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H2020Individual fellowship2016–2018

Bioinformatics4Breeding · Harnessing the power of bioinformatic analysis to improve genetic selection for fertility in dairy cows

Horizon 2020 — Marie Skłodowska-Curie Actions

Duration
2016-05-01 → 2018-04-30
EU contribution
€195,455
Participants
1
Scheme
MSCA-IF-EF-CAR

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Results in brief

Harnessing the power of bioinformatic analysis to improve genetic selection for fertility in dairy cows

The future of a sustainable dairy industry is dependent on increased efficiency of production per cow. Economic analysis shows that profitability of dairy enterprises increases with increased longevity and fertility, however diseases as well as adaptation to different environmental conditions are heavily affecting the average life span in cattle. Dealing with these interlinked problems requires genetic selection for more fertile and robust and so long-lasting cows. The first objective was for the fellow to obtain intensive training on using diverse bioinformatic methodologies (ranging from genome alignments to detection of evolutionary conserved elements) enabling two main comparative genomics projects to be carried out: i) enrichment for conserved non-coding elements and transcription factor binding sites in ruminant genomes, ii) whole genome resequencing of two highly adapted to harsh environment but phylogenetically distinct cattle breeds. The aim, in the first project, was to explore the potential role of conserved non-coding elements in ruminants’ evolution, gene regulation, and formation of phenotypic traits. Genome sequence comparisons of transcription factor binding sites among several mammalian species was performed, and several ruminants-specific motifs were found to be enriched in regulatory domain of genes involved in reproduction. In the second project, genomes from two highly adapted to harsh (cold) environment and resistant to various pathogens cattle breeds were compared to each other and other breed genomes . Whole genome resequencing of Yakut and Kholmogory native cattle breeds was performed and contrasted to Holstein and Hanwoo breeds in order to identify signatures of selection in genomic regions potentially responsible for adaptation to harsh climate as well as disease resistance. Detection of genomic regions under selection pinpointed potential causative SNPs which might be used further as markers to select for adaptation to harsh environments. This can be used to improve other European breeds to make them adapted to the “fast acting” climate change, as well as disease resistance, leading to longer lasting cows.

Data: CORDIS, © European Union

Project objective

Genetic selection for high yielding dairy cows has been associated with reduced fertility. Infertility remains the major reason for culling, decreasing longevity and reducing production efficiency. We propose that this trend could be reversed by identifying key genes involving reproductive function and selective breeding of more longlasting cows. The specific research objectives are: 1) to train the incoming researcher in bioinformatics methodologies related to analysis of large genomic datasets including SNP detection, genotyping, and evolutionary conserved DNA elements detection; 2) to use the methodologies to analyse dairy phenotypic and genomic data to highlight potential genic and regulatory regions of the cattle genome containing polymorphisms which are beneficial, with a particular focus on fertility; 3) to use appropriate tools to investigate the likely effects of both coding and regulatory variants on the expression of the candidate genes found in these regions; 4) to use pathway analysis to understand how the candidate genes may influence key molecular events and larger gene networks involved in reproductive phenotypes; 5) to recommend appropriate selection procedures to the EU dairy breeding industry to supplement current genomic methods. The project combines the expertise of Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia agraria, Italy (CREA) and the Royal Veterinary College, UK (RVC) in farm animal genetics and genomics and dairy cow production. The objectives will be met by the mobility of Dr L Buggiotti to the UK, where she will work closely alongside two senior RVC scientists, Dr DM Larkin and Professor DC Wathes. She will transfer this expertise back to CREA on her return. Both groups are experienced in knowledge transfer to the dairy industry and are committed to use the information generated to breed more fertile cows, so improving longevity and promoting sustainability of the EU dairy industry.

Original text from CORDIS.

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Data: CORDIS, © European Union