title: Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids.
abstract: 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'×'Louise 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.
authors.affiliation: Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France.
authors.forename: Sara
authors.initials: S
authors.lastname: Montanari
authors.forename: Munazza
authors.initials: M
authors.lastname: Saeed
authors.forename: Mareike
authors.initials: M
authors.lastname: Knäbel
authors.forename: YoonKyeong
authors.initials: Y
authors.lastname: Kim
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.forename: Mickael
authors.initials: M
authors.lastname: Malnoy
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.forename: Paolo
authors.initials: P
authors.lastname: Fontana
authors.forename: KyungHo
authors.initials: K
authors.lastname: Won
authors.forename: Charles-Eric
authors.initials: CE
authors.lastname: Durel
authors.forename: Laure
authors.initials: L
authors.lastname: Perchepied
authors.forename: Robert
authors.initials: R
authors.lastname: Schaffer
authors.forename: Claudia
authors.initials: C
authors.lastname: Wiedow
authors.forename: Vincent
authors.initials: V
authors.lastname: Bus
authors.forename: Lester
authors.initials: L
authors.lastname: Brewer
authors.forename: Susan E
authors.initials: SE
authors.lastname: Gardiner
authors.forename: Ross N
authors.initials: RN
authors.lastname: Crowhurst
authors.forename: David
authors.initials: D
authors.lastname: Chagné
mesh_terms: D000483:Alleles; D001483:Base Sequence; D002874:Chromosome Mapping; D020090:Chromosome Segregation / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D003433:Crosses, Genetic; D005060:Europe; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics; D060005:Genotyping Techniques; D006824:Hybridization, Genetic; D027845:Malus / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D031989:Pyrus / Q000235:genetics*; D012641:Selection, Genetic; D013045:Species Specificity
chemical_list: D005819:Genetic Markers