Whole-genome analysis of diversity and SNP-major gene association in peach germplasm

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.
This work has been funded by the EU seventh Framework Programme (http://ec.europa.eu/research/fp7/index_en.cfm) through the project “FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops” (Grant #FP7- 265582; http://fruitbreedomics.com/); by the Ministero delle Politiche Agricole Alimentari e Forestali -Italy (MiPAAF, http://www.politicheagricole.it) through the project ‘‘DRUPOMICS: Sequenziamento del genoma del pesco ed utilizzo della sequenza in programmi di miglioramento della qualita` del frutto del pesco e della resistenza alle malattie’’ (Grant # DM14999/7303/08) and “ESPLORA: Esplorazione della biodiversità vegetale ed animale alla ricerca di alleli superiori da inserire nei programmi avanzati di miglioramento genetico a sostegno dell’agricoltura nazionale” (Grant #DM 14658/7303/10); by the Spanish Ministry of Science and Innovation (http://www.micinn.es/) through the project AGL2012-40228-C02-01 (uso de la secuencia genomica para la caracterizacion de la variabilidad intraclonal e interespecifica en Melocotonero y almendro) and by the INIA (http://www.inia.es/) through the Project RF2012-00024-C04-04 (“conservación y caracterización de germoplasma introducido”).