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Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm

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https://ir.library.oregonstate.edu/concern/articles/fq977v46s

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  • Correction 21 Jun 2012: Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, et al. (2012) Correction: Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm. PLOS ONE 7(6): 10.1371/annotation/33f1ba92-c304-4757-91aa-555de64a0768.
  • 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.
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  • Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, et al. (2012) Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm. PLoS ONE 7(4): e35668. doi:10.1371/journal.pone.0035668
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  • 7
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  • 4
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  • This work was funded by: United States Department of Agriculture’s National Institute of Food and Agriculture - Specialty Crop Research Initiative project (http://www.csrees.usda.gov/fo/specialtycropresearchinitiative.cfm), ‘‘RosBREED: Enabling marker-assisted breeding in Rosaceae’’ (Grant # 2009-51181-05808); Ministero delle Politiche Agricole Alimentari e Forestali -Italy (MiPAAF, http://www.politiche agricole.it) through the project ‘‘DRUPOMICS: Sequenziamentodel genoma del pesco ed utilizzo della sequenza in programmi di miglioramento della qualita` del frutto del pesco e della resistenza alle malattie’’ (Grant # DM14999/7303/08). European Union-funded project "FruitBreedomics: Integrated approach for increasing breeding efficiency in fruit tree crops" (Grant #FP7-265582; http://fruitbreedomics.com/; http://ec.europa.eu/research/fp7/index_en.cfm). AGL2009-07305 project and Consolider-Ingenio 2010 Program project (grant # CSD2007-00036) both funded by the Spanish Ministry of Science and Innovation (http://www.micinn.es/).
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