Correction: Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm
Year: 2012
Type: erratum
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 markerassisted 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 InfiniumH 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 GoldenGateH 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.
Source: PLoS ONE
Authors: Ignazio Verde, Nahla Bassil, Simone Scalabrin, Barbara Gilmore, Cynthia T. Lawley, Ksenija Gasic, Diego Micheletti, Umesh R. Rosyara, Federica Cattonaro, Elisa Vendramin, Dorrie Main, Valeria Aramini, Andrea L. Blas, Todd C. Mockler, Douglas W. Bryant, Larry Wilhelm, Michela Troggio, Bryon Sosinski, Maria José Aranzana, Pere Arús, Amy Iezzoni, Michele Morgante, Cameron Peace
Institutions: Agricultural Research Service, United States Department of Agriculture, National Clonal Germplasm Repository, Istituto di Genomica Applicata, Illumina (United States), Clemson University, Universitat Autònoma de Barcelona, Consejo Superior de Investigaciones Científicas, Center for Research in Agricultural Genomics, Michigan State University, Washington State University, Oregon State University, Donald Danforth Plant Science Center, Oregon Health & Science University, Fondazione Edmund Mach, North Carolina State University, University of Udine
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $2,382
OpenAlex ID: W4233903858