Investigating genetic diversity and population structure of Egyptian goats across four breeds and seven regions

This study investigated the genetic diversity and population structure of 157 Egyptian adult goat females from four breed groups (Saidi, Barki, Wahati, and E. Nubian / Zaraibi), and distributed over eight geographic regions. Results from various analyses revealed high levels of genotypic diversity. Shannon values ranging from 3.89 in the Serw region population (within the Zaraibi breed) to 2 in the Kharga region population(within Wahati goats), and low linkage disequilibrium. The Simpson index for diversity varied with values ranging from 0.97 in the Serw population to 0.875 in Kharga population. Analysis of gene diversity using Nei’s unbiased method found high levels of heterozygosity, with values ranging from 0.38 in Aswan and Assuit to 0.3 in Serw populations. Principal component analysis separated the studied populations into three groups. The first group displayed Zaraibi and Saidi populations as genetically distinct populations, and the second group showed interbreeding between Barki desert breed, and Wahati oasis breed. Bayesian Information Criterion identified four distinct subpopulations, and the discriminant analysis of principal components revealed intermingling between Wahati and Barki populations, as well as the independence of Zaraibi population. Structure analysis of the subpopulations revealed six gene pools with admixture of Wahati and Barki goats, which were confirmed by the kinship analysis. In conclusion, the study revealed clear diversity between the studied populations, with the regions having their own distinct breeds. These findings suggest that interbreeding between some populations may be due to the exchange of genetic stocks and hybridization programs could be necessary to sustain Egyptian breeds and produce offspring that can survive environmental diversity and CC. •The study assessed genetic diversity and population structure of Egyptian adult goatfrom four breeds (Saidi, Barki, Wahati, and E. Nubian), over eight geographic regions.•Results revealed high levels of genotypic diversity, and low linkage dis- equilibrium.•PCA divided the populations into three groups, with the first group showing significant interbreeding.•BIC identified four distinct subpopulations, and revealed intermingling of Wahati and Barki populations and independency of Zaraibi population.•The structure analysis of the subpopulations revealed six gene pools.