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Armillaria and Desarmillaria spp. are causal agents of a devastating root-borne disease of peach. Breeding resistant rootstock requires a reliable screening tool. An in vitro co-culture screen designed for almond was modified by replacing agar-gelled medium with a more aerated phenolic foam and combining resistant and susceptible rootstocks (i.e., common garden experiment) and minimizes variation in inoculum pressure or rooting substrate among replicate vessels. Eight Prunus rootstocks tested (peach, plum, peach × plum, and choke cherry) were rooted and had no decline in health. Susceptible peach rootstock, ‘GF 305’, was cultured for 15 wk in phenolic foam in the same vessel with a resistant peach × plum hybrid, ‘MP-29’, inoculated with Armillaria mellea at week 5, that led to more severe shoot symptoms in the former after an additional 8 wk. This method accommodated peach genotypes that were difficult to root in agar medium. The difference during a uniform challenge with the A. mellea fungus recapitulates resistant/susceptible reactions. The phenolic foam-based co-culture method will work on many Prunus spp. of potential use in rootstock breeding.

Variation in susceptibility of 28 Prunus rootstock genotypes to the causal agents of Armillaria root rot, Armillaria mellea, A. solidipes, and Desarmillaria tabescens, were studied by conducting in vitro root screening assays. Root segments with wounded and intact periderm were placed next to and on the top of the fungal cultures. At day 21, the percent success of fungal penetration and the circumferential and longitudinal lengths of fungal growth were measured. A parallel investigation using the inoculated root segments was carried out to characterize the active host defense mechanisms involved, including anatomical responses in bark and wood. Overall, the success of penetration and the longitudinal and circumferential spread of Armillaria spp. and D. tabescens were significantly different among various Prunus rootstock genotypes. None of the tested rootstock genotypes were completely resistant to infection. However, plum and plum derived rootstocks, and some of the cherry genotypes were less susceptible to infection compared to the peach genotypes. The host’s ability to limit infection by Armillaria spp. and D. tabescens was not limited to a single mechanism but appeared to be regulated by several collective nonspecific host responses acting together. Differential levels of a series of non-specific coordinated events were triggered in Prunus genotypes such as the formation of new callus tissue on the root surface, a colored reaction zone, necrophylactic periderm, new cells, and new vascular cambium to compartmentalize the pathogen. The host responses were elevated in the genotypes with low level of infection as compared to highly infected genotypes.

14 Pags.- 9 Figs.- 2 Tabls.- Supplementary information is available for this paper at https://doi.org/10.1038/s41598-020-58271-5. The dataset generated for this study is available in the NCBI-SRA database, BioProject number PRJNA489327. © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder., Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,382 high quality SNPs (MAF >0.05; missing data, This research was funded by CONICYT-REGIONAL/GORE O’HIGGINS/CEAF/R19A10003; FONDECYT 3160316; FONDECYT 1160706; CONICYT R16F20006; and the Spanish Ministry of Science, Innovation and Universities (MICINN) grants RFP2015-00019 and RTI2018-094176-R-C33, cofunded by FEDER.

BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica(L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F1low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet cherry, the fruticosa subgenome of sour cherry, and cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and the avium and the fruticosa subgenomes of sour cherry, respectively. For sweet cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in cherry.

Genetic control and location of QTLs associated with phytochemical compounds and fruit quality in peach [Prunus persica (L.) Batsch] were evaluated using an F2 mapping population (ZC2) derived from cross between ‘Zin Dai’ × ‘Crimson Lady’. Antioxidant capacity, accumulation of phenolic compounds (total phenolics, flavonoids, and anthocyanins), and fruit quality traits (fruit diameter, fruit weight, fruit firmness, soluble solids concentration, titratable acidity, and ripening index) were evaluated for 2 years (2013–2014). Fourteen QTLs for phytochemical and fruit quality traits were identified in 5 LGs, with two QTL clusters (qPC.ZC_5.1_2014 and qPC.ZC_7.1) observed on LGs 5 and 7. The QTL cluster qPC.ZC_5.1_2014 was associated with antioxidant capacity, flavonoids, anthocyanin content, and SSC, while qPC.ZC_7.1 exhibited association only with flavonoids and fruit ripening index. QTL clusters associated with different fruit quality traits were observed on LGs 1 and 6. Candidate gene analyses of the QTL cluster on LG5 (qPC.ZC_5.1_2014) revealed 14 candidate genes in peach with functional annotation related to biosynthesis pathway of phytochemical compounds.

BackgroundFruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica(L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time.ResultsPhenotypic data of seven F1low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40–46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles.ConclusionsA multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.

9 Pags.- 3 Figs.- 1 Tabl. The definitive version is available at: https://www.actahort.org/index.htm. Article from a original paper presented by the authors at IV International Symposium on Molecular Markers in Horticulture (March 7, 2017 - March 10, 2017), Modern plant breeding utilizes a large number of molecular markers for segregation analysis, gene mapping and marker discovery to facilitate marker-assisted selection (MAS). Genotyping-by-sequencing (GBS) is a cost-effective next-generation sequencing technology that provides a platform for detection of a large number of single nucleotide polymorphisms (SNPs) in a large sample pool. The Centro de Estudios Avanzados en Fruticultura (CEAF), located in Rengo, Región de O'Higgins, Chile, initiated a Prunus rootstock breeding program in 2010. Consequently, different interspecific crosses have been carried out utilizing the Prunus rootstock germplasm collection established at CEAF and available pollen obtained from Prunus rootstock germplasm of the Spanish Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC). In the present study, 53 diploid Prunus rootstocks and five scion cultivars were genotyped using GBS for genome-wide SNP identification, enabling the assessment of the genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,391 high-quality SNPs (minor allele frequency (MAF) GROTERDAN0.05; missing data, This research was funded by CONICYT-REGIONAL/GORE O’HIGGINS/CEAF/ R08I1001, FONDECYT 3160316, FONDECYT 1160706, and the Spanish Ministry of Economy and Competitiveness (MINECO) grants RFP2012-00020 and AGL2014-52063-R.

Genotyping by sequencing (GBS) is a flexible and cost-effective strategy for genome-wide SNP discovery and high-throughput genotyping. Here, we employed the GBS approach to explore population structure, genetic variability, and patterns of linkage disequilibrium (LD) among 220 peach genotypes (Prunus persica), representative of the Brazilian breeding germplasm. This selected panel is mainly composed by locally adapted peaches developed in mild winter and high relative humidity conditions, and represents a worldwide reference of peach germplasm for low-chilling areas. A total of 93,353 SNP markers were discovered, and after filtering, 18,373 high-quality SNPs were used in analyses. Thirty-four percent of selected SNPs were located in genic regions and about 70% of these in the coding sequence. Principal coordinate analysis (PCoA) and Bayesian clustering (fastSTRUCTURE) successfully detected population genetic structure in our germplasm panel, supporting the identification of three main distinct subpopulations. The distribution of the genotypes within subpopulations reflected their fruit-related traits: melting and non-melting flesh cultivars. LD patterns revealed a medium LD level in peach, with the extent of LD highly dependent on the subpopulation and genome regions. The use of GBS-SNPs to perform genome-wide association studies (GWAS) was also exploited by using phenotypic information from five fruit quality traits. The observed significant SNP-trait associations were always in the regions previously predicted by linkage and association mapping analysis, providing valuable insights to incorporate the use of marker-assisted selection in the breeding program.

High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation in ploidy levels can lead to spurious marker-locus-trait associations and incorrect origin assignment of alleles to individuals. High-throughput genotyping requires automated scoring, as manual inspection of thousands of scored loci is too time-consuming. However, automated SNP scoring can result in errors that should be corrected to ensure recorded genotypic data are accurate and thereby ensure confidence in downstream genetic analyses. To enable quick identification of errors in a large genotypic data set, we have developed a comprehensive workflow. This multiple-step workflow is based on inheritance principles and on removal of markers and individuals that do not follow these principles, as demonstrated here for apple, peach, and sweet cherry. Genotypic data was obtained on pedigreed germplasm using 6-9K SNP arrays for each crop and a subset of well-performing SNPs was created using ASSIsT. Use of correct (and corrected) pedigree records readily identified violations of simple inheritance principles in the genotypic data, streamlined with FlexQTL™ software. Retained SNPs were grouped into haploblocks to increase the information content of single alleles and reduce computational power needed in downstream genetic analyses. Haploblock borders were defined by recombination locations detected in ancestral generations of cultivars and selections. Another round of inheritance-checking was conducted, for haploblock alleles (i.e., haplotypes). High-quality genotypic data sets were created using this workflow for pedigreed collections representing the U.S. breeding germplasm of apple, peach, and sweet cherry evaluated within the RosBREED project. These data sets contain 3855, 4005, and 1617 SNPs spread over 932, 103, and 196 haploblocks in apple, peach, and sweet cherry, respectively. The highly curated phased SNP and haplotype data sets, as well as the raw iScan data, of germplasm in the apple, peach, and sweet cherry Crop Reference Sets is available through the Genome Database for Rosaceae.

Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry., A fruitful genomic resource Detailed genomic maps from the fruit-bearing trees of the Prunus genus should greatly accelerate the breeding of superior cultivars. These plants produce a variety of popular fruits, but until relatively recently, breeders had only limited genetic information with which to work. Pere Arús of Spain’s Institute of Agrifood Research and Technology and colleagues have now reviewed the rapid advances in Prunus genomics that have taken place since 2010, when researchers completed the first genome assembly for this genus. In the ensuing decade, increasingly high-quality genomes from the peach, Japanese apricot, and cherry have allowed scientists to home in on chromosomal regions associated with key traits such as fruit quality and disease resistance. These data also offer valuable genetic markers that agronomists can use to guide the production of healthier trees and more commercially desirable fruits.

It has recently been described that the Japanese plum "Santa Rosa" bud sport series contains variations in ripening pattern: climacteric, suppressed-climacteric and non-climacteric types. This provides an interesting model to study the role of ethylene and other key mechanisms governing fruit ripening, softening and senescence. The aim of the current study was to investigate such differences at the genomic level, using this series of plum bud sports, with special reference to genes involved in ethylene biosynthesis, signal transduction, and sugar metabolism. Genomic DNA, isolated from leaf samples of six Japanese plum cultivars ("Santa Rosa", "July Santa Rosa", "Late Santa Rosa", "Sweet Miriam", "Roysum", and "Casselman"), was used to construct paired-end standard Illumina libraries. Sequences were aligned to the Prunus persica genome, and genomic variations (SNPs, INDELS, and CNV's) were investigated. Results determined 12 potential candidate genes with significant copy number variation (CNV), being associated with ethylene perception and signal transduction components. Additionally, the Maximum Likelihood (ML) phylogenetic tree showed two sorbitol dehydrogenase genes grouping into a distinct clade, indicating that this natural group is well-defined and presents high sequence identity among its members. In contrast, the ethylene group, which includes ACO1, ACS1, ACS4, ACS5, CTR1, ERF1, ERF3, and ethylene-receptor genes, was widely distributed and clustered into 10 different groups. Thus, ACS, ERF, and sorbitol dehydrogenase proteins potentially share a common ancestor for different plant genomes, while the expansion rate may be related to ancestral expansion rather than species-specific events. Based on the distribution of the clades, we suggest that gene function diversification for the ripening pathway occurred prior to family extension. We herein report all the frameshift mutations in genes involved in sugar transport and ethylene biosynthesis detected as well as the gene CNV implicated in ripening differences.

Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars ‘Zin Dai’ and ‘Crimson Lady’ (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae., This project was supported in part by the USDA-NIFA-Specialty Crop Research Initiative project, RosBREED: Enabling marker-assisted breeding in Rosaceae (2009-51181-05808) to KG, and RosBREED 2: Combining disease resistance with horticultural quality in new rosaceous cultivars (2014-51181-22378) to KG. The Spanish Ministry of Economy and Competitiveness (project RTA2015-00050-00-00, Severo Ochoa Program for Centres of Excellence in R&D 201-2019 (SEV-2015-0533) and CERCA Programme-Generalitat de Catalunya). This work was in part supported by the Ministero delle Politiche Agricole Alimentari e Forestali (MiPAAF, Italy) through the projects DRUPOMICS (grant DM14999/7303/08), and 'MAS.PES: apricot and peach breeding by molecular-assisted selection' a project funded by private and public agencies.

Blush, the proportion of red overcolor on the skin surface of fruit, is highly variable in peach breeding germplasm and is important in the marketing of peach fruit. The fresh market peach industry demands a high level of blush to entice consumers, while the processing peach industry requires minimal blush. Therefore, blush is a major selection criterion in breeding programs. The use of DNA-based information could improve breeding efficiency and accuracy for fruit blush coverage, but a predictive DNA test is required. The objective of this study was to develop a DNA test for the prediction of blush coverage by targeting the major locus, R f , associated with blush variation. Initially, haplotypes were developed based on five SNP markers associated with variation in blush coverage. To convert the 5-SNP haplotype test into a single, simple PCR-based assay, 11 simple sequence repeat markers were designed and used to screen individuals representing all SNP haplotypes. The most informative assay, named Ppe-Rf-SSR, was chosen to screen 200 individuals of the RosBREED peach reference germplasm set that incorporated germplasm from four breeding programs. Ppe-Rf-SSR accurately differentiated individuals with high-, medium-, and low-blush coverage in most lineages. Outcomes highlighted that DNA tests can be quite predictive for some breeding programs or specific germplasm sets, while for others the predictiveness can falter. Therefore, the confirmation of genotype effects for any DNA test is recommended in new germplasm before routine use. The prediction accuracy and breeding utility of Ppe-Rf-SSR in the University of Arkansas breeding program were subsequently confirmed by screening 443 seedlings, independent of the initial DNA test development process, derived from 18 cross-combinations of 28 parents. Ppe-Rf-SSR can be used to efficiently and accurately predict fruit blush coverage, especially in fresh market germplasm, and has been deployed for routine use in the University of Arkansas peach breeding program.

The narrow genetic base of peach (Prunus persica L. Batsch) challenges efforts to accurately dissect the genetic architecture of complex traits. Standardized phenotypic assessment of pedigree-linked breeding germplasm and new molecular strategies and analytical approaches developed and conducted during the RosBREED project for enabling marker-assisted breeding (MAB) in Rosaceae crops has overcome several aspects of this challenge. The genetic underpinnings of fruit size (fruit equatorial diameter (FD)) and weight (fresh weight (FW)), two most important components of yield, were investigated using the pedigree-based analysis (PBA) approach under a Bayesian framework which has emerged as an alternative strategy to study the genetics of quantitative traits within diverse breeding germplasm across breeding programs. In this study, a complex pedigree with the common founder “Orange Cling” was identified and FD and FW data from 2011 and 2012 analyzed. A genetic model including genetic additive and dominance effects was considered, and its robustness was evaluated by using various prior and initial values in the Markov chain Monte Carlo procedure. Five QTLs were identified which accounted for up to 29 and 17 % of the phenotypic variation for FD and FW, respectively. Additionally, genomic breeding values were obtained for both traits, with accuracies >85 %. This approach serves as a model study for performing PBA across diverse pedigrees. By incorporating multiple breeding programs, the method and results presented support and highlight the ability of this strategy to identify genomic resources as targets for DNA marker development and subsequent MAB within each program.

The complete genome sequences of apple, peach, and diploid strawberry - one member of each of the three main fruit-producing branches of the Rosaceae tree - were available in 2010. Despite this achievement, virtually none of this genomics knowledge was being used to assist breeding efforts of these crops. Four years later, this gap has been bridged, with genetic information routinely used in many US apple, peach, and cherry breeding programs. For example, DNA tests predict apple crispness, peach maturity date, and cherry fruit size, enabling breeders to determine the best parents to combine and the best seedlings to advance. This application significantly reduces the wasted effort to eliminate entirely poor families and reduces the costs to grow and evaluate thousands of seedlings genetically destined to have unacceptable fruit quality or maturity date. This achievement was enabled by international community efforts, including the RosBREED project, funded by the USDA-National Institute of Food and Agriculture Specialty Crop Research Initiative (SCRI). DNA tests are now applied for high-value attributes where the targeted loci explain a large proportion of the trait variation. However, limitations to widespread adoption of these predictive tests still exist. Some limitations are due to lack of knowledge, such as an understanding of genotype by environment (G×E) interactions and loci associated with variation for other valuable attributes. Technical limitations include streamlined phasing of alleles from multiple families of pedigree-connected breeding germplasm and access to suitable commercial service providers.

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., 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.politicheagricole.it) 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). 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/).