Genetic polymorphisms at candidate genes affecting fat content and fatty acid composition in Modicana cows: effects on milk production traits in different feeding systems.

Feeding greatly affects milk yield and composition. The research is highlighting the potential of genetic polymorphism at some loci to affect milk yield and quality traits. These loci can be up/down regulated depending on the production environment; therefore, we hypothesized that milk yield and composition could differ when cows with different genotype at SCD, DGAT1 and ABCG2 loci are reared in different feeding systems. The polymorphisms of SCD, DGAT1 and ABCG2 genes were investigated in Modicana breed. In all, three polymorphic sites, responsible for the genetic variation of quantitative trait loci and therefore defined quantitative trait nucleotides, were genotyped: the transition g.10329C>T in 5th exon determines a substitution p.A293V in the SCD, the dinucleotide mutation g.10433-10434AA>GC in 8th exon responsible for p.K232A substitution in the DGAT1 and the transition g.62569A>C in the 14th exon responsible for p.Y581S substitution in the ABCG2 gene. In the sample of 165 Modicana cows, SCD and DGAT1 genes resulted polymorphic; the alleles g.10329T and g.10433-10434GC were the most frequent in SCD and DGAT1 (0.73 and 0.91) respectively, whereas ABCG2 locus was monomorphic for allele A (p.581Y). Sequencing analysis was carried out on 14 samples with different genotypes to confirm the results of the PCR-RFLP protocols. Based on the genotypes at SCD locus, 47 Modicana cows were selected for the nutritional trial: 24 cows in a semi-intensive farm, with 2 h/day grazing on natural pasture, and 23 cows in an extensive farm, with 8 h/day grazing on natural pasture. Monthly, milk yield and composition were evaluated and individual milk samples were analyzed for fatty acids composition by gas chromatography. No differences in milk yield, fat, protein, lactose, casein and urea were associated to SCD genotype. Feeding systems affected milk yield and composition. No significant genotype×feeding system interaction was observed for milk yield and composition. Fatty acids composition was significantly affected only by the feeding system. Significant interactions were found between SCD genotype and feeding system for six fatty acids: 4:0, 6:0, 8:0, 10:0, 12:0 and t11 18:1. We concluded that the feeding system was the factor that mostly affected milk production and composition; moreover, our results do not confirm what reported in literature as regard the effect of the SCD polymorphism on milk fatty acid composition. The high amount of pasture seemed to have resized the SCD polymorphism effects because of the different fatty acids composition of the diet.

Genome-wide variability and selection signatures in Italian island cattle breeds.

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo-Bruna and Sardo-Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within-breed genetic heterogeneity. The FST comparison revealing the largest number of significant SNPs was Sardo-Bruna vs. Sardo-Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo-Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo-Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi-dimensional scaling and the admixture analysis the Sardo-Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo-Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.

Genetic relationships among American donkey populations: insights into the process of colonization.

This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model-based methods. These populations were then compared to a database containing information on 476 individuals from 11 European breeds to identify the most likely ancestral donor populations. Results showed the presence of two distinct genetic pools, with confluence of the two in Colombia. The southern pool showed a unique genetic signature subsequent to an older founder event, but lacked any significant influence of modern gene flow from Europe. The northern pool, conversely, may have retained more ancestral polymorphisms and/or have experienced modern gene flow from Spanish breeds. The Andalusian and, to a lesser extent, the Catalan breeds have left a more pronounced footprint in some of the American donkey populations analysed.

A genetic analysis of the Italian Salernitano horse.

Salernitano (SAL) is an ancient Italian horse breed developed over the course of the ages together with Napoletano and, during the 20th century, by crossing with Thoroughbred horse lines. Excellent in hurdle jumping, this breed is currently facing a concrete risk of extinction due to the lack of appropriate management strategies. This research is the first SAL genetic characterization that aims to set up the basic knowledge for a conservation plan. A representative sample of 61 SALs was analyzed by means of a set of 16 microsatellites markers (short tandem repeats (STRs)). The sequence of hypervariable D-loop mtDNA region was also performed on a subset of 24 mares in order to study the maternal diversity and obtain a complete picture of the internal genetic variation. All the molecular data were analyzed together with those obtained from three Sicilian horse breeds investigated in a previous research (Siciliano, Sanfratellano and Sicilian Oriental Purebred). STRs markers revealed a moderate level of genetic diversity in SAL (alleles/locus 5.1, He 0.67) and confirmed the hunch of genetic erosion. Autosomal variability highlighted a very light deficit of homozygotes (FIS=-0.067). Experimental D-loop sequences were compared by multiple alignments with those retrieved from biological databases and revealed two unreported haplotypes. The phylogenetic network, which was built on mtDNA sequences, included various cosmopolitan and European horses and showed SAL haplotypes distributed among different mtDNA lineages.

Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds.

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.

The mathematical modeling of the lactation curve for dairy traits of the donkey (Equus asinus).

In recent years, an increase in the number of donkeys farmed in Italy as a consequence of the growing demand for donkey milk for direct consumption has been observed. Some research has been carried out on jenny milk composition and on its nutritional properties, whereas milk production features are scarcely described for this species. In this work, the lactation curve shape of donkeys for milk yield and composition was investigated. A total of 453 test-day records for milk yield, fat and protein percentage, and somatic cell count of 62 lactations measured on 46 multiparous jennies of the Ragusano breed were considered. Effects of herd, age, and foaling season were assessed by using a mixed model analysis. Average and individual lactation curves were fitted using the Wood incomplete gamma function, the Cappio-Borlino modified gamma, and a third-order Legendre orthogonal polynomial model. Donkeys foaling between 6- and 10-yr-old had the highest test-day milk yield (about 1.85 kg/d). Donkeys foaling in winter and autumn had a higher daily milk yield compared with those foaling in summer and spring. Less defined results were obtained for composition traits. The general pattern of the donkey lactation curve is similar to the standard shape reported for the main dairy ruminant species, with a peak yield occurring at about 5 wk from parturition. Younger jennies tended to have lower production peaks and higher lactation persistency. Similarly to what is reported for dairy cattle, a large variability in individual patterns has been observed. No differences in goodness of fit have been observed between the models in the case of average lactation curves, whereas orthogonal polynomials were more efficient in fitting individual patterns.

Evolutionary study of a potential selection target region in the pig.

Domestication, modern breeding and artificial selection have shaped dramatically the genomic variability of domestic animals. In livestock, the so-called FAT1 quantitative trait locus (QTL) in porcine chromosome 4 was the first QTL uncovered although, to date, its precise molecular nature has remained elusive. Here, we characterize the nucleotide variability of 13 fragments of ∼500 bp equally spaced in a 2 Mb region in the vicinity of the FAT1 region in a wide-diversity panel of 32 pigs. Asian and European animals, including local Mediterranean and international pig breeds, were sequenced. Patterns of genetic variability were very complex and varied largely across loci and populations; they did not reveal overall a clear signal of a selective sweep in any breed, although FABP4 fragment showed a significantly higher diversity. We used an approximate Bayesian computation approach to infer the evolutionary history of this SSC4 region. Notably, we found that European pig populations have a much lower effective size than their Asian counterparts: in the order of hundreds vs hundreds of thousands. We show also an important part of extant European variability is actually due to introgression of Asian germplasm into Europe. This study shows how a potential loss in diversity caused by bottlenecks and possible selective sweeps associated with domestication and artificial selection can be counterbalanced by migration, making it much more difficult the identification of selection footprints based on naive demographic assumptions. Given the small fragment analyzed here, it remains to be studied how these conclusions apply to the rest of the genome.

Genetic diversity and admixture analysis of Sanfratellano and three other Italian horse breeds assessed by microsatellite markers.

Sanfratellano is a native Sicilian horse breed, mainly reared in the north east of the Island, developed in the 19th century from local dams and sires with a restricted introgression of Oriental, African and, more recently, Maremmano stallions. In this study, the genetic relationships and admixture among Sanfratellano, the other two Sicilian autochthonous breeds and Maremmano breed were assessed using a set of microsatellites. The main goals were to infer the impact of Maremmano breed in the current Sanfratellano horse and to provide genetic information useful to improve the selection strategies of the Sanfratellano horse. The whole sample included 384 horses (238 Sanfratellano, 50 Sicilian Oriental Purebred, 30 Sicilian Indigenous and 66 Maremmano), chosen avoiding closely related animals. A total of 111 alleles from 11 microsatellite loci were detected, from four at HTG7 to 15 at ASB2 locus. The mean number of alleles was the lowest in Oriental Purebred (6.7), the highest in Sanfratellano (8.3). All the breeds showed a high level of gene diversity (He) ranging from 0.71 ± 0.04 in Sicilian Oriental Purebred to 0.81 ± 0.02 in Sicilian Indigenous. The genetic differentiation index was low; only about 6% of the diversity was found among breeds. Nei's standards (DS) and Reynolds' (DR) genetic distances reproduced the same population ranking. Individual genetic distances and admixture analysis revealed that: (a) nowadays Maremmano breed does not significantly influence the current Sanfratellano breed; (b) within Sanfratellano breed, it is possible to distinguish two well-defined groups with different proportions of Indigenous blood.

Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers.

The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20-122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within-breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. The mean molecular coancestry of the entire population examined was 0.205, Losino being the breed that contributed most. In addition to Nei's standard and Reynolds' genetic distances, pair-wise kinship distance and molecular coancestry were estimated. Remarkably similar breed rankings were obtained with all methods. Clustering analysis provided an accurate representation of the current genetic relationships among the breeds. Determining coancestry is useful for analysing genetic diversity distribution between and within breeds and provides a good framework for jointly analysing molecular markers and pedigree information. An integrated analysis was undertaken to obtain information on the population dynamics in western Mediterranean native horse populations, and to better determine conservation priorities.

Characterization of single nucleotide polymorphisms in sheep and their variation as evidence of selection.

The discovery of SNPs was performed using animals from eight European sheep breeds. Eleven SNPs were further characterized using about 1,700 sheep belonging to 57 breeds. A method for the identification of loci that were likely subject to selection was applied; three of the 11 SNPs lying outside the 95% confidence region of the conditional joint distribution of F(ST) and mean heterozygosity were identified as outliers.

Assessment of population structure by single nucleotide polymorphisms (SNPs) in goat breeds.

Single nucleotide polymorphisms (SNPs) may be used in biodiversity studies and commercial tasks like traceability, paternity testing and selection for suitable genotypes. Twenty-seven SNPs were characterized and genotyped on 250 individuals belonging to eight Italian goat breeds. Multilocus genotype data were used to infer population structure and assign individuals to populations. To estimate the number of groups (K) to test in population structure analysis we used likelihood values and variance of the bootstrap samples, deriving optimal K from a drop in the likelihood and a rise in the variance plots against K.

Effects of shearing and supplemental level on intake of dry ewes grazing on barley stubble.

Twenty-eight Comisana dry ewes were utilised to evaluate the effect of shearing (14 shorn and 14 unshorn ewes) and supplemental level (100 and 300g of concentrate) on intake of barley stubble. Shorn ewes showed a small increase in dry matter intake (at the end of August: 1.32 vs. 1.10kg/day; p<0.01). Intake of barley stubble decreased as supplement level increased (mean: 1.18 vs. 1.29; p<0.01). On average, substitution effect was 0.63. Total lamb weight per ewe was greater in the group receiving 300g of concentrate (7.38 vs. 5.85; p<0.05). Shearing induced a small, but not significant decrease in total lamb weight per ewe (6.18 vs. 7.05kg/ewe). Results seem to indicate that unshorn ewes react better to environmental stress and that 300g improve reproductive performance.

Characterization of the CSN1AG allele of the bovine alpha s1-casein locus by the insertion of a relict of a long interspersed element.

The bovine CSN1AG allele is associated with a lower proportion of alpha s1-casein in milk and is characterized by an insertion in the last noncoding exon (19th). According to DNA sequence analysis, the location, length, and origin of the insertion characterizing the bovine CSN1AG allele have been identified. This insertion interrupts the 19th exon between nucleotides 58 and 59, is 371 bp long, and has a high level of homology with relicts of long interspersed elements of retropositional origin. Northern blot analysis shows that the inserted element is transcribed and that the number of transcripts of the CSN1AG allele is less than one-half of the number of transcripts of the CSN1AB allele. The lower amount of alpha s1-casein in milk obtained from cows carrying the CSN1AG allele can be explained by a reduced mRNA stability. Furthermore, a method has been developed using polymerase chain reaction for identification of the carriers of the CSN1AG allele.

Effect of sustained-release somatotropin on performance and grazing behavior of ewes housed at different stocking rates.

This study evaluated the effects of recombinant bovine somatotropin (bST; one injection of 320 mg per ewe) on milk production and composition and on the grazing behavior of multiparous ewes in the third to fourth lactation. Forty Comisana lactating ewes were divided into four groups: 1) untreated, grazing on natural pasture (botanical composition: 35% of Graminaceae, 49% of Fabaceae, 6% of Cruciferae, 10% of other families) at a low stocking rate (16 m2/d); 2) untreated, grazing at a high stocking rate (8 m2/d); 3) treated with bST, grazing at a low stocking rate; and 4) treated with bST, grazing at a high stocking rate. The diets of the ewes were supplemented with vetch and oat hay (500 g/d) and with concentrate (500 g/d). Treatment increased milk production (923.8 vs. 669.5 g/d) but had little effect on fat and protein contents. Administration of bST significantly increased herbage intake; the effect on intake was more marked at the high stocking rate. Under these grazing conditions, the treated ewes reduced selective intake behavior and, thus, achieved good feed intake despite the low biomass availability.