Utilisation of the whole mitogenome in cattle breeding and conservation genetics
Funded by the Croatian Science Foundation.
Posted on 06.06.15
The public presentation of the project will be held on Thursday the 11th of June at 12pm at the Faculty of Agriculture, "Large Council Hall" by prof. Ino Čurik.
The main goal of this proposal is to sequence mitochondrial whole genome (mtWGS) in a 500 to 600 bulls or cows (440 to 540 belonging to Istrian cattle, Busha cattle, Slavonian-Syrmian Podolian cattle and Holstein population in Croatia) in order to: 1) identify polymorphic sites within mtWGS in genetically small populations and to analyse (confirm) the presence of selection for the whole mitochondrial genome as well as for each single gene (comparison of non-synonymous versus synonymous mutations); 2) Identify potentially detrimental mutations and to estimate detrimental load in all analysed populations; 3) develop computerised approach (set of algorithms) that will, in terms of probability or likelihood, enable imputation of sequenced mtWGS haplotypes for other pedigree members as well as to point to animals that are wrongly assigned to the pedigree, 4.) Identify mutations that are associated with phenotypic variability of milk production and fertility traits and to estimate the magnitude of the mtWGS effects (haplotypes) in terms of variance components and 5.) Identify private (specific) mutations that can be used in traceability or genetic bar-coding of species and breeds (this is of particular interest for endangered populations).
In performing these comprehensive analyses we will use newly developed methodologies of high-throughput sequencing and complex computing analyses. We believe that this research will stimulate other researchers involved in animal genetics and breeding of other species (dog, horse, swine, rabbit, etc…) for similar research. Furthermore, results of the project will be commercially utilised in cattle breeding as well as conservation management of endangered Croatian breeds. At the same time, we hope that innovative and technologically advanced component of this research will result in good publication record for all scientists involved which will further increase our competitiveness to approach to EU funded projects.
The paradigm of DNA sequencing, first introduced by Sanger, revolutionary changed in 2005 with the advent of the “next-generation” sequencing technologies which afford sequencing of large regions (even genomes) at a low price in a short time. This technological advance enabled us to open the “genetic black box” and to provide the first insight into understanding of genetic background of phenotypic variation (height, body mass index, blood pressure, predisposition to diseases, genetic defects, growth, milk production, etc…). The commercial potentials and opportunities of newly obtained knowledge are huge in the human and veterinary medicine, pharmaceutical industry and agriculture. This is the reason for the fast growth of research concentrated on the genomic dissection of phenotypic variability, and the focus is mainly on the impact of nuclear genome. As stated by Manolio (2013): "In the past 7 years, more than 1,600 publications have identified ~2,000 robust associations with more than 300 complex diseases and traits". On the other hand, the potential impact of mitochondrial genome has not been properly recognised and there are just several pioneering researches done in humans and mouse as a model animal. At the same time, we are not aware of comprehensive research designed to study the impact of mitochondrial genome on phenotypic variability in commercially exploited domestic animals. This is even more surprising as phenotypic variability in domestic animals has been exploited for a long time. Only in the last five years tremendous resources have been provided for analyses of nuclear genome impacts on the phenotypic variability. Thus, for example, at a "9th World Congress on Genetics Applied to Livestock Production" in Leipzig (August 2010) there were 276 (out of 846) papers related to the genomic selection and this trend is rapidly increasing. In this proposal we decided to analyse the impact of mitogenome on the phenotypic variability, detection of regions under selection and estimation of mitohondrial detrimental load as well as to build a program for haplotype imputation, detection of pedigree errors and detection of breed specific markers that might be used in traceability and labelling of the endangered breed products. We believe that this research will stimulate other researchers involved in conservation genetics and animal breeding of other species (dog, horse, pig, sheep, rabbit, etc…) for similar researches as results obtained do have high potential of being commercially utilised.of particular interest for endangered populations).
While the research will be based on cattle populations, the obtained results will be of a more general interest. More directly, we expect to provide evidence of non-neutrality over the whole mitochondrial sequence variation. This would have an impact on phylogenetic studies which are mainly based on the assumption of neutrality. Furthermore, the analyses would also point to genes (mtDNA segments) that are under strong selection pressure, which will, further, open new hypotheses related to the functional properties of genes inherited from mtDNA. We also expect to prove the impact of mtWGS, in a magnitude of 2 to 10%, on phenotypic variability for at least one trait important in cattle breeding, such as sperm motility or cattle longevity. Furthermore, we expect to provide the evidence on the presence of detrimental mutations (deletions, mutations at termination codons, etc.) within mtWGS that segregate in endangered populations. Confirmation of this hypothesis would have an impact on the conservation programs. By the whole mitogenome sequencing of cattle populations, we expect to identify polymorphisms that are specific for Croatian endangered breeds. This would enable traceability and labelling of the cattle products (meat, milk, leather, etc.) originating from endangered breeds. At the end, we will develop computer program that would help pruning of pedigree errors. The importance of such program should not be neglected as correct pedigree is an important factor in cattle breeding and conservation programs. At the end, we are closely collaborating with Dejana Brajković, PhD, Siniša Radović, PhD and Ankica Oroš-Sršen, PhD, from the Institute for Quaternary Paleontology and Geology, Croatian Academy of Sciences and Arts, Zagreb, Croatia as well as Prof. Preston T. Miracle from the Department of Archaeology, University of Cambridge, Cambridge, United Kingdom, and the proposed research would be a valuable pre-work with the respect to archeogenetic analyses of ancient cattle bones taken from the Croatian sites.
WP1: Sampling, molecular genetics and sequence analysis
WP2: Detection of selection through the sequence analyses
WP3: Identification of detrimental mutations
WP4: Algorithmic imputation of haplotypes
WP5: Estimation of mitogenome impact on the phenotypic variability
WP6: Dissemination of the project results
Expert Associate (2014) University of Zagreb, Faculty of Agriculture Department of Animal Science phone: +385 01 239 4008 e-mail: email@example.com
Head of Central Animal Gene Bank Department Croatian Agricultural Agency Central Animal Gene Bank Department phone: +385 01 3903 187 fax: +385 01 3903 127 e-mail: firstname.lastname@example.org; email@example.com web: www.hpa.hr
Assistant Professor (2011) University of Zagreb, Faculty of Agriculture Department of Animal Science phone: +385 01 239 4010 e-mail: firstname.lastname@example.org
Professor (2010) University of Zagreb, Faculty of Agriculture Department of Animal Science phone: +385 01 239 4008 e-mail: email@example.com
Assistant (2014) University of Zagreb, Faculty of Agriculture Department of Animal Science phone: +385 01 239 3915 e-mail: firstname.lastname@example.org
Docent University of Zagreb, Faculty of Agriculture Department of Animal Science phone: +385 01 239 3915 e-mail: email@example.com
Assistant Professor University of J.J. Strossmayer, Faculty of Agriculture Kralja Petra Svačića 1d, 31000 Osijek phone: +385 031 554 942 email: firstname.lastname@example.org
PhD Student (2015) University of Zagreb, Faculty of Agriculture Department of Animal Science phone: +385 239 3929 e-mail: email@example.com
Senior Associated Researcher Ruđer Bošković Institute Laboratory for Stochastic Signals and Processes phone: +385 01 456 1029 e-mail: firstname.lastname@example.org
Expert associate Croatian Agricultural Agency
University of Zagreb, Faculty of AgricultureSvetošimunska 25, 10000, Zagreb, Croatia
Tel:+385 01 239 4008
Fax:+385 1 239 3947