Persistent Identifier
|
doi:10.15454/IOPGYF |
Publication Date
|
2019-10-22 |
Title
| FruitBreedomics apple high-density SNP genotyping dataset |
Point of Contact
|
Use email button above to contact.
Denancé, Caroline (INRA - Institut National de la Recherche Agronomique)
Muranty, Hélène (INRA - Institut National de la Recherche Agronomique) |
Author
| Denancé, Caroline (INRA - Institut National de la Recherche Agronomique)
Muranty, Hélène (INRA - Institut National de la Recherche Agronomique) - ORCID: 0000-0003-3956-3807
Durel, Charles-Eric (INRA - Institut National de la Recherche Agronomique) - ORCID: 0000-0003-3856-2837 |
Description
| This dataset contains SNP data obtained by using the Axiom®Apple480K array (Bianco et al., 2016) on 1355 apple accessions from nine mostly European institutions and 92 apple progeny individuals from two parental combinations. Among the accessions, 1341 are diploid, 12 are triploid, and two are doubled haploid. These data were mainly obtained in the frame of the EU seventh Framework Programme project FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com/). Two dataset versions are available (see tab "Versions"). In Dataset 1.0, the files with root "FruitBreedomics_apple_253K_SNP" are those used for studying apple pedigrees as described in Muranty et al (2020). In Dataset 2.1, the files with root "FruitBreedomics_apple_320K_SNP" are those used for generating high density SNP data for the apple reference population, as described in Jung et al (2020 ; see Métadonnées/Metadata for this publication). The files with the suffix ".bed" are genotyping matrix in plink binary format, the files with the suffix ".bim" contain positions of loci in plink binary format and the files with the suffix ".fam" contain identifiers of the genotypes plink binary format. This format is described at http://zzz.bwh.harvard.edu/plink/data.shtml#bed. (2020-11-04) |
Language
| English |
Subject
| Agricultural Sciences |
Keyword
| Apple
Genotyping
Malus x domestica
Axiom(R)Apple480K SNP array |
Topic Classification
| Plant Breeding and Plant Products |
Data Type
| Dataset |
Data Origin
| experimental data |
Life cycle step
| Deposit; New version release |
Related Publication
| Hélène Muranty, Caroline Denancé, Laurence Feugey, Jean-Luc Crépin, Yves Barbier, Stefano Tartarini, Matthew Ordidge, Michela Troggio, Marc Lateur, Hilde Nybom, Frantisek Paprstein, François Laurens, Charles-Eric Durel (2020) Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. BMC Plant Biology 20:2. doi: 10.1186/s12870-019-2171-6 https://doi.org/10.1186/s12870-019-2171-6
Michaela Jung, Morgane Roth, Maria José Aranzana, Annemarie Auwerkerken, Marco Bink, Caroline Denancé, Christian Dujak, Charles-Eric Durel, Carolina Font i Forcada, Celia M. Cantin, Walter Guerra, Nicholas P. Howard, Beat Keller, Mariusz Lewandowski, Matthew Ordidge, Marijn Rymenants, Nadia Sanin, Bruno Studer, Edward Zurawicz, François Laurens, Andrea Patocchi, Hélène Muranty (2020) The apple REFPOP - a reference population for genomics-assisted breeding in apple. Horticulture Research 7:189. doi: 10.1038/s41438-020-00408-8 https://rdcu.be/b9xwK |
Related Dataset
| The Malus UNiQue genotype codes (MUNQ) for the 1355 accessions are listed in the dataset “MUNQ - Malus UNiQue genotype code for grouping apple accessions corresponding to a unique genotypic profile”.: doi: 10.15454/HKGMAS https://doi.org/10.15454/HKGMAS |
Funding Information
| European Commission: FP7-KBBE-2010 No. 265582 |
Project Information
| FruitBreedomics (Integrated Approach for increasing breeding efficiency in fruit tree crops) |
Depositor
| Hélène Muranty, Charles-Eric Durel |
Deposit Date
| 2020-11-04 |