A genome-wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent selection

About three decades of breeding and selection in the Valle del Belìce sheep are expected to have left several genomic footprints related to milk production traits. In this study, we have assembled a dataset with 451 individuals of the Valle del Belìce sheep breed: 184 animals that underwent directional selection for milk production and 267 unselected animals, genotyped for 40,660 single-nucleotide polymorphisms (SNPs). Three different statistical approaches, both within (iHS and ROH) and between (Rsb) groups, were used to identify genomic regions potentially under selection. Population structure analyses separated all individuals according to their belonging to the two groups. A total of four genomic regions on two chromosomes were jointly identified by at least two statistical approaches. Several candidate genes for milk production were identified, corroborating the polygenic nature of this trait and which may provide clues to potential new selection targets. We also found candidate genes for growth and reproductive traits. Overall, the identified genes may explain the effect of selection to improve the performances related to milk production traits in the breed. Further studies using high-density array data, would be particularly relevant to refine and validate these results

Exploring genome-wide differentiation and signatures of selection in Italian and North American Holstein populations

Among Italian dairy cattle, the Holstein is the most reared breed for the production of Parmigiano Reggiano protected designation of origin cheese, which represents one of the most renowned products in the entire Italian dairy industry. In this work, we used a medium-density genome-wide data set consisting of 79,464 imputed SNPs to study the genetic structure of Italian Holstein breed, including the population reared in the area of Parmigiano Reggiano cheese production, and assessing its distinctiveness from the North American population. Multidimensional scaling and ADMIXTURE approaches were used to explore the genetic structure among populations. We also investigated putative genomic regions under selection among these 3 populations by combining 4 different statistical methods based either on allele frequencies (single marker and window-based) or extended haplotype homozygosity (EHH; standardized log-ratio of integrated EHH and cross-population EHH). The genetic structure results allowed us to clearly distinguish the 3 Holstein populations; however, the most remarkable difference was observed between Italian and North American stock. Selection signature analyses identified several significant SNPs falling within or closer to genes with known roles in several traits such as milk quality, resistance to disease, and fertility. In particular, a total of 22 genes related to milk production have been identified using the 2 allele frequency approaches. Among these, a convergent signal has been found in the VPS8 gene which resulted to be involved in milk traits, whereas other genes (CYP7B1, KSR2, C4A, LIPE, DCDC1, GPR20, and ST3GAL1) resulted to be associated with quantitative trait loci related to milk yield and composition in terms of fat and protein percentage. In contrast, a total of 7 genomic regions were identified combining the results of standardized log-ratio of integrated EHH and cross-population EHH. In these regions candidate genes for milk traits were also identified. Moreover, this was also confirmed by the enrichment analyses in which we found that the majority of the significantly enriched quantitative trait loci were linked to milk traits, whereas the gene ontology and pathway enrichment analysis pointed to molecular functions and biological processes involved in AA transmembrane transport and methane metabolism pathway. This study provides information on the genetic structure of the examined populations, showing that they are distinguishable from each other. Furthermore, the selection signature analyses can be considered as a starting point for future studies in the identification of causal mutations and consequent implementation of more practical application

Observation of classically `forbidden' electromagnetic wave propagation and implications for neutrino detection

Ongoing experimental efforts in Antarctica seek to detect ultra-high energy neutrinos by measurement of radio-frequency (RF) Askaryan radiation generated by the collision of a neutrino with an ice molecule. An array of RF antennas, deployed either in-ice or in-air, is used to infer the properties of the neutrino. To evaluate their experimental sensitivity, such experiments require a refractive index model for ray tracing radio-wave trajectories from a putative in-ice neutrino interaction point to the receiving antennas; this gives the degree of signal absorption or ray bending from source to receiver. The gradient in the density profile over the upper 200 meters of Antarctic ice, coupled with Fermat's least-time principle, implies ray "bending" and the existence of "forbidden" zones for predominantly horizontal signal propagation at shallow depths. After re-deriving the formulas describing such shadowing, we report on experimental results that, somewhat unexpectedly, demonstrate the existence of electromagnetic wave transport modes from nominally shadowed regions. The fact that this shadow-signal propagation is observed both at South Pole and the Ross Ice Shelf in Antarctica suggests that the effect may be a generic property of polar ice, with potentially important implications for experiments seeking to detect neutrinos.Comment: 33 pages, 14 figures, accepted for publication in JCA

Probing the angular and polarization reconstruction of the ARIANNA detector at the South Pole

The sources of ultra-high energy (UHE) cosmic rays, which can have energies up to 10^20 eV, remain a mystery. UHE neutrinos may provide important clues to understanding the nature of cosmic-ray sources. ARIANNA aims to detect UHE neutrinos via radio (Askaryan) emission from particle showers when a neutrino interacts with ice, which is an efficient method for neutrinos with energies between 10^16 eV and 10^20 eV. The ARIANNA radio detectors are located in Antarctic ice just beneath the surface. Neutrino observation requires that radio pulses propagate to the antennas at the surface with minimum distortion by the ice and firn medium. Using the residual hole from the South Pole Ice Core Project, radio pulses were emitted from a transmitter located up to 1.7 km below the snow surface. By measuring these signals with an ARIANNA surface station, the angular and polarization reconstruction abilities are quantified, which are required to measure the direction of the neutrino. After deconvolving the raw signals for the detector response and attenuation from propagation through the ice, the signal pulses show no significant distortion and agree with a reference measurement of the emitter made in an anechoic chamber. Furthermore, the signal pulses reveal no significant birefringence for our tested geometry of mostly vertical ice propagation. The origin of the transmitted radio pulse was measured with an angular resolution of 0.37 degrees indicating that the neutrino direction can be determined with good precision if the polarization of the radio-pulse can be well determined. In the present study we obtained a resolution of the polarization vector of 2.7 degrees. Neither measurement show a significant offset relative to expectation

White Paper: ARIANNA-200 high energy neutrino telescope

The proposed ARIANNA-200 neutrino detector, located at sea-level on the Ross Ice Shelf, Antarctica, consists of 200 autonomous and independent detector stations separated by 1 kilometer in a uniform triangular mesh, and serves as a pathfinder mission for the future IceCube-Gen2 project. The primary science mission of ARIANNA-200 is to search for sources of neutrinos with energies greater than 10^17 eV, complementing the reach of IceCube. An ARIANNA observation of a neutrino source would provide strong insight into the enigmatic sources of cosmic rays. ARIANNA observes the radio emission from high energy neutrino interactions in the Antarctic ice. Among radio based concepts under current investigation, ARIANNA-200 would uniquely survey the vast majority of the southern sky at any instant in time, and an important region of the northern sky, by virtue of its location on the surface of the Ross Ice Shelf in Antarctica. The broad sky coverage is specific to the Moore's Bay site, and makes ARIANNA-200 ideally suited to contribute to the multi-messenger thrust by the US National Science Foundation, Windows on the Universe - Multi-Messenger Astrophysics, providing capabilities to observe explosive sources from unknown directions. The ARIANNA architecture is designed to measure the angular direction to within 3 degrees for every neutrino candidate, which too plays an important role in the pursuit of multi-messenger observations of astrophysical sources

A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds

BACKGROUND: To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS: The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS: To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes