Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data.

Simple Summary: The Carpatina goat breed from Romania is very well adapted to a range of contrasting and very different environments compared to highly specialized breeds. This adaptability makes them an important source of genetic variability for future breeding programs. To improve breeding strategies, it is necessary to evaluate the genetic diversity of the Carpatina breed. The aim of this study was therefore to investigate genetic diversity and inbreeding of old native Carpatina goat populations from different geographical areas in Romania using single nucleotide polymorphism (SNP) data for 67 individuals. Diversity, measured by average expected heterozygosity (H_E), was 0.418, and average observed heterozygosity (H_o) was 0.420. Linkage disequilibrium (LD) estimation showed that the average r² value was 0.32. The effective population size (N_e) estimate 13 generations ago ranged between 98 and 185. These results based on SNP data are very useful for the application of proper management and for designing goat breeding programs. Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (H_E), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The N_e has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the N_e trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed. [ABSTRACT FROM AUTHOR]