SNP and microsatellite genotype data for the characterization of the Lipizzan horse population from Lipica Stud
Data files
Aug 17, 2026 version files 68.67 MB
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Lipizzan_horses_Lipica_STR.txt
12.50 KB
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Lipizzan_horses_Lipica.map
1.91 MB
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Lipizzan_horses_Lipica.ped
66.74 MB
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README.md
3.01 KB
Abstract
This dataset contains SNP and microsatellite (STR) genotype data generated for 233 Lipizzan horses from Lipica Stud, Slovenia. The data were used to assess genetic diversity, genomic inbreeding, population structure, and signatures of selection in the Lipizzan horse population. The repository includes genotype datasets and accompanying metadata required to reproduce the molecular analyses presented in the associated manuscript. Detailed file descriptions and data formats are provided in the accompanying README file.
Dataset DOI: 10.5061/dryad.s4mw6m9nb
Description of the data and file structure
Blood samples were collected from 233 Lipizzan horses from the Lipica Stud Farm (Slovenia), born between 1992 and 2018. DNA was extracted from peripheral blood and genotyped by Neogen using the GGP Equine 70K BeadChip.
Files and variables
File: Lipizzan_horses_Lipica.map
Description: PLINK MAP file containing 71,607 SNP markers. Genomic coordinates are based on the EquCab3.0 reference genome assembly. The file is whitespace-delimited and contains four columns:
- Chromosome or genomic sequence identifier
- SNP marker identifier
- Genetic distance in centimorgans
- Physical position in base pairs
File: Lipizzan_horses_Lipica.ped
Description: PLINK PED file containing unfiltered SNP genotype data for 233 Lipizzan horses. The file is whitespace-delimited.
The first six columns are:
- Family ID, coded as 0 for all individuals
- Individual ID, coded consecutively from 1 to 233
- Paternal ID, coded as 0 because pedigree information is not included
- Maternal ID, coded as 0 because pedigree information is not included
- Sex, coded as 0 because sex information is not included
- Phenotype, coded as -9 because phenotype information is not included
The remaining columns contain two allele codes for each of the 71,607 SNP markers. Genotypes are represented using A/B allele coding. Missing genotypes are coded as 0 0.
File: Lipizzan_horses_Lipica_STR.txt
Description: Tab-delimited text file containing microsatellite genotype data for 233 Lipizzan horses.
The first column, ID, contains numerical individual identifiers from 1 to 233. These identifiers correspond to the individual identifiers used in the SNP PED file.
The remaining columns contain genotype calls for 18 microsatellite loci:
vhl20: VHL20
htg4: HTG4
aht4: AHT4
hms7: HMS7
htg6: HTG6
aht5: AHT5
hms6: HMS6
asb23: ASB23
asb2: ASB2
htg10: HTG10
htg7: HTG7
hms3: HMS3
hms2: HMS2
asb17: ASB17
lex3: LEX3
hms1: HMS1
ca425: CA425
ucd437: UCD437
Microsatellite alleles are reported using the letter-based allele codes present in the original laboratory records. Each cell contains the genotype call for one individual at one locus. Blank cells indicate missing microsatellite genotype calls.
Code/software
The data are provided as standard PLINK PED/MAP files and can be viewed with any plain-text editor. For data analysis, the files can be imported into software PLINK 1.9 or later.
The microsatellite data are provided as a tab-delimited text file and can be viewed using a plain-text editor.
Access information
Other publicly accessible locations of the data:
- None. The dataset is not currently available in any other public repository.
Data was derived from the following sources:
- Not applicable.