The coordinator’s team has a substantial track record in livestock molecular genetics and in particular in characterising and interpreting, using newly developed methods, genetic diversity within and among livestock populations with different demographic histories. Bruford is a population geneticist who has worked on livestock diversity, domestication and evolution for the last 15 years. Orozco-terWengel is a new member of academic staff at Cardiff and is a population geneticist who uses whole genome datasets to infer demographic and selective processes. Both members of the team have been members of the FP7 Nextgen project (http://nextgen.epfl.ch) that is investigating signatures of adaptation in livestock populations and their wild ancestors in heterogeneous and environments challenging environments. Within this project the team has been analysing large-scale whole genome and high density SNP array data to detect selection in Moroccan sheep and goats that are farmed in mesic, high altitude and xeric landscapes, north and south of the Atlas mountains. In addition, Bruford recently coordinated the FP7 Support Action project ConGRESS (Conservation of Genetic Resources for Effective Species Survival – www.congressgenetics.eu) – a highly successful program involving 13 partners aimed at making genetic concepts and data available more easily for European biodiversity managers and policy makers. This project produced an easy to use web portal, providing data, simulation and decision tools and information, which has been well-received by the academic and end-user community alike.
Within ClimGen, Cardiff coordinates the project, being responsible for project delivery, reporting, meetings and interaction with the Steering Committee, including all monitoring activities of the project. The Cardiff team has extensive experience with European funding, from FP3 – FP7, and have recent coordination experience on a highly successful FP7 project (ConGRESS) that has so far delivered eight ISI publications, some of which are already of high profile. In addition, Partner 1 is closely involved in all other work packages, with the exception of WP3 and will be especially closely involved in WPs 4 and 5 (database and analysis pipeline [WP4]; integrated data analysis [WP5]), being the partner responsible for WP5. Specifically, in WP4 the team will extend current methodologies to compile and facilitate analysis of the medium and high density SNP array, whole genome and transcriptome data available. These approaches have been developed with Partner 3 and have facilitated the efficient handling and transformation of large datasets, allowing analysis of demographic history and genomic selection in a computationally feasible way. Cardiff will lead WP5 on integrated data analysis, applying and extending current methods to detect selection from genomic data using established methods and now methods accounting for demographic history being developed by Orozco-terWengel.
Paolo Ajmone Marsan is Professor of Animal Genetics and Director of the Institute of Zootechnics and the Proteomic and Nutrigenomic Research Center (PRONUTRIGEN) of the Università Cattolica del Sacro Cuore. He has participated in seven EU projects and coordinated GLOBALDIV (GenRes, 2007-2009) “A global view of livestock biodiversity and conservation” and ECONOGENE (FP5-2002-2004) “Sustainable conservation of animal genetic resources in marginal rural areas: integrating molecular genetics, socio-economic and geostatistical approaches”. He is scientific Advisor of FAO/IAEA projects, and member of the Technical Commission of ANAFI (Italian Holstein cattle breeder association) and has been member of the Italian delegation of the EU FP7 Programme Committe in Area 2. He is section editor of Genetics Selection Evolution, member of the editorial board of Animal Genetics and author of more than 80 ISI papers. His research is focused on using DNA for reconstructing livestock domestication; estimating farm animal diversity for conservation purposes; tracing the origin of animal products; identifying useful genes sustaining beef and dairy milk production, genome wide selection approaches and detecting the effects of diet and nutrients on gene expression in animal models.
Within ClimGen, UNICATT will participate in: WP2 – coordinating case study collection; WP4, collecting and harmonising available cattle SNP data and genotyping newly collected samples to complete datasets; in WP3, by carrying out metabolomic analyses in the pig heat stress experiment carried our at PTP; in WP5 by contributing in data analyses, in particular for the detection of selection signatures in cattle and in the identification of candidate genes and metabolic pathways involved in animal response to environmental stress; in WP7 by participating in the dissemination of results towards different stakeholders.
PTP is a small independent enterprise that carries out research and development activities in the field of agriculture and food. PTP has active research groups in plant and animal molecular genetics and breeding, statistics and bioinformatics. The Statistical Genomics and Bioinformatics Unit develops and implements new statistical methods for the analysis of complex data, creates project management bioinformatics systems and pipelines for analysing next generation sequence information and develops databases for large data sets. PTP s.r.l. runs a high-throughput molecular technology service platform which is SIGNAL and ISO9000 accredited and is equipped to provide high throughput “next generation” sequence based applications (genome sequencing and re-sequencing, transcriptomics, epigenetics, metagenomics etc), proteomics and chemical analysis as contract testing for companies and research organisations in the agri-food sector. Dr Alessandra Stella is a quantitative geneticist and genome specialist with 65 publications to date including in the highest impact journals. She has participated in a number of high profile animal and plant genome projects and in stress experiments in livestock species.
Within ClimGen, PTP will lead WP3, by setting up a heat stress experiment in pig; will contribute to WP2, collecting and harmonising available genomic and phenotypic data from which PTP has participated in a number of projects; and will also contribute to both WP4 and WP5 by contributing to pipeline development and data analysis, in particular for the detection of selection signatures in cattle and in the identification of candidate genes and metabolic pathways involved in animal response to environmental stress; PTP will also participate in WP7 by bridging the gap among different stakeholders from an SME perspective.
Ezequiel Luis Nicolazzi
At UJF, the ‘Laboratoire d’Ecologie Alpine’ has 15 year’s experience in studying the genetics of domestication by characterizing the variability of wild and domestic Capra and Ovis. Pompanon and Taberlet are renowned experts in developing methods based on Next Generation Sequencing (including genome scans) for characterizing biodiversity and for landscape genomics studies. The team is specialised in conservation genetics, both at the empirical and theoretical levels, and have participated in four recent EU projects linked to biodiversity of wild species and farm animals and dealing with innovative approaches for preserving biodiversity (ECONOGENE, INTRABIODIV, ECOCHANGE, NEXTGEN). A bioinformatics unit works on the characterization of DNA sequences and comparative genomics in close collaboration with the European Bioinformatics Institute (Vertebrate Genomics Group). Besides their skills in population genomics and conservation genetics, the group develops internationally recognized biodiversity models integrating recent advances in ecology and evolutionary theories in order to develop sound scenarios of biodiversity distribution with regards to climate changes. Francois Pompanon, assistant professor and author of 50 ISI publications, has a broad background in population genetics and evaluation of genetic diversity using molecular marker information. He works on the genetics of domestication of small ruminants and on the genomics of livestock species, focusing on adaptation to environmental factors. Pierre Taberlet, senior scientist, has a broad expertise in the development of innovative molecular tools to characterize genetic diversity and in conservation genetics. He has coordinated several National and European projects, including NEXTGEN (FP7 20010-2014: Next generation methods to preserve farm animal biodiversity). Frederic Boyer is a bioinformatician, specialised in developing methods for genome analyses and comparative genomics. He has a long experience in algorithm development dedicated to the study of genomes.
Within ClimGen, UJF will strongly contribute and coordinate WP4, contribute to WP2, retrieving whole genome data from previous projects, and in producing genomic data for completing the sampling. In WP3, UJF will characterise the methylation patterns in sheep and goats living in contrasting heat conditions to assess their epigenetic response under field conditions. In WP5, UJF will analyse data for identifying genomic regions and genes associated with climate variables and carrying signatures of climate-mediated selection. In WP6, UJF will use these data to help predict the impact of global change on current genotypic distributions to assess which breed could be mostly affected, and then evaluate breeding programs designed according to the distribution of adaptive genotype with regards to future climatic conditions.
UASMV is specialized in sheep and cattle breeding programmes, DNA analyses, population genetics, quantitative genetics and animal breeding by selection and crossing, animal genotyping at major milk and blood protein loci and their association with economic traits, and also in genotype x environment interactions under different microclimatic and nutritional conditions. Dr. Antonia Cristina Maria Odagiu has experience in environmental monitoring and climate change analysis, but also has laboratory background in molecular genetics, and implementation of quality systems in livestock genotyping laboratories and in assessment of environment quality. Bogdan Vlaic is geneticist with background in quantitative genetics and molecular analysis. UASMV has over 15 year’s experience as a team in national and international projects. They have been involved in national projects for the identification of polymorphisms of milk proteins in livestock and their use as markers for identification of milk product authenticity, and also in founding and coordinating regional laboratories for livestock genotyping and environmental quality assessment. The international activity of the team is emphasized by sheep breeding research, developed within two bilateral cooperation grants (Romania – Belgium, and Romania – Hungary), which evaluated production traits Merino Tsigai crosses with Suffolk and Laitière Belge and Booroola rams. Partner 5 has experience with EU funded collaboration, being involved in EU ECONOGENE Project (2002 – 2004) FW 5 (QLK5-CT-2001-02461) as a subcontractor.
The main role of partner 5 in ClimGen is to coordinate WP 7 Dissemination, together with Partner 7. They will focus on three areas, establishing a community of target beneficiaries and coordinating the roll-out of workshops, conferences, popular dissemination of project scientific results, website content, the design of lectures for relevant stakeholders (farmers associations, livestock breeders, industry and governmental actors. UASMV will also be involved in other two work packages, WP 2 and WP 5. Within WP 2 (database assembly, assessment and gap identification) we will mainly contribute to sample collection and assembly of the primary database, while within WP 5 (data analysis and comparison) will perform raw data analysis, and will participate to data comparisons.
UCM has expertise in quantitative genetics applied to beef cattle breeding programs and the use of molecular information (autosomal and sex-specific microsatellite loci, mitochondrial DNA sequencing information, single nucleotide polymorphism) to unravel the pattern of geographic distribution of livestock genetic diversity, and to implement strategies for its management. Ongoing laboratory research activities include: a) the molecular characterization of candidate genes for quality meat and carcass traits in beef cattle and the development and validation of SNPs markers; b) the application of NGS tools to sequence the transcriptome of the partridge (Alectoris ssp.) aiming to study unspecific stress resistance. UCM leads of a Certified Genetic Laboratory (ISO 9001:2008) (www.ucm.es/genetvet). The team has twenty-five years experience in animal breeding and fifteen years applied to the investigation of genetic diversity and to the identification of genes associated with economic traits. JC, SD and OC are authors and co-authors of more than 100 peer-reviewed papers. The team has participated in a number of EU projects including RESGEN (CT-98-118; 2000- 2002). Towards a strategy for the conservation of the genetic diversity of European cattle. GEMQUAL (QLK5-CT2000-0147; 2001-2006). Assessment of genetic variation in meat quality and the evaluation of the role of candidate genes in beef characteristics with a view on breeding for improved product quality and ECONOGENE (QLRT2000-02461; 2002-2004). Sustainable conservation of animal genetic resources in marginal rural areas: integrating molecular genetics, socio-economic and geostatistical approaches.
Within ClimGen, UCM will participate in the stress experiment (WP3) using a game bird species (Alectoris rufa) as an animal model. The UCM team also have experience on breeding programs applied to livestock and will contribute to WP6 – breeding program design, simulating complex genotyped populations to investigate the impact of alternative marker based selection schemes on the selection response under several scenarios.
Natural Resources Institute Finland (Luke) is a non-profit public research organisation operating under the Ministry of Agriculture and Forestry and Finland’s leading research institute in all areas of the bioeconomy, including agriculture, food, forestry, natural resource management and biotechnology. Luke was created by the merge of several entities: MTT Agrifood Research Finland, the Finnish Forest Research Institute (Metla), the Finnish Game and Fisheries Research Institute (RKTL), and the statistical services of the Information Centre of the Ministry of Agriculture and Forestry (Tike), and commenced its operation on 01 January 2015. Luke brings together expertise in renewable natural resources and responsible food production and provides innovative solutions that promote new business activities. The cross-disciplinary research data and expertise support responsible decisionmaking both domestically and internationally. Research on natural resources benefits the consumers by providing information on health and well-being, and by supporting the vitality of Finnish nature.
The Luke-research team has long experience in molecular and population genetics, quantitative genetics and biometric methods applied to investigate and conserve farm animal genetic resources, animal breeding and to recognize quantitative trait gene effects. The team has adopted novel technologies, such as whole-genome SNP analyses, whole-genome DNA sequencing, transcriptomics and bioinformatics to the investigations of domestic animal genomes and special characters of breeds. The team has interest towards multidisciplinary studies, such as archaeological genetics and examining non-genetic values (social, socio-economic and cultural) of locally adapted native farm animal breeds. The team’s research has focused on cattle, sheep, horse and chicken breeds. The members have actively collaborated in various national, Nordic, European and Asian research networks and national and international projects. In addition, the team is coordinating the Finnish National Action Plan for in situ and ex situ conservation of genetic resources of cattle, dog, goat, horse, pig, poultry, reindeer and sheep genetic resources. Professor Juha Kantanen, a team leader, is a population and animal geneticist, Professor Ismo Strandén is a mathematician experienced in Bayesian statistics, biometry, simulation studies and animal breeding methods, and researcher Kisun Pokharel is a bioinformatician who has worked on genomics, transcriptomics, and proteomics.
Within ClimGen, Luke will be responsible for WP6 where future breeding programs will be designed to promote mitigation and adaptation of animal production to climate change and cost/benefit analyses of different breeding strategies performed. This will involve simulations using the QMSim software, which Luke has experience in using for genome assisted breeding programs. In addition, the Partner will be closely involved in WPs 4 and 5 where large-scale genomic databases and analysis pipelines for them will be set up for integrated and comparative data analysis. In addition, the Partner will be involved in WP7 to disseminate results and will organize and host one of the ClimGen workshops in Finland.
The Geographical Information Systems Laboratory (LASIG) is a unit within the Ecole Polytechnique Fédérale de Lausanne (EPFL), one of the two Ecoles Polytechniques fédérales in Switzerland. LASIG is within the School of Architecture, Civil and Environmental Engineering (ENAC) and its research takes place in the Institute of Environmental Engineering.
The landscape genetics’ group at LASIG is specialized in the contribution of Geographic Information Science for the conservation of plant and animal genetic resources. We apply spatial analysis, spatial statistics, spatial modelling, and geocomputation methods to conservation and landscape genetics, with core research activities landscape genomics, a field that aims to study and discover the genetic basis of adaptation by processing many simultaneous DNA-environment association models.