Apple REFPOP progeny mid-density genotypic data (ICPSR doi:10.15454/1ERHGX)

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Document Description

Citation

Title:

Apple REFPOP progeny mid-density genotypic data

Identification Number:

doi:10.15454/1ERHGX

Distributor:

Portail Data INRAE

Date of Distribution:

2020-10-22

Version:

1

Bibliographic Citation:

Muranty, Hélène; Howard, Nicholas P.; Denancé, Caroline; Le Paslier, Marie-Christine; Berard, Aurélie, 2020, "Apple REFPOP progeny mid-density genotypic data", https://doi.org/10.15454/1ERHGX, Portail Data INRAE, V1

Study Description

Citation

Title:

Apple REFPOP progeny mid-density genotypic data

Identification Number:

doi:10.15454/1ERHGX

Authoring Entity:

Muranty, Hélène (INRA - Institut National de la Recherche Agronomique)

Howard, Nicholas P. (Department of Horticultural Science, University of Minnesota, St Paul, USA)

Denancé, Caroline (INRA - Institut National de la Recherche Agronomique)

Le Paslier, Marie-Christine (INRA - Institut National de la Recherche Agronomique)

Berard, Aurélie (INRA - Institut National de la Recherche Agronomique)

Distributor:

Portail Data INRAE

Access Authority:

Muranty, Helene

Depositor:

Muranty, Helene

Date of Deposit:

2020-09-08

Study Scope

Keywords:

Plant Breeding and Plant Products, apple, genotyping, Malus domestica, 20K SNP array

Abstract:

This dataset corresponds to the curated genotypic data used for the progeny group of the apple reference population used by Jung et al (2020) "The apple REFPOP - a reference population for genomics-assisted breeding in apple" Horticulture Research, 7:189. The dataset was obtained using the 20K apple SNP array (Bianco et al, 2014). These data were obtained partly 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/) and partly in the frame of the INRAE SelGen project GDivSelGen: "Efficient use of genetic diversity in genomic selection".

Kind of Data:

Dataset

Methodology and Processing

Sources Statement

Data Access

Notes:

<img src="https://www.etalab.gouv.fr/wp-content/uploads/2011/10/licence-ouverte-open-licence.gif" alt="Licence Ouverte" height="100"><a href="https://www.etalab.gouv.fr/licence-ouverte-open-licence">Licence Ouverte / Open Licence Version 2.0</a> compatible CC BY

Other Study Description Materials

Related Publications

Citation

Identification Number:

10.1038/s41438-020-00408-8

Bibliographic Citation:

Jung Michaela, Roth Morgane, Aranzana Maria José, Auwerkerken Annemarie, Bink Marco, Denancé Caroline, Dujak Christian, Durel Charles-Eric, Font i Forcada Carolina, Cantin Celia M., Guerra Walter, Howard Nicholas P., Keller Beat, Lewandowski Mariusz, Ordidge Matthew, Rymenants Marijn, Sanin Nadia, Studer Bruno, Zurawicz Edward, Laurens François, Patocchi Andrea, Muranty Hélène (2020) The apple REFPOP - a reference population for genomics-assisted breeding in apple. Horticulture Research, 7:189

Other Reference Note(s)

Bianco L, Cestaro A, Sargent DJ, et al. (2014) Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh). PLoS ONE 9:e110377. doi: 10.1371/journal.pone.0110377

Bianco L, Cestaro A, Linsmith G, et al. (2016) Development and validation of the Axiom®Apple480K SNP genotyping array. Plant J 86:62–74. doi: 10.1111/tpj.13145

Bink MCAM, Jansen J, Madduri M, et al. (2014) Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor Appl Genet 127:1073–1090. doi: 10.1007/s00122-014-2281-3

Daccord N, Celton J-M, Linsmith G, et al. (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49:1099–1106.

Di Pierro EA, Gianfranceschi L, Di Guardo M, et al. (2016) A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species. Horticulture Research 3:16057. doi: 10.1038/hortres.2016.57

Howard NP, Troggio M, Durel C-E, et al. (2020) Integration of Infinium and Axiom SNP array data in the outcrossing species <em>Malus</em> × <em>domestica</em> and causes for seemingly incompatible calls. bioRxiv 2020.09.01.276758. doi: 10.1101/2020.09.01.276758

Other Study-Related Materials

Label:

apple_REFPOP_progeny_individuals.txt

Text:

List of the 259 progeny individuals with 20K data used for the apple REFPOP. Column "Index" indicates the name of the individual used in the file "apple_REFPOP_progeny_marker_data.txt". Column "Genotype_code" indicates the code for the individual listed in Supplementary Table S1 in Jung et al (2020) Horticultural Research, in press. Column "data_origin" indicates which project founded the genotyping of the individual. Column "Bink_et_al_2014" indicates the name under which data for 87 SSR loci were published for this individual in Supplementary Material 1 of Bink et al (2014) doi:10.1007/s00122-014-2281-3. Column "Di_Pierro_et_al_2016_genotype_code" indicates the name under which segregation data for this individual were published in Supplementary Datasets of Di Pierro et al (2016) doi:10.1038/hortres.2016.57, and column "Di_Pierro_et_al_2016_Dataset" indicates in which Dataset these data can be found. In the last three columns, a dash ("-") indicates the individual did not appear in these previous datasets.

Notes:

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Other Study-Related Materials

Label:

apple_REFPOP_progeny_marker_data.txt

Text:

Genotypic data for 10295 SNP loci on 259 apple progeny genotypes obtained with the Illumina Infinium 20K SNP array. Names of individuals are in column "Index". The names of their parents are in columns "P1" and "P2". More information about individuals is given in the file "apple_REFPOP_progeny_individuals.txt". More information about SNP loci is given in the file "apple_REFPOP_progeny_marker_position_data.txt". Genotypes are encoded as AA, AB, BB, AC, BC and CC. A stands for A or T, B stands for C or G, and C represents a null allele.

Notes:

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Other Study-Related Materials

Label:

apple_REFPOP_progeny_marker_position_data.txt

Text:

List of the 10295 SNP loci genotyped with the Illumina Infinium 20K array on the apple REFPOP progeny. The column "Index_20K" indicates the SNP index number on the 20K array that is used as column name in the file apple_REFPOP_progeny_marker_data.txt. The column "Original_Locus_Name" indicates the full name of the SNP; the column "Affymetrix_id" indicates the name of the SNP on the Affymetrix Axiom 480K SNP array (Bianco et al 2016); the columns "chr" and "position" indicate the position of the SNP on GDDH13 v1.1 reference genome (Daccord et al 2017). A value of "0" in column "chr" means the SNP is located on an unmapped portion of GDDH13 v1.1 genome. A value of "19" in column "chr" means the position of the SNP could not be deduced from BLAST results. A value "not robust on 480K" in columns "chr" and "position" means the SNP was not considered robust when genotyped on the Affymetrix Axiom 480K SNP array and thus not used for the apple REFPOP. The column "Used ot not" indicates if the SNP was used in the work on the apple REFPOP by Jung et al (2020). The subset of 10295 robust SNPs was filtered from the 20K genotyping results as described in Howard et al (2020).

Notes:

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