Jabal Akhtar goats SNP genotypes
Data files
Jun 26, 2025 version files 17.91 MB
Abstract
The objectives of the study were to identify SNPs associated with body size measurements in Jabal Akhdar Omani female goats. Seventy-two Jabal Akhdar Omani female goats were genotyped for the current study using the Illumina GoatSNP50 BeadChip, which contains 53,347 SNPs. After genotypic data filtration, the number of SNPs remaining for analysis was 46,035 SNPs belonging to 29 autosomes. Body size phenotypes used in the present study were withers height (WH), rump height (RH), Body Length (BL), Sternum height (SH), body depth (BD), Bicoastal diameter (BID), Ear Length (EL), Rump width (RW), Head width (HW), Rump Length (RL), Head Length (HL), Head Girth (HG), Cannon bone circumference (CC), Muzzle Diameter (MD), and finally the first principal component for all previous body measurements (PC1). Genome Wide Association Analysis (GWAS) of body measurements was performed using the GenABEL package in R software. A multiple testing correction approach (simpleM) was used to adjust for multiple testing of SNPs. Later, BioMart-Ensamble was used to look for candidate genes within 100 kb upstream and downstream of the significant SNPs. Fifty-one SNPs were identified in the current study for all studied traits except WH, BL, HG and CC. The identified SNPs were linked to 90 genes that have different functions related to protein, lipid, and carbohydrate metabolism, in addition to ion binding, mineral transportation, early growth and reproduction. Consequently, these genes could play vital roles in Jabal Akhdar goats' growth and possibly other goat breeds. To our knowledge, this is the first GWAS in body measurements in Omani goats.
The dataset includes the genotypes files of 72 female Jabal Akhdar Omani goats in PLINK format.
The animals were genotyped using the Illumina GoatSNP50 BeadChip and the data can be viewed and analyzed using the freely available PLINK software with the file formats being PLINK standard format. The research was carried out and funded by Sultan Qaboos University and the samples were obtained from Jabal Akhdar in Oman.
Description of the data and file structure
The dataset consists of two files, a Sultan_Qaboos_University_GOAT53KV1_20190531_ManifestChrUpdate.ped and Sultan_Qaboos_University_GOAT53KV1_20190531_ManifestChrUpdate.map file.
Below is a detailed description of the PLINK .ped and .map file formats
PLINK .ped and .map File Descriptions
📁 1. PLINK .ped File
The .ped file is a space-delimited plain text file that contains individual-level genotype data. Each row represents one individual, and the columns are structured as follows:
Columns:
| Column | Description |
|---|---|
| 1 | Family ID (FID) – Identifier for the family (can be dummy if not using family-based analysis) |
| 2 | Individual ID (IID) – Unique identifier for the individual |
| 3 | Paternal ID – ID of the father (use 0 if unknown or not applicable) |
| 4 | Maternal ID – ID of the mother (use 0 if unknown or not applicable) |
| 5 | Sex – 1 = male, 2 = female, 0 = unknown |
| 6 | Phenotype – Quantitative value, case/control status (1=control, 2=case), or -9 for missing |
| 7+ | Genotypes – Each SNP is represented by two alleles (e.g., A A, A G, C T). Missing alleles are denoted by 0 0 |
🔹 Genotype columns start from column 7 and continue as two columns per SNP (allele 1 and allele 2 for SNP 1, allele 1 and allele 2 for SNP 2, etc.)
📌 Example:
FAM001 IND001 0 0 1 2 A A G G C T ...
FAM001 IND002 0 0 2 1 A G G G C C ...
📁 2. PLINK .map File
The .map file is a plain text file that contains SNP-level information, with one row per SNP, in the same order as the SNPs in the .ped file.
Columns:
| Column | Description |
|---|---|
| 1 | Chromosome – Chromosome number (1–22, X=23, Y=24, MT=25) |
| 2 | SNP ID – Identifier for the SNP (rsID or any label) |
| 3 | Genetic Distance – Usually set to 0 (can be used for recombination distance in cM if known) |
| 4 | Base-pair Position – Physical position on the chromosome in base pairs |
📌 Example:
1 rs123456 0 12345678
1 rs234567 0 12345999
2 rs345678 0 23456789
The .ped and .map files are standard formats used in genome-wide association studies (GWAS), compatible with PLINK software (Purcell et al., 2007).
Sharing/Access information
You can access the data via the following URL:https://datadryad.org/dataset/doi:10.5061/dryad.2v6wwpzvz
OR
By emailing the authors at: abri1st@squ.edu.om
Code/Software
This submission contains no code.
- Al-Abri, Mohammed; Kharousi, Khadhia Al; Hamrashdi, Abeer Al et al. (2023). Genome wide association analysis for twinning ability in Jabal Akhdar Omani goats. Small Ruminant Research. https://doi.org/10.1016/j.smallrumres.2023.106951