Browsing by Author "Colli, Licia"

Now showing 1 - 6 of 6
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    Combining Landscape Genomics and Ecological Modelling to Investigate Local Adaptation of Indigenous Ugandan Cattle to East Coast Fever
    (Frontiers in Genetics, 2018) Vajana, Elia; Barbato, Mario; Colli, Licia; Milanesi, Marco; Rochat, Estelle; Fabrizi, Enrico; Mukasa, Christopher; Del Corvo, Marcello; Masembe, Charles; Muwanika, Vincent B.; Kabi, Fredrick; Stewart Sonstegard, Tad; Huson, Heather Jay; Negrini, Riccardo; Consortium, NextGen; Joost, Stéphane; Ajmone-Marsan, Paolo
    East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes’ proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.
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    Genomic diversity and disease prevalence in Ugandan cattle
    (ReColAd Workshop, 2015) Colli, Licia; Bomba, Lorenzo; Milanesi, Marco; Vajana, Elia; Negrini, Riccardo; Eufemi, Elisa; Capomaccio, Stefano; Mazza, Raffaele; Stella, Alessandra; Joost, Stephane; Stucki, Sylvie; Taberlet, Pierre; Pompanon, François; Kabi, Fred; Muwanika, Vincent; Masembe, Charles; Ajmone Marsan, Paolo
    Ugandan cattle are represented by three main types: the long-horned Ankole, the short-horned zebu, and the Ankole-zebu crosses called “Nganda”. In the course of the EU-funded project Nextgen, Ugandan cattle have been extensively sampled over the whole country to investigate the association between genotypes and resistance/tolerance to endemic diseases (e.g. tsetse fly- and tick-born diseases).
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    Genomic diversity and Population Structure of Ugandan Taurine and Zebuine Cattle Breeds
    (XXI ASPA Congress, 2015) Colli, Licia; Milanesi, Marco; Bomba, Lorenzo; Vajana, Elia; Negrini, Riccardo; Eufemi, Elisa; Capomaccio, Stefano; Mazza, Raffaele; Stella, Alessandra; Joost, Stephane; Stucki, Sylvie; Taberlet, Pierre; Pompanon, François; Kabi, Fred; Muwanika, Vincent; Masembe, Charles; Ajmone Marsan, Paolo
    An extensive sampling of Ugandan cattle was carried out in the course of the European project Nextgen to identify possible associations between geno types, livestock endemic diseases and environmental variables.
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    Modeling the spatial distribution of Theileriaparva(Theiler 1904), causative agent of East Coast Fever disease in cattle
    (NEXTGEN Consortium, 2015) Vajana, Elia; Colli, Licia; Milanesi, Marco; Bomba, Lorenzo; Negrini, Riccardo; Capomaccio, Stefano; Eufemi, Elisa; Kabi, Fred; Muwanika, Vincent; Masembe, Charles; Ajmone-Marsan, Paolo
    The ileriaparvais a protozoan emo-parasite affecting sub-Saharan Bostaurusand Bosindicuspopulations. It is the causative agent of East Coast Fever, a major cattle disease causing the death of ~1.1∙106 animals per year and an annual loss of ~168∙106USD (Norvalet. al., 1992). T. parvageographical occurrence is bound to the presence of susceptible bovine host populations, the main tick vector Rhipicephalusappendiculatus(Neumann 1901), as well assuitable ecological conditions for the survival of both the vector and the parasite. While tick habitat requirements have been extensively investigated (see e.g. Cumming, 2002), studies focusing solely on the environmental conditions determining the parasite occurrence are still lacking.
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    SamBada in Uganda: landscape genomics study of traditional cattle breeds with a large SNP dataset
    (n The IALE 2013 European Congress, 2013) Sylvie, Stucki; Orozco-terWengel, Pablo; Colli, Licia; Kabi, Fredrick; Masembe, Charles; Negrini, Riccardo; Bruford, Michael W.; NEXTGEN, Consortium; Joost, Stéphane
    Since its introduction [9], landscape genomics has developed quickly with the increasing availability of both molecular and topoclimatic data. The current challenges involve processing large numbers of models and disentangling selection from demography. Several methods address the latter, either by estimating a neutral model from population structure [3] or by inferring simultaneously environmental and demographic effects [6]. Here we present Sam ada, an integrated software for landscape genomic analysis of large datasets. This tool was developed in the framework of NextGen with the objective of characterising traditional Ugandan cattle breeds using single nucleotide polymorphisms (SNPs) data.
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    VarGoats project: a dataset of 1159 whole‑genome sequences to dissect Capra hircus global diversity
    (Genetics Selection Evolution, 2021) Denoyelle, Laure; Talouarn, Estelle; Bardou, Philippe; Colli, Licia; Alberti, Adriana; Danchin, Coralie; Corvo, Marcello Del; Engelen, Stéfan; Orvain, Céline; Palhière, Isabelle; Rupp, Rachel; Sarry, Julien; Salavati, Mazdak; Amills, Marcel; Wandui Masiga, Clet; Pompanon, François; Rosen, Benjamin D.
    Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies.