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.
IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.
Diego
D
Micheletti
Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy.
Maria Teresa
MT
Dettori
Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy.
Sabrina
S
Micali
Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy.
Valeria
V
Aramini
Università degli Studi di Milano, DiSAA, Milan, Italy.
Igor
I
Pacheco
Università degli Studi di Milano, DiSAA, Milan, Italy.
Cassia
C
Da Silva Linge
Centro Ricerche Produzioni Vegetali, Cesena (FC), Italy.
Stefano
S
Foschi
Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy.
Elisa
E
Banchi
INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France; Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France.
Teresa
T
Barreneche
INRA UR1052 GAFL, Domaine Saint Maurice, Montfavet, France.
Bénédicte
B
Quilot-Turion
INRA UR1052 GAFL, Domaine Saint Maurice, Montfavet, France.
Patrick
P
Lambert
INRA UR1052 GAFL, Domaine Saint Maurice, Montfavet, France.
Thierry
T
Pascal
IRTA, Estació Experimental de Lleida, Parc de Gardeny, Edifici Fruitcentre, Lleida, Spain.
Ignasi
I
Iglesias
IRTA, Estacio Experimental Mas Badia, La Tallada d'Empordà, Girona, Spain.
Joaquim
J
Carbó
Zhenzhou Fruit Research Institute, CAAS, Zhengzhou, China.
Li-Rong
LR
Wang
Horticultural Institute, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
Rui-Juan
RJ
Ma
Department of Horticulture, Zhejiang University, Hangzhou, China.
Xiong-Wei
XW
Li
Department of Horticulture, Zhejiang University, Hangzhou, China.
Zhong-Shan
ZS
Gao
Parco Tecnologico Padano, Lodi, Italy.
Nelson
N
Nazzicari
Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy.
Michela
M
Troggio
Università degli Studi di Milano, DiSAA, Milan, Italy.
Daniele
D
Bassi
Università degli Studi di Milano, DiSAA, Milan, Italy; Parco Tecnologico Padano, Lodi, Italy.
Laura
L
Rossini
Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy.
Ignazio
I
Verde
INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France; Université d'Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France; AgroCampus-Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, Angers, France.
François
F
Laurens
IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.
Pere
P
Arús
IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.
Maria José
MJ
Aranzana
D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D000068239:Prunus persica / Q000235:genetics*