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Summary: 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The genetic variation at four milk protein lociαs1-casein (CSN1S1),β-casein (CSN2),κ-casein (CSN3) andβ-lactoglobulin (LGB) was investigated in 358 animals belonging to seven populations well adapted to hot climatic conditions, reared in Africa and Italy.Bos taurus(Somba, Lagune and Modicana),Bos indicus(Sudanese Zebu Peul, Azaouak and Adamawa), andB. taurus × B. indicus(Borgou) were studied by adapting different molecular methodologies to evaluate their genetic variability. All loci were polymorphic and a newCSN2synonymous variant, namedA2′, was detected and characterized. Noteworthy differences in the distribution of alleles and haplotypes were observed between zebuine and taurine cattle showing that milk protein polymorphism is suited for discriminatingB. taurusfromB. indicusefficiently, and also taurine breeds. Milk protein loci, being positively selected loci, can also provide information about the occurrence of germplasm particularly useful for breeding strategies and production improvement. [ABSTRACT FROM AUTHOR]

In goat at CSN1S2 locus, seven alleles have been observed, characterized by different levels of expression, and, in particular, a null allele CSN1S2O that significantly influences protein composition of milk.In a local goat breed reared in the North East of Sicily, “Argentata dell’Etna”, the combined use of electrophoretic milk analysis (SDS-PAGE) and 11th exon genomic analysis (PCR-RFLP) made it possible to identify three genotypes respectively normal (CSN1S2NN), heterozygote for the null allele (CSN1S2NO) and homozygote for the null allele (CSN1S2OO). In 214 “Argentata dell’Etna” goats, CSN1S2O allele has shown a frequency of 0.033.An immunological test, REAST-inhibition assay (REAST, reverse enzyme allergo sorbent test), was carried out on three lyophilized milk samples (casein and seroprotein fractions) produced by goats with different genotypes at CSN1S2 locus, in order to assess their allergenic potency. By comparing the C50, the casein fraction CSN1S2NN turned out to be the most allergenic, followed by the fraction CSN1S2OO with 60% potency compared to the first one, while the fraction CSN1S2NO presented 54% potency compared to the first one. [Copyright &y& Elsevier]

In this study we surveyed two endangered Sicilian goat breeds (Girgentana and Argentata dell'Etna) for genetic polymorphism at the CSN1S2 locus. In a total of 537 goats, we detected CSN1S2A, CSN1S2B, CSN1S2C° (CSN1S2C + CSN1S2E), CSN1S2D, CSN1S2F and CSN1S2O alleles by means of various polymerase chain reaction (PCR), allele specific-PCR (AS –PCR) and PCR-restriction fragment length polymorphism (RFLP) reactions with the aim of improving the knowledge of the genetic resource of these two breeds. Three and five alleles, with six and twelve genotypes, were identified at CSN1S2 locus, in Girgentana and Argentata, respectively. Argentata dell'Etna showed a higher degree of genetic variation. The allelic and genotypic distribution seems to be significantly different (p < 0.001) in the two breeds. In Argentata the rare null allele (CSN1S2O) was found at low frequency (0.033); this genetic peculiarity makes its preservation worthwhile. [ABSTRACT FROM AUTHOR]

Abstract: 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. [Copyright &y& Elsevier]