title: A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species.
abstract: Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domesticaBorkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.
authors.affiliation: Department of Biosciences, University of Milan , Milan 20133, Italy.
authors.forename: Erica A
authors.initials: EA
authors.lastname: Di Pierro
authors.affiliation: Department of Biosciences, University of Milan , Milan 20133, Italy.
authors.forename: Luca
authors.identifier: 0000-0002-7644-5968
authors.initials: L
authors.lastname: Gianfranceschi
authors.affiliation: Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands; Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige 38010, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: Di Guardo
authors.affiliation: Plant Breeding, Wageningen University and Research , Wageningen 6700AJ, The Netherlands.
authors.forename: Herma Jj
authors.initials: HJ
authors.lastname: Koehorst-van Putten
authors.affiliation: Biometris, Wageningen University and Research , Wageningen 6700AA, The Netherlands.
authors.forename: Johannes W
authors.initials: JW
authors.lastname: Kruisselbrink
authors.affiliation: Plant Breeding, Wageningen University and Research , Wageningen 6700AJ, The Netherlands.
authors.forename: Sara
authors.initials: S
authors.lastname: Longhi
authors.affiliation: Research and Innovation Centre, Edmund Mach Foundation , San Michele all'Adige 38010, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.affiliation: Research and Innovation Centre, Edmund Mach Foundation , San Michele all'Adige 38010, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bianco
authors.affiliation: IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV , Beaucouzé 49071, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Muranty
authors.affiliation: Department of Agricultural Sciences, University of Bologna , Bologna 40127, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Pagliarani
authors.affiliation: Department of Agricultural Sciences, University of Bologna , Bologna 40127, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Tartarini
authors.affiliation: Department of Molecular Biology, Laimburg Research Centre for Agriculture and Forestry , Ora 39040, Italy.
authors.forename: Thomas
authors.initials: T
authors.lastname: Letschka
authors.affiliation: Department of Molecular Biology, Laimburg Research Centre for Agriculture and Forestry , Ora 39040, Italy.
authors.forename: Lidia
authors.initials: L
authors.lastname: Lozano Luis
authors.affiliation: Department of Plant Breeding, Swedish University of Agricultural Sciences , Alnarp 23053, Sweden.
authors.forename: Larisa
authors.initials: L
authors.lastname: Garkava-Gustavsson
authors.affiliation: Research and Innovation Centre, Edmund Mach Foundation , San Michele all'Adige 38010, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Micheletti
authors.affiliation: Biometris, Wageningen University and Research , Wageningen 6700AA, The Netherlands.
authors.forename: Marco Cam
authors.initials: MC
authors.lastname: Bink
authors.affiliation: Plant Breeding, Wageningen University and Research , Wageningen 6700AJ, The Netherlands.
authors.forename: Roeland E
authors.initials: RE
authors.lastname: Voorrips
authors.affiliation: Plant Breeding, Wageningen University and Research , Wageningen 6700AJ, The Netherlands.
authors.forename: Ebrahimi
authors.initials: E
authors.lastname: Aziz
authors.affiliation: Research and Innovation Centre, Edmund Mach Foundation , San Michele all'Adige 38010, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.affiliation: IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV , Beaucouzé 49071, France.
authors.forename: François
authors.initials: F
authors.lastname: Laurens
authors.affiliation: Plant Breeding, Wageningen University and Research , Wageningen 6700AJ, The Netherlands.
authors.forename: W Eric
authors.initials: WE
authors.lastname: van de Weg