma, Rui-Juan, Li, Xiong-Wei, Gao, Zhong-Shan, Nazzicari, Nelson, Troggio, Michela, Bassi, Daniele, Rossini, Laura, Verde, Ignazio, Laurens, François, Arús, Pere, Aranzana, Maria José
• Format: Article
• Language: English
• Subjects: Agricultural sciences; Biodiversity; Bioinformatics; Breeding; Chromosome Mapping; Chromosomes, Plant; Consortia; Data collection; Diagnostic systems; Domestication; Fruits; Gene pool; Genetic aspects; Genetic diversity; Genetic variability; Genetic Variation; Genome, Plant; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Genotype; Genotype & phenotype; Germplasm; Haplotypes; Horticulture; Life Sciences; Linkage analysis; Linkage disequilibrium; Marker-assisted selection; Morphology; Myzus persicae; Parents; Peaches; Phenotype; Phylogeny; Physiological aspects; Polymorphism, Single Nucleotide; Population structure; Population studies; Populations; Prunus; Prunus persica; Prunus persica - genetics; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies; Variability; Vegetal Biology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0136803

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.