Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 510355
Title A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species
Author(s) Pierro, Erica A. Di; Gianfranceschi, Luca; Guardo, Mario Di; Koehorst-Van Putten, Herma J.J.; Kruisselbrink, Johannes W.; Longhi, Sara; Troggio, Michela; Bianco, Luca; Muranty, Hélène; Pagliarani, Giulia; Bink, Marco C.A.M.; Voorrips, Roeland E.; Weg, Eric van de
Source Horticulture Research 3 (2016). - ISSN 2052-7276
DOI https://doi.org/10.1038/hortres.2016.57
Department(s) WUR Plant Breeding
Laboratory of Plant Breeding
Sports Centre Algemeen
WUR PB Siergewassen, Tissue Culture
Biometris (PPO/PRI)
PE&RC
WUR PB Kwantitatieve Aspecten
WUR PB Biodiversiteit en Genetische Variatie
EPS
Publication type Refereed Article in a scientific journal
Publication year 2016
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 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 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.

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