![]() ![]() Simultaneous genotyping of hundreds of thousands of SNPs in a single assay has become feasible due to innovative combinations of assay and array platform multiplexing. Alignment of the short NGS reads obtained from diverse and unrelated varieties to a reference genome allows the identification of large numbers of Single Nucleotide Polymorphisms (SNPs) and small Deletion/Insertion Polymorphisms (DIPs) and the contextual estimation of their minor allele frequencies (MAF). The growing number of draft genome sequences of many species coupled with Next Generation Sequencing (NGS) technologies has quickly changed the paradigm of plant genome analysis. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist.ĭissection of the genetic components underlying complex agricultural traits in plants has so far used mainly experimental bi-parental crosses and a limited number of genetic markers. ![]() AGL2009-07305 project and Consolider-Ingenio 2010 Program project (grant # CSD2007-00036) both funded by the Spanish Ministry of Science and Innovation ( ). ![]() European Union-funded project “FruitBreedomics: Integrated approach for increasing breeding efficiency in fruit tree crops" (Grant #FP7-265582 ). The work is made available under the Creative Commons CC0 public domain dedication.įunding: This work was funded by: United States Department of Agriculture's National Institute of Food and Agriculture - Specialty Crop Research Initiative project ( ), “RosBREED: Enabling marker-assisted breeding in Rosaceae" (Grant # 2009-51181-05808) Ministero delle Politiche Agricole Alimentari e Forestali -Italy (MiPAAF, ) through the project “DRUPOMICS: Sequenziamento del genoma del pesco ed utilizzo della sequenza in programmi di miglioramento della qualità del frutto del pesco e della resistenza alle malattie" (Grant # DM14999/7303/08). This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Received: JanuAccepted: MaPublished: April 20, 2012 PLoS ONE 7(4):Įditor: Rongling Wu, Pennsylvania State University, United States of America (2012) Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm. 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.Ĭitation: Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, et al. 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. ![]() 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. 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. 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. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. 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. 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 and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. ![]()
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