ANALYSIS OF GENOMIC DATA IN RUMINANT SPECIES FOR PARENTAGE, PRODUCT TRACING AND POPULATION STRUCTURE STUDIES

The availability of genomic and high performance computing technologies gave access to new approaches and methods to exploit the high number of genetic information provided, even in livestock species. These new tools can be used to unveil the relationships between different populations or individuals, to understand the genetic background of breeds, to define the genetic architecture of phenotypes or pathologies and to detect selection signatures that shaped the cattle, sheep and goat reared today. In this context, these technologies may provide breeders and breeders\u2019 associations with new tools that may be used in livestock management. In fact, the estimation of genomic parentage among individuals can help in defining the least related animals in case of identical values of additive parentage and detect errors in pedigree declarations as well. Moreover, since DNA is immutable within animal life but very polymorphic between individuals, these tools may be of help in the definition of the breed or the individual of origin, improving food safety. In this thesis, I faced the complexity of genomic data in ruminant species, focusing in particular on goats. I reported three studies with distinct aims: i) study the signatures of selection in 369 animals of 16 Italian populations, and then focusing on the Valdostana goat breed which presents a breed-specific broad signature of selection in chromosome 7; ii) define a new method to develop panels of SNPs for parentage assessment that could be applied on species with unreliable genomic assembly; and iii) study the selection signatures in 929 animals of 41 Pakistani and Italian goat populations associated with a specific pigmentation pattern, the roan, detecting a candidate gene important in understanding the coat color genetics in goats and which could be also used as a marker for traceability of breeds that carry this peculiar phenotypic pattern

Extremal functions for the anisotropic Sobolev inequalities

The existence of multiple nonnegative solutions to the anisotropic critical problem - \sum_{i=1}^{N} \frac{\partial}{\partial x_i} (| \frac{\partial u}{\partial x_i} |^{p_i-2} \frac{\partial u}{\partial x_i}) = |u|^{p^*-2} u {in} \mathbb{R}^N is proved in suitable anisotropic Sobolev spaces. The solutions correspond to extremal functions of a certain best Sobolev constant. The main tool in our study is an adaptation of the well-known concentration-compactness lemma of P.-L. Lions to anisotropic operators. Futhermore, we show that the set of nontrival solutions \calS is included in $L^\infty(\R^N)$ and is located outside of a ball of radius $\tau >0$ in $L^{p^*}(\R^N)$

Asymptotic behaviour of a semilinear elliptic system with a large exponent

Consider the problem \begin{eqnarray*} -\Delta u &=& v^{\frac 2{N-2}},\quad v>0\quad {in}\quad \Omega, -\Delta v &=& u^{p},\:\:\:\quad u>0\quad {in}\quad \Omega, u&=&v\:\:=\:\:0 \quad {on}\quad \partial \Omega, \end{eqnarray*} where $\Omega$ is a bounded convex domain in $\R^N,$ $N>2,$ with smooth boundary $\partial \Omega.$ We study the asymptotic behaviour of the least energy solutions of this system as $p\to \infty.$ We show that the solution remain bounded for $p$ large and have one or two peaks away form the boundary. When one peak occurs we characterize its location.Comment: 16 pages, submmited for publicatio

Detection of selection signatures for ear carriage in Maltese goat breed

Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity

AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap

Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Thus the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission. This work was supported by a grant from the CB Dennis British Beekeepers’ Research Trust awarded to MB and DW, and through strategic investment funding to the Roslin Institute from the Biotechnology and Biological Sciences Research Council (BBS/E/D/30002276). MP was supported by a Basque Government grant (IT1233-19)

Ground States for Diffusion Dominated Free Energies with Logarithmic Interaction

Replacing linear diffusion by a degenerate diffusion of porous medium type is known to regularize the classical two-dimensional parabolic-elliptic Keller-Segel model. The implications of nonlinear diffusion are that solutions exist globally and are uniformly bounded in time. We analyse the stationary case showing the existence of a unique, up to translation, global minimizer of the associated free energy. Furthermore, we prove that this global minimizer is a radially decreasing compactly supported continuous density function which is smooth inside its support, and it is characterized as the unique compactly supported stationary state of the evolution model. This unique profile is the clear candidate to describe the long time asymptotics of the diffusion dominated classical Keller-Segel model for general initial data.Comment: 30 pages, 2 figure

Ground state solutions to the nonlinear Schrodinger-Maxwell equations

We prove the existence of ground state solutions for the nonlinear Schrodinger-Maxwell equations.Comment: 27 page

Sharp Global Bounds for the Hessian on Pseudo-Hermitian Manifolds

We find sharp bounds for the norm inequality on a Pseudo-hermitian manifold, where the L^2 norm of all second derivatives of the function involving horizontal derivatives is controlled by the L^2 norm of the sub-Laplacian. Perturbation allows us to get a-priori bounds for solutions to sub-elliptic PDE in non-divergence form with bounded measurable coefficients. The method of proof is through a Bochner technique. The Heisenberg group is seen to be en extremal manifold for our inequality in the class of manifolds whose Ricci curvature is non-negative.Comment: 13 page

Short-Term Bisphosphonate Therapy Could Ameliorate Osteonecrosis: A Complication in Childhood Hematologic Malignancies

Osteonecrosis (ON) is a critical complication in the treatment of childhood leukemia and lymphoma. It particularly affects survivors of acute lymphoblastic leukemia and non-Hodgkin lymphoma reflecting the cumulative exposure to glucocorticosteroid therapy. ON is often multiarticular and bilateral, specially affecting weight-bearing joints. A conventional approach suggests a surgical intervention even if pharmacological options have also recently been investigated. We reported two cases of long time steroid-treated patients who underwent Bone Marrow Transplantation (BMT) for hematological disease. Both patients developed femoral head osteonecrosis (ON) that was diagnosed by magnetic resonance imaging (MRI) and the ON was also accompanied with pain and a limp. Despite of the conventional strategies of therapy, we successfully started a short-term treatment with bisphosphonates in order to decrease the pain and the risk of fracture