The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine genetic diversity to date, providing an important resource for the design and development of livestock production. We studied this dataset, comprising more than 30,000 Single Nucleotide Polymorphisms (SNPs) for 19 breeds (13 taurine, three zebu, and three hybrid breeds), seeking to identify small panels of genetic markers that can be used to trace the breed of unknown cattle samples. Taking advantage of the power of Principal Components Analysis and algorithms that we have recently described for the selection of Ancestry Informative Markers from genomewide datasets, we present a decision-tree which can be used to accurately infer the origin of individual cattle. In doing so, we present a thorough examination of population genetic structure in modern bovine breeds. Performing extensive cross-validation experiments, we demonstrate that 250-500 carefully selected SNPs suffice in order to achieve close to 100% prediction accuracy of individual ancestry, when this particular set of 19 breeds is considered. Our methods, coupled with the dense genotypic data that is becoming increasingly available, have the potential to become a valuable tool and have considerable impact in worldwide livestock production. They can be used to inform the design of studies of the genetic basis of economically important traits in cattle, as well as breeding programs and efforts to conserve biodiversity. Furthermore, the SNPs that we have identified can provide a reliable solution for the traceability of breed-specific branded products.
The purpose of this study was to determine the occurrence and antimicrobial resistance of Streptococcus spp. isolated from fresh ewe's milk and consequently to draw conclusions concerning the health condition of the animal flocks and the current trends of antibiotic use in small ruminants. A total of 77 mountainous sheepfolds were investigated representing 10% of all transhumant sheep and goats flocks in the area. Duplicate milk samples were collected from January to February transferred to the laboratory and analyzed for the presence of Streptococcus spp. by using the serial dilution method and plating on the surface of Slanetz and Bartley agar. The isolates were tested against nine antimicrobial agents with the Kirby-Bauer disk diffusion method. The results showed that Streptococcus spp. occurred in 84.4% of the samples and in counts ranged between 1.8 log CFU/mL and 4.6 log CFU/mL. Concerning susceptibility, only 1.3% of the isolates were resistant to all antimicrobials while 27.3% were fully susceptible. Resistance to cefepime was the most common (93.1%) observation followed by resistance to ampicillin (82.1%), ciprofloxacine (58.3%) and meropenem (51.9%). The isolates were vancomycin susceptible at a rate of 83.6%. Multidrug resistance to at least three antibiotics was observed to be 22.1% of Streptococcus spp.. Given the prevalence of Streptococcus spp. and the elevated resistance of isolates to various antibiotics it is concluded that further examinations and even interventions are required in order to pertain the appropriate animal health and milk quality.
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