The African introgression of Murciano Granadina goats has a Moroccan origin and displays remarkable levels of inter-individual variability.

There is evidence that Murciano Granadina (MG), the most important caprine dairy breed in Spain, has been introgressed by African goats, but the precise geographic origin of such introgression has not been identified yet. Moreover, an accurate estimate of the magnitude of this African introgression is lacking, since current estimates are based on small numbers of sampled individuals. The aim of our work was to tackle these two issues by genotyping 500 MG goats with the Goat SNP50 BeadChip and comparing their genotypes with those of reference populations from Spain (Bermeya), France (Saanen), Morocco (Barcha, Draa, Ghazalia, Noire de Atlas, Nord, Moroccan), Egypt (Barki, Oasis, Saidi), Algeria (Arabia, Makatia, M'Zabite, Kabyle), Tunisia (Tunisian native breeds) and Sudan (Desert, Nilotic, Taggar). The population of 500 MG goats was subdivided into 10 datasets of 50 individuals to ensure that sample sizes of the target (MG) and reference populations are balanced. Performance of an unsupervised ADMIXTURE analysis demonstrated that MG goats have a North African ancestry, with an average proportion of 4.4 ± 2.3%. Next, we did a supervised ADMIXTURE analysis that revealed that the Moroccan genetic component reaches a proportion of 4.01 ± 3.9% in MG goats, while the Algerian (0.001 ± 0.001%), Egyptian (0.2 ± 0.1%), Sudanese (0.1 ± 0.1%) and Tunisian (0.3 ± 0.4%) components are present in extremely small proportions. The historical circumstances of this introgression event are currently unknown, but several plausible scenarios are outlined. Moreover, our results show considerable inter-individual heterogeneity regarding the magnitude of the Moroccan introgression of MG goats (0%- 12% depending on the MG data set under analysis). This result implies that reliable estimates about the introgression of autochthonous livestock by exotic breeds can only be obtained by extensively sampling target populations.

Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene.

The Mangalitza lard-type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow-Belly Mangalitza and Red Mangalitza. The Swallow-Belly line has a black coat combined with yellow-blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci whose frequencies have been modified by artificial selection. The results of selection scans, with HapFLK and BayeScan, and of a GWAS for coat colour highlighted the existence of one region on SSC16 (18-20 Mb) with potential effects on hair pigmentation (Red vs. Blond contrast). The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) locus as a candidate gene for this trait. The polymorphism of the SLC45A2 locus has been associated with reduced levels or the absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G > A and rs693695020:G > A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.

Detecting the footprint of selection on the genomes of Murciano-Granadina goats.

Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. We aimed to identify genomic regions targeted by selection for dairy and pigmentation traits in Murciano-Granadina goats. Performance of a selection scan based on the integrated haplotype score test in a population of 1183 Murciano-Granadina goats resulted in the identification of 77 candidate genomic regions/SNPs. The most significant selective sweeps mapped to chromosomes 1 (69.86 Mb), 4 (41.80-49.95 Mb), 11 (65.74 Mb), 12 (31.24 and 52.51 Mb), 17 (34.76-37.67 Mb), 22 (31.75 Mb), and 26 (26.69-31.05 Mb). By using previously generated RNA-Seq data, we built a catalogue of 6414 genes that are differentially expressed across goat lactation (i.e. 78 days post-partum, early lactation; 216 days post-partum, late lactation; 285 days post-partum, dry period). Interestingly, 183 of these genes mapped to selective sweeps and several of them display functions related with lipid, protein, and carbohydrate metabolism, insulin signaling, cell proliferation, as well as mammary development and involution. Of particular interest are the CSN3 and CSN1S2 genes, which encode two major milk proteins. Additionally, we found three pigmentation genes (GLI3, MC1R, and MITF) co-localizing with selective sweeps. Performance of a genome-wide association study and Sanger sequencing and TaqMan genotyping experiments revealed that the c.801C>G (p.Cys267Trp) polymorphism in the melanocortin 1 receptor (MC1R) gene is the main determinant of the black (GG or GC genotypes) and brown (CC genotypes) colorations of Murciano-Granadina goats.

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep.

We aimed to determine whether casein variants that are currently segregating in ovine populations existed before the domestication of sheep or, to the contrary, if their emergence is much more recent. To this end, we have retrieved whole-genome sequences from Iranian and domestic sheep from Africa, Europe, South and East Asia and West Asia. Population structure analysis based on 55,352,935 SNPs revealed a clear separation between Iranian mouflons and domestic sheep. Moreover, we also observed a strong genetic differentiation between Iranian mouflons sampled in geographic areas close to Tehran and Tabriz. Based on sequence data, hundreds of SNPs mapping to the casein αS1 (CSN1S1, 248 SNPs), casein αS2 (CSN1S2, 268 SNPs), casein ß (CSN2, 146 SNPs) and casein κ (CSN3, 112 SNPs) genes were identified. Approximately 25-63.02% of the casein variation was shared between Iranian mouflons and domestic sheep, and the four domestic sheep populations also shared 44.2-57.4% of the casein polymorphic sites. These findings suggest that an important fraction of the casein variation present in domestic sheep was already segregating in the mouflon prior to its domestication. Genomic studies performed in horses and dogs are consistent with this view, suggesting that much of the diversity that we currently detect in domestic animals comes from standing variation already segregating in their wild ancestors.

Detection of homozygous genotypes for a putatively lethal recessive mutation in the porcine argininosuccinate synthase 1 (ASS1) gene.

The sequencing of the pig genome revealed the existence of homozygous individuals for a nonsense mutation in the argininosuccinate synthase 1 (ASS1) gene (rs81212146, c.944T>A, L315X). Paradoxically, an AA homozygous genotype for this polymorphism is expected to abolish the function of the ASS1 enzyme that participates in the urea cycle, leading to citrullinemia, hyperammonemia, coma and death. Sequencing of five Duroc boars that sired a population of 350 Duroc barrows revealed the segregation of the c.944T>A polymorphism, so we aimed to investigate its phenotypic consequences. Genotyping of this mutation in the 350 Duroc barrows revealed the existence of seven individuals homozygous (AA) for the nonsense mutation. These AA pigs had a normal weight despite the fact that mild citrullinemia often involves impaired growth. Sequencing of the region surrounding the mutation in TT, TA and AA individuals revealed that the A substitution in the second position of the codon (c.944T>A) is in complete linkage disequilibrium with a C replacement (c.943T>C) in the first position of the codon. This second mutation would compensate for the potentially damaging effect of the c.944T>A replacement. In fact, this is the most probable reason why pigs with homozygous AA genotypes at the 944 site of the ASS1 coding region are alive. Our results illustrate the complexities of predicting the consequences of nonsense mutations on gene function and phenotypes, not only because of annotation issues but also owing to the existence of genetic mechanisms that sometimes limit the penetrance of highly harmful mutations.

Low genome-wide homozygosity in 11 Spanish ovine breeds.

The population of Spanish sheep has decreased from 24 to 15 million heads in the last 75 years due to multiple social and economic factors. Such a demographic reduction might have caused an increase in homozygosity and inbreeding, thus limiting the viability of local breeds with excellent adaptations to harsh ecosystems. The main goal of our study was to investigate the homozygosity patterns of 11 Spanish ovine breeds and to elucidate the relationship of these Spanish breeds with reference populations from Europe, Africa and the Near East. By using Ovine SNP50 BeadChip data retrieved from previous publications, we have found that the majority of studied Spanish ovine breeds have close genetic relatedness with other European populations; the one exception is the Canaria de Pelo breed, which is similar to North African breeds. Our analysis has also demonstrated that, with few exceptions, the genomes of Spanish sheep harbor fewer than 50 runs of homozygosity (ROH) with a total length of less than 350 Mb. Moreover, the frequencies of very long ROH (>30 Mb) are very low, and the inbreeding coefficients (FROH ) are generally small (FROH  < 0.10), ranging from 0.008 (Rasa Aragonesa) to 0.086 (Canaria de Pelo). The low levels of homozygosity observed in the 11 Spanish sheep under analysis might be due to their extensive management and the high number of small to medium farms.