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

Diego Micheletti (1) , Maria Teresa Dettori (2) , Sabrina Micali (2) , Valeria Aramini (2) , Igor Pacheco (3) , Cassia da Silva Linge (3) , Stefano Foschi (4) , Elisa Banchi (5) , Teresa Barreneche (6) , Bénédicte Quilot-Turion (7) , Patrick Lambert (7) , Thierry Pascal (7) , Iglesias Ignasi (8) , Joachim Carbo (9) , Li-Rong Wang (10) , Rui-Juan Ma (11) , Xiongwei Li (3) , Zhong-Shan Gao (12) , Nelson Nazzicari (13) , Michela Troggio (5) , Danièle Bassi (3) , Laura Rossini (3, 13) , Ignazio Verde (2) , Francois Laurens (14) , Pere Arús (1) , Maria José Aranzana (1)

1 Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB
2 Centro di Ricerca per la Frutticoltura
3 DISAA
4 CRPV - Centro Ricerca Produzione Vegetale
5 Fondazione Edmund Mach (FEM)
6 BFP - Biologie du fruit et pathologie
7 GAFL - Génétique et Amélioration des Fruits et Légumes
8 Estació Experimental de Lleida
9 Estacio Experimental Mas Badia
10 Zhenzhou Fruit Research Institute
11 Horticultural Institute
12 Department of Horticulture
13 Parco Tecnologico Padano
14 IRHS - Institut de Recherche en Horticulture et Semences

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 program

Domaines: Sciences agricoles; Biologie végétale

Diego Micheletti, Maria Teresa Dettori, Sabrina Micali, Valeria Aramini, Igor Pacheco, et al.. Whole-genome analysis of diversity and SNP-major gene association in peach germplasm. PLoS ONE, 2015, 10 (9), 19 p. ⟨10.1371/journal.pone.0136803⟩. ⟨hal-01210020⟩