Apple REFPOP progeny mid-density genotypic data

Version 1.1

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

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Description	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". (2020-11-05)
Subject	Plant Breeding and Plant Products
Keyword	apple, genotyping, Malus domestica, 20K SNP array
Related Publication	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 doi: 10.1038/s41438-020-00408-8

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	apple_REFPOP_progeny_individuals.txt text/plain - 13.6 KB - Oct 22, 2020 - 5 Downloads MD5: fe721c3a852f9a80e8603c471e6f158c 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.	Read Text Download
	apple_REFPOP_progeny_marker_data.txt text/plain - 7.7 MB - Oct 22, 2020 - 4 Downloads MD5: c7c4efc6b6841086e405273714983ff2 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.	Read Text Download
	apple_REFPOP_progeny_marker_position_data.txt text/plain - 680.2 KB - Oct 22, 2020 - 4 Downloads MD5: cf2c8863f52fef5c0e8e8118f88b0b45 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).	Read Text Download

Citation Metadata

Dataset Persistent ID	doi:10.15454/1ERHGX
Publication Date	2020-10-22
Title	Apple REFPOP progeny mid-density genotypic data
Author	Muranty, Hélène (INRA - Institut National de la Recherche Agronomique) - ORCID: 0000-0003-3956-3807 Howard, Nicholas P. (Department of Horticultural Science, University of Minnesota, St Paul, USA) - ORCID: 0000-0001-7094-2229 Denancé, Caroline (INRA - Institut National de la Recherche Agronomique) Le Paslier, Marie-Christine Berard, Aurélie
Contact	Use email button above to contact. Muranty, Helene (INRA - Institut National de la Recherche Agronomique)
Description	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". (2020-11-05)
Kind of Data	Dataset
Data Origin	experimental data
Subject	Plant Breeding and Plant Products
Life cycle step	Deposit
Keyword	apple genotyping Malus domestica 20K SNP array
Related Publication	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 doi: 10.1038/s41438-020-00408-8 https://rdcu.be/b9xwK
Language	English
Depositor	Muranty, Helene
Deposit Date	2020-09-08
Other References	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 Malus × domestica and causes for seemingly incompatible calls. bioRxiv 2020.09.01.276758. doi: 10.1101/2020.09.01.276758

Life Sciences Metadata

Other Organism	Malus domestica
Measurement Type	SNP analysis
Technology Type	DNA microarray
Technology Platform	Illumina
Sample type	clones

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