DOI: 10.5061/dryad.2v6wwpzvz
title: Jabal Akhtar goats SNP genotypes

description: 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.
description: # Jabal Akhtar goats SNP genotypes [Access this dataset on
 Dryad](https://datadryad.org/dataset/doi:10.5061/dryad.2v6wwpzvz) 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](https://datadryad.org/dataset/doi:10.5061/dryad.2v6wwpzvz) OR By emailing the authors at: [abri1st@squ.edu.om](mailto:abri1st@squ.edu.om) ## Code/Software This submission contains no code.