Genetic diversity, population structure, and combined detection of selection signatures in Iranian versus Afghan Baluchi sheep

Selection to increase the frequency of useful mutations has left marks on animal genomes, genetic diversity, and population structure within populations. The study and investigation of these genomic regions can lead to the identification of genes related to economic traits or competence and adaptability. This study aimed to recognize genetic diversity, population structure, and selection signatures in Iranian (IB) and Afghan (AB) Baluchi sheep populations. In this study, 86 Iranian Baluchi and 15 Afghan Baluchi sheep were genotyped using Illumine Ovine SNP50K Beadchip arrays. Note that the sample size imbalance (IB n = 86 vs. AB n = 15) may reduce statistical power and potentially bias population structure and selection scan results. Additionally, use of the Ovine 50K array may introduce ascertainment bias; analyses were based on 38,193 shared SNPs, potentially missing population-specific variants. Generally, moderate genetic diversity was observed in both the Afghan Baluchi (AB) and Iranian Baluchi (IB) sheep populations, using various assessment methods. However, the IB population showed the lowest level of genetic diversity and the highest rate of linkage disequilibrium decay, despite having a better effective population size in recent generations. The ADMIXTURE analysis indicated that the optimal number of genetic clusters was K = 2, which was determined based on the lowest cross-entropy error of 0.603 observed during cross-validation. At K = 2 and NJ tree analysis, a clear genetic distinction between the AB and IB populations was evident. Additionally, the IB population demonstrated significant genetic uniformity when compared to the AB population in terms of genetic distance. Also, FST and XP-EHH were used to identify selection signatures. Some putative candidate genes for FST, including HDAC9, CSMD3, DAB1, FGF12, and PCDH9 were associated with important economic traits such as body weight, hot carcass weight, muscle weight in carcass, reproductive seasonality, and carcass fat percentage, respectively. Also, XP-EHH putative candidate genes were KCNIP4, FGF11, CNTROB, and ROBO2 in AB population, which were related to body weight, hot carcass weight, milk yield, and muscle weight in carcass. Moreover, XP-EHH putative candidate genes in IB population were GRIK3, NCOA1, and FGD3, that related to muscle weight in carcass, staple length, and milk fat percentage. Selection signals were identified using top 1% FST thresholds and XP-EHH without genome-wide multiple-testing correction; results require experimental validation. We observed very similar outcomes in terms of similar signatures related to economic traits in both FST and XP-EHH methods, indicating the robustness of analysis in this study. It can be concluded that selection has made a major distinction between Afghan and Iranian Baluchi sheep populations for reproduction, milk production, and growth traits. These could be due to the managed breeding programme in Iranian Baluchi sheep. Utilizing validated QTLs as described in this study could be applied to reveal the direction of breeding plans in livestock species.