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A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

Horticulture Research 2016年第1期3卷 30-42页

作者： Erica A Di Pierro Luca Gianfranceschi Mario Di Guardo herma jj koehorst-van putten Johannes W Kruisselbrink Sara Longhi Michela Troggio Luca Bianco Hélène Muranty Giulia Pagliarani Stefano Tartarini Thomas Letschka Lidia Lozano Luis Larisa Garkava-Gustavsson Diego Micheletti Marco CAM Bink Roeland E Voorrips Ebrahimi Aziz Riccardo Velasco François Laurens W Eric van de Weg Department of Biosciences University of MilanMilan20133Italy Plant Breeding Wageningen University and ResearchWageningen6700AJThe Netherlands Research and Innovation Centre Edmund Mach FoundationSan Michele all’Adige38010Italy Biometris Wageningen University and ResearchWageningen6700AAThe Netherlands IRHS INRAAGROCAMPUS-OuestUniversitéd’AngersSFR 4207 QUASAVBeaucouzé49071France Department of Agricultural Sciences University of BolognaBologna40127Italy Department of Molecular Biology Laimburg Research Centre for Agriculture and ForestryOra39040Italy Department of Plant Breeding Swedish University of Agricultural SciencesAlnarp23053Sweden Hendrix Genetics Research Technology&ServicesBoxmeer 5830 ACThe Netherlands

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 *** apple(Malus domestica Borkh),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 *** 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 *** map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 ***,chromosome 5 was oriented according to its homoeologous chromosome *** map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL *** collinearity with the genome sequences v1 and v3 are *** our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and *** result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.

关键词： breeding linkage mapping

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