Identification of Pyrus Single Nucleotide Polymorphisms (SNPs) and Evaluation for Genetic Mapping in European Pear and Interspecific Pyrus Hybrids

We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear (‘Old Home’בLouise Bon Jersey’) and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality

Apple, from genome to breeding

Genome resources for apple (Malus×domestica Borkh), the main fruit crop of temperate regions, have been developed over the past 10 years, culminating in the sequencing of the ‘Golden Delicious’ genome. The apple genome sequence anchored to a high-density linkage map provides the apple community with new tools to identify genes and other functional elements that will enable the study of the evolution of plant genome structure, as well as facilitating genomic-assisted breeding. Transcriptomics, proteomics and metabolomics studies are greatly benefiting from the availability of an annotated genome. In this review, we report on the status of the apple genome and on current molecular and genetic tools available in apple that will improve the efficiency of the process of cultivar development; we discuss how an integrative ‘omics’ approach could greatly enhance the understanding of biological processes that determine agronomically and economically favorable phenotypes; we review the databases and bioinformatics tools that are available to manage and exploit the large amounts of biological data generated for apple and other plant genome

Apple, from genome to breeding

Genome resources for apple (Malus  7 domestica Borkh), the main fruit crop of temperate regions, have been developed over the past 10 years, culminating in the sequencing of the \u2018Golden Delicious\u2019 genome. The apple genome sequence anchored to a high-density linkage map provides the apple community with new tools to identify genes and other functional elements that will enable the study of the evolution of plant genome structure, as well as facilitating genomic-assisted breeding. Transcriptomics, proteomics and metabolomics studies are greatly benefiting from the availability of an annotated genome. In this review, we report on the status of the apple genome and on current molecular and genetic tools available in apple that will improve the efficiency of the process of cultivar development; we discuss how an integrative \u2018omics\u2019 approach could greatly enhance the understanding of biological processes that determine agronomically and economically favorable phenotypes; we review the databases and bioinformatics tools that are available to manage and exploit the large amounts of biological data generated for apple and other plant genomes

A draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’)

We have sequenced the genome of European pear, Pyrus communis cultivar ‘Bartlett’/‘William Bon Chrétien’ using second generation sequencing technology (Roche 454) A draft assembly was produced from single end reads, 2 kb, and 8 kb insert paired end reads using Newbler (version 2.7). The assembly contained 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.29Mb) covering a total of 577.3 Mb, representing 96.1% of the expected 600 Mb Pyrus genome. Preliminary analysis indicated that 549 SNP markers anchored 105 Mb (17.5%) of the assembled genome to a consensus genetic map of ‘Old Home’ x ‘Louise de Bonne Jersey’ and P019R054T042 x P037R048T081 segregating populations. Synteny with the apple genome primary assembly of ‘Golden Delicious’, and other rosaceous genomes is being used to extend putative anchoring. Gene prediction was performed and the use of the gene family of expansins will be reported as an example of assessment of the quality of the gene prediction. This ‘Bartlett’ genome sequence is a unique tool for identifying the genetic control of key horticultural traits and developing better pear cultivars, enabling wide application of marker‐assisted (MAS) and genomic selection (GS)

A sequence-anchored integrated genetic linkage map for apple, Malus X domestica Borkh

International audienceGenome resources for apple (Malus x domestica Borkh), the main fruit crop of temperate regions, have built up over the past five years, culminating in the sequencing of the apple cultivar ‘Golden Delicious’ (GD) genome. In spite of the availability of a high-quality genome sequence, a large collection of expressed sequence tags, and a physical map, high-resolution genetic maps remain crucial resources for molecular breeding programs as well as for fine-mapping quantitative trait loci. We describe here the construction of an apple dense integrated genetic map derived from six F1 populations and, for the first time, its physical anchor to the sequenced genome of GD. Polymorphisms discovered by assembling the two haplotypes of the GD genome were used to develop markers for each metacontig to correlate them with linkage groups. The map included 1,730 polymorphic markers, 196 SSRs, 1,500 genomic-derived SNPs and 34 EST-derived SNPs. In total, 17 linkage groups were identified based on SSR markers mapping to existing apple linkage maps. All sequenced markers, well positioned on the genetic map, were used to order and to orient metacontigs along the appropriate linkage groups. In addition, marker information was used to avoid building chimerical metacontigs from different linkage groups. Many genes related to disease resistance, fruit quality, plant development, and reaction to environment have been identified and mapped to chromosomes. Region-dependent estimations of physical and recombinational distance, and correlation of recombination with specific sequence parameters are also presented