Genetic variability in a Holstein population using SNP markers and their use for monitoring mating strategies

As genotyping costs continue to decrease, the demand for genotyping has increased among farmers. In most livestock herds, an important issue is controlling the increase in inbreeding coefficient. While this remains a large motive to genotype, producers are often unaware of the other benefits that genotyping could bring. The aim of this study was to demonstrate that SNP chips could be used as an effective herd management tool by utilizing a population of Italian Holstein-Friesian cattle. After filtering, the total number of animals and SNPs retained for analyses were 44 and 27,365, respectively. The principal component analyses (PCA) were able to identify a sire and origin-of-sire effect within the herd, while determining that sires do not influence individual genomic selection index values. The inbreeding coefficients calculated from genotypes (FIS) provided a glimpse into the herd\u2019s heterozygosity and determined that the genetic variability is being well maintained. On the other hand, inbreeding coefficients on the genomic level were deduced from runs of homozygosity (FROH) and were compared to the inbreeding coefficients based on pedigree (FPED). Furthermore, 1,950 runs of homozygosity (ROH) were identified with the average length of ROH being 4.66 Mb. Genes and QTL within the genomic regions most commonly associated (top 1% and top 5% of SNP) with ROH were characterized. These results indicate that genotyping small herds, albeit at low-density, provides insights to the genetic variability within the herd and thus allows producers the ability to manage their stock from a genetic standpoint

The missing whales: relevance of “struck and lost” rates for the impact assessment of historical whaling in the southwestern Atlantic Ocean

The massive impact that open-boat historical whaling (18th to 20th centuries) had on whale populations has been traditionally estimated from records of oil and baleen plate production. However, an unknown proportion of hunted whales were struck, wounded, eventually killed, but lost, and not included in these records, suggesting that whaling impact may be critically underestimated. Whaling logbooks provide a key source for assessing past catches and losses. Here, we extract detailed records of 19875 days of activity in the southwestern Atlantic Ocean from 255 logbooks of offshore whaling voyages. During the period considered (1776–1923), whalers first targeted southern right whales (Eubalaena australis, 2497 sightings and 658 catches), gradually substituted by sperm whales (Physeter macrocephalus, 1157 sightings and 843 catches) after 1840. Loss rate factors, calculated to account for the number of “struck and lost” whales, decreased across time for both species, and were particularly high (ranging 1.09–1.6) for the southern right whale, whose population was drastically reduced by whaling, as compared to previous estimates based on rough catch records. Accurate accounting for these “lost” individuals is essential for reconstructing the impact of whaling on cetacean populations and for a proper assessment of their initial population size and demographic trends.Postprint2,27

A new design for the CERN-Fr\'ejus neutrino Super Beam

We present an optimization of the hadron focusing system for a low-energy high-intensity conventional neutrino beam (Super-Beam) proposed on the basis of the HP-SPL at CERN with a beam power of 4 MW and an energy of 4.5 GeV. The far detector would be a 440 kton Water Cherenkov detector (MEMPHYS) located at a baseline of 130 km in the Fr\'ejus site. The neutrino fluxes simulation relies on a new GEANT4 based simulation coupled with an optimization algorithm based on the maximization of the sensitivity limit on the $\theta_{13}$ mixing angle. A new configuration adopting a multiple horn system with solid targets is proposed which improves the sensitivity to $\theta_{13}$ and the CP violating phase $\delta_{CP}$.Comment: 11 pages, 18 figures, 2 table