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

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 

机构地区：[1]Department of Biosciences,University of Milan,Milan,20133,Italy [2]Plant Breeding,Wageningen University and Research,Wageningen,6700AJ,The Netherlands [3]Research and Innovation Centre,Edmund Mach Foundation,San Michele all’Adige,38010,Italy [4]Biometris,Wageningen University and Research,Wageningen,6700AA,The Netherlands [5]IRHS,INRA,AGROCAMPUS-Ouest,Universitéd’Angers,SFR 4207 QUASAV,Beaucouzé,49071,France [6]Department of Agricultural Sciences,University of Bologna,Bologna,40127,Italy [7]Department of Molecular Biology,Laimburg Research Centre for Agriculture and Forestry,Ora,39040,Italy [8]Department of Plant Breeding,Swedish University of Agricultural Sciences,Alnarp,23053,Sweden [9]Hendrix Genetics Research,Technology&Services,Boxmeer 5830 AC,The Netherlands

出　　处：《Horticulture Research》2016年第1期30-42,共13页园艺研究（英文）

基　　金：We thank Yolanda Noordijk for the isolation of DNA from all samples at Wageningen-UR and Elisa Banchi for her work on the genotyping of these samples with the 20 K Infinium SNP array at the Fondazione Edmund Mach;This work has been co-funded by the EU seventh Framework Programme by the FruitBreedomics project N°.265582:Integrated Approach for increasing breeding efficiency in fruit tree crops(www.FruitBreedomics.com).

摘　　要：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 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 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 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 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.

关 键 词：BREEDING LINKAGE MAPPING 

分 类 号：S51[农业科学—作物学]