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Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm
Verde, Ignazio (Centro di Ricerca per la Frutticoltura (Roma))
Bassil, Nahla (United States Department of Agriculture. National Clonal Germplasm Repository)
Scalabrin, Simone (Istituto di Genomica Applicata)
Gilmore, Barbara (United States Department of Agriculture. National Clonal Germplasm Repository)
Lawley, Cynthia T. (Illumina Inc. (California))
Gasic, Ksenija (Clemson University. School of Agricultural, Forest and Environmental Sciences)
Micheletti, Diego (Centre de Recerca en Agrigenòmica)
Rosyara, Umesh R. (Michigan State University. Department of Horticulture)
Cattonaro, Federica (Istituto di Genomica Applicata)
Vendramin, Elisa (Centro di Ricerca per la Frutticoltura (Roma))
Main, Dorrie (Washington State University. Department of Horticulture & Landscape Architecture)
Aramini, Valeria (Centro di Ricerca per la Frutticoltura (Roma))
Blas, Andrea L. (Centre de Recerca en Agrigenòmica)
Mockler, Todd C. (The Donald Danforth Plant Science Center)
Bryant, Douglas W. (The Donald Danforth Plant Science Center)
Wilhelm, Larry (Oregon Health Sciences University)
Troggio, Michela (The Istituto Agrario di San Michele all'Adige)
Sosinski, Bryon (North Carolina State University. Department of Horticultural Science)
Aranzana, Maria José (Centre de Recerca en Agrigenòmica)
Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica)
Iezzoni, Amy (Michigan State University. Department of Horticulture)
Morgante, Michele (Istituto di Genomica Applicata)
Peace, Cameron (Washington State University. Department of Horticulture & Landscape Architecture)

Date: 2012
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.
Abstract: 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.
Grants: European Commission 265582
Ministerio de Economía y Competitividad AGL2009-07305
Ministerio de Ciencia e Innovación CSD2007-00036
Rights: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Language: Anglès
Document: Article ; recerca ; Versió publicada
Published in: PloS one, Vol. 7, issue 4 (April 2012) , e35668, ISSN 1932-6203

DOI: 10.1371/journal.pone.0035668
PMID: 22536421

13 p, 1.2 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles

 Record created 2017-11-06, last modified 2022-03-24

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