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.
Highlights
Dissection 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
The accessions were founders, intermediate ancestors, and important breeding parents used in international peach breeding programs, chosen both for the significance of their contribution to breeding germplasm according to pedigree records, and for genetic diversity based upon relatedness estimates from simple sequence repeats (SSRs) studies [21], [14], (Verde I. unpublished data)
single nucleotide polymorphism (SNP) detection A total of 25.4 Gb of DNA sequence (111.76 coverage of the peach genome) was obtained from 279.7 million reads (Illumina and 454) generated for the 56 peach accessions multiplexed among 12 pools (Table 1)
Summary
Dissection 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. Illumina’s InfiniumH BeadArray Technology platform is an extremely high-throughput SNP genotyping system that allows the detection of up to 2.5 million SNPs per single DNA sample [2]. Multiplex SNP genotyping enables cost effective marker-assisted selection strategies, whole genome fingerprinting, genome-wide association studies (GWAS), map-based gene cloning and population-based analyses. The availability of such tools fosters the application of GWAS in plants and animals [3], [4], [5], [6] and provides the opportunity to apply genomic selection (GS) methods to agricultural species, including Prunus. High-density SNP genotyping arrays have been designed for several domestic animals including cattle [3], pig [4] and chicken [5]; arrays are being developed in several plant species including apple [6], maize, tomato, and cherry (http://www.illumina.com/agriculture)
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