A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle
Data files
Jun 08, 2023 version files 4.92 MB
-
README.md
-
Ugandan_indegenous_cattle_gnotypes.map
-
Ugandan_indegenous_cattle_gnotypes.ped
Abstract
The cattle industry contributes to Uganda’s agricultural output. It however faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent developments in genomics and bioinformatics technologies. In the current study, we provided a proof-of-concept conflict resolution method based on the available bovine genomic tools. Briefly, two farmers we refer to as A and B contested for ownership of a group of 9 cattle. To offer objective and data-based guidance to resolving this conflict, we sampled hair samples of the 9 contested cattle as well as 7 and 2 cattle from farmers A and B respectively that were identified by these farmers as the closest relatives of the contested animals. DNA was extracted from each of the collected hair samples and subsequently genotyped on the Illumina BovineSNP50-24 version 3 BeadChip for 53218 DNA Single Nucleotide Polymorphisms (SNP) variants. Upon genotype data cleaning we retained ~30,000 SNPs which were used for different genomic analyses including principal component analysis, identity by state (IBS) analysis, and hierarchical clustering analysis, to establish the genetic relationships within and between the investigated animal groups.
Methods
In this study, genetic analyses of 18 indigenous Ugandan cattle were performed to establish genetic relationships between cattle from 3 different groups. Hair samples of the 9 contested cattle as well as 7 and 2 cattle from farmers A and B respectively that were identified by these farmers as the closest relatives of the contested animals were collected. DNA was extracted from each of the collected hair samples and subsequently genotyped on the Illumina BovineSNP50-24 version 3 BeadChip for 53218 DNA Single Nucleotide Polymorphisms (SNP) variants. Upon genotype data cleaning we retained ~30,000 SNPs which were used for different genomic analyses including principal component analysis, identity by state (IBS) analysis, and hierarchical clustering analysis, to establish the genetic relationships within and between the investigated animal groups.
Usage notes
Plink1.9, R, vegan package in R