title: Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm.
abstract: Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs.The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.
authors.affiliation: CRA - Fruit Tree Research Center, Rome, Italy. ignazio.verde@entecra.it
authors.forename: Ignazio
authors.initials: I
authors.lastname: Verde
authors.forename: Nahla
authors.initials: N
authors.lastname: Bassil
authors.forename: Simone
authors.initials: S
authors.lastname: Scalabrin
authors.forename: Barbara
authors.initials: B
authors.lastname: Gilmore
authors.forename: Cynthia T
authors.initials: CT
authors.lastname: Lawley
authors.forename: Ksenija
authors.initials: K
authors.lastname: Gasic
authors.forename: Diego
authors.initials: D
authors.lastname: Micheletti
authors.forename: Umesh R
authors.initials: UR
authors.lastname: Rosyara
authors.forename: Federica
authors.initials: F
authors.lastname: Cattonaro
authors.forename: Elisa
authors.initials: E
authors.lastname: Vendramin
authors.forename: Dorrie
authors.initials: D
authors.lastname: Main
authors.forename: Valeria
authors.initials: V
authors.lastname: Aramini
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Blas
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Bryant
authors.forename: Larry
authors.initials: L
authors.lastname: Wilhelm
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.forename: Bryon
authors.initials: B
authors.lastname: Sosinski
authors.forename: Maria José
authors.initials: MJ
authors.lastname: Aranzana
authors.forename: Pere
authors.initials: P
authors.lastname: Arús
authors.forename: Amy
authors.initials: A
authors.lastname: Iezzoni
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Cameron
authors.initials: C
authors.lastname: Peace
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D005787:Gene Frequency; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing; D007391:International Cooperation; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D027861:Prunus / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers