Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data.

Carina Visser,Este Van Marle-Köster,Simon F Lashmar,Daniel Allain,Mario A Poli

doi:10.1371/journal.pone.0154353

Carina Visser, Este Van Marle-Köster + Show 3 more

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The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.

Highlights

The use of animal fibres from sheep and goats date back to the Biblical age, where wool was often used to make clothing, and goat hair for decoration in the temples [1]
The call rates were high for all three populations genotyped varying from 0.981 for the Argentinian population to 0.996 for the South African goats
Most markers failed based on MAF and HWE in the South Africa (SA) population, while sample call rate was a major cause of loss in the AR population

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Introduction

The use of animal fibres from sheep and goats date back to the Biblical age, where wool was often used to make clothing, and goat hair for decoration in the temples [1]. The ancient Roman Empire facilitated the continued breeding of sheep and goats into the modern world, due in part to the continued importance of skins and hair in the making of clothing and water skins, as well as tents and stuffing for pillows [2]. The Angora goat originates from the district of Ankara in Turkey [1]. Similar to many other goat breeds, Angora goats have since spread throughout Europe, the Americas and Australasia via human-mediated distribution [3]. Other countries with notable mohair industries include Turkey, Lesotho, and Argentina [4]

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