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

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.

Effects of α s1-casein (CSN1S1) and κ-casein (CSN3) genotypes on milk coagulation properties in Murciano-Granadina goats.

The effects of the caprine α s1-casein (CSN1S1) polymorphisms on milk quality and cheese yield have been widely studied in French and Italian goat breeds. Much less is known about the consequences of κ-casein (CSN3) genotype on the technological and coagulation properties of goat milk. In the current study, we have performed an association analysis between polymorphisms at the goat CSN1S1 and CSN3 genes and milk coagulation (rennet coagulation time, curdling rate and curd firmness) and technological (time to cutting of curd and cheese yield) properties. In this analysis, we have included 193 records from 74 Murciano-Granadina goats (with genotypes constituted by different combinations of alleles B, E and F of the gene CSN1S1 and alleles A and B of the gene CSN3) distributed in three herds, which were collected bimonthly during a whole lactation. Data analysis, using a linear mixed model for repeated observations, revealed significant associations between CSN1S1 genotypes and the rate of the curdling process. In this way, milk from EE goats had a significantly higher curdling rate than milk from BB individuals (P<0·05). Contrary to previous experiments performed in French breeds, cheese yield was not significantly different in BB, EE and EF goats. Moreover, we have shown that CSN3 genotype has a significant effect on the rennet coagulation time (BB>AB, P<0·05) but not on cheese yield. No interaction between the CSN1S1 and CSN3 genotypes was observed.

Use of Principal Component Analysis to Combine Genetic Merit for Heat Stress and for Fat and Protein Yield in Spanish Autochthonous Dairy Goat Breeds.

We studied the effect of the Temperature Humidity Index (THI) (i.e., the average of temperature and relative humidity registered at meteorological stations) closest to the farms taken during the test day (TD), for total daily protein and fat yields (fpy) of the three main Spanish dairy goats. The data were from Florida (11,244 animals and 126,825 TD), Malagueña (12,215 animals and 141,856 TD) and Murciano Granadina (5162 animals and 62,834 TD) breeding programs and were studied by different linear models to estimate the nature of the fpy response throughout the THI and the weeks of lactation (Days in Milk, DIM) trajectories. The results showed an antagonism between THI and DIM, with a marked depression in the fpy level in animals kept in the hot zone of the THI values (THI > 25) compared with those in the cold zone (THI ≤ 16), with a negative impact equivalent to production of 13 to 30 days. We used a Reaction Norm model (RN), including THI and DIM as fixed covariates and a Test Day Model (TDM), to estimate the genetic (co)variance components. The heritability and genetic correlations estimated with RN and TDM showed a decreased pattern along the scale of THI and DIM, with slight differences between breeds, meaning that there was significant genetic variability in the animal's ability to react to different levels of THI, which is not constant throughout the DIM, showing the existence of genotype-environment interaction. The breeding values (BV) of all animals for each level of THI and DIM were subject to a principal component analysis, and the results showed that 89 to 98% of the variance between the BV was explained by the two first eigenvalues. The standardized BV were weighted with the corresponding eigenvector coefficients to construct an index that showed, in a single indicator, the most complete expression of the existing genetic variability in the animals' ability to produce fpy along the trajectories of THI and DIM. This new option will make it easier to select animals which are more productive, and with better adaptability to heat stress, as well as enabling us to exploit genetic variations in the form of the response to heat stress to be adapted to different production systems.

Effect of alphas1-casein ( CSN1S1) genotype on milk CSN1S1 content in Malagueña and Murciano-Granadina goats.

There is substantial evidence showing that the polymorphism of the goat alphas1-casein (CSN1S1) gene has a major effect on milk protein, casein and fat content as well as on cheese yield. However, its influence on the synthesis rate of CSN1S1 has been less studied, with measurements only available in French breeds. In this article, we have measured milk CSN1S1 content in 89 Malagueña and 138 Murciano-Granadina goats with 305 and 460 phenotypic registers, respectively. In the Malagueña breed, average values of CSN1S1 content estimated for BB, BF, EE and FF genotypes were 6.94+/-0.38, 5.36+/-0.22, 4.58+/-0.13 and 3.98+/-0.27 g/l, respectively, being all significantly different (P<0.05). Conversely, in the Murciano-Granadina breed only the BB genotype (8.50+/-0.60 g/l) was significantly associated with increased levels of CSN1S1 (P<0.05), whereas BF (6.56+/-0.82 g/l), EE (6.39+/-0.60 g/l) and EF (6.91+/-0.76 g/l) genotypes displayed non-significant differences when compared with each other. Our results highlight the existence of breed-specific genetic and/or environmental factors modulating the impact of the CSN1S1 gene polymorphism on the synthesis rate of the corresponding protein.