A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

Abstract

Background: The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes.

Results: Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect.

Conclusions: Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations.

Fig. 1

Multidimensional scaling plot for 12 caprine populations. Caprine populations analysed: Spain (Bermeya, Blanca de Rasquera, Malagueña, Murciano-Granadina, Florida, Mallorquina and Palmera), Tunisia, Burkina Faso (Sahel and Djallonké), Romania (Carpathian) and Switzerland (Saanen). This analysis is based on genome-wide identity-by-state pairwise distances calculated with the PLINK software [11] on the basis of 39,257 SNPs. Three main clusters are observed: (1) Spanish and European breeds, (2) African breeds, and (3) the Palmera breed from the Canary Islands

Fig. 2

Maximum likelihood estimation of individual ancestries calculated with the admixture software. We assumed a K-value 7 because it had the lowest cross-validation error. We took into consideration data from 39,257 SNPs used to genotype 12 caprine populations from Spain (Bermeya, Blanca de Rasquera, Malagueña, Murciano-Granadina, Florida, Mallorquina and Palmera), Tunisia, Burkina Faso (Sahel and Djallonké), Romania (Carpathian) and Switzerland (Saanen). This analysis shows that the Southern Spanish breeds, Malagueña and Murciano-Granadina, together with the Carpatian breed from Romania show evidence of potential introgression with North African (Tunisian) goats

Fig. 3

Runs of homozygosity (ROH) identified for 12 caprine populations. The number of ROH found for each individual genome (y-axis) is plotted against ROH total size (i.e. the number of Mb covered by ROH in each genome, x-axis). We analysed goats from Spain (Bermeya, Blanca de Rasquera, Malagueña, Murciano-Granadina, Florida, Palmera and Mallorquina), Tunisia, Burkina Faso (Sahel and Djallonké), Romania (Carpathian) and Switzerland (Saanen). For the Mallorquina and Blanca de Rasquera breeds, we observed many individuals with a large number of ROH (>40) and that a substantial fraction of the genome is covered by ROH (>400 Mb). In contrast, for the Palmera breed, the number of ROH is relatively large (20 to 40) but the fraction of the genome covered by ROH is quite small (<400 Mb)

Fig. 4

Classification of ROH in seven categories (x-axis) according to size (from 1 to 5 Mb to more than 30 Mb) and mean sum of ROH (y-axis, measured in megabases) within each ROH category and averaged per breed. We analysed 12 caprine populations from Spain (Bermeya, Blanca de Rasquera, Malagueña, Murciano-Granadina, Florida, Palmera and Mallorquina), Tunisia, Burkina Faso (Sahel and Djallonké), Romania (Carpathian) and Switzerland (Saanen). This figure shows that for the Mallorquina breed, the mean sum of ROH with sizes greater than 30 Mb is several times larger than that for the remaining breeds. In contrast, in Palmera goats, ROH with sizes between 5 to 10 and 10 to 15 Mb display the largest mean sums (>60 Mb for each category)