Transfer learning meets livestock genomics

April 16, 2018, Peter the Great Saint-Petersburg Polytechnic University
Researchers at Peter the Great St. Petersburg Polytechnic University (SPbPU) have developed a new computational method that predicts harmful mutations in mammalian species. Credit: Peter the Great St.Petersburg Polytechnic University

Researchers at Peter the Great St. Petersburg Polytechnic University (SPbPU) have developed a new computational method that predicts harmful mutations in mammalian species. As more livestock producers are using genetic tests to improve their herds, this method will help to optimize and guide the animal breeding programmes, as well as increase the profitability and yields of livestock. Published in Evolutionary Applications, the method follows closely in the footsteps of the most recent innovations in human genomics and translates the knowledge about genetics risk factors in humans to companion animals, thus having a transformative potential for genetics and genomics of livestock species.

Efficient selection in farm that will produce offspring with desirable phenotypes and ensure less reliance on hormones and antibiotics has been in the spotlight of many livestock genomic and gene-editing projects. However, their success has been hindered by unknown effects produced by genomic variants. Scientists, led by Profs. Maria Samsonova, Sergey Nuzhdin and Lev Utkin (Mathematical Biology and Bioinformatics Lab and Machine Learning Group) took the full advantage of available information on human variation with deleterious potential and used transfer learning methods to enable classification of damaging mutations in other . The approach was extensively validated using dog and mouse models. "The developed methodology could be used to identify deleterious, unwanted mutations in genomes of other farm animals, thus facilitating the design of finely tuned metabolic pathways that allow animals to thrive under a wide range of conditions," said Maria Samsonova, head of the Laboratory of Mathematical Biology and Bioinformatics SPbPU.

From the earliest domestication of animals, humans have selected for desirable characteristics or traits in livestock, and conversely, selection against undesirable phenotypes. A side effect of controlled breeding is rapid accumulation of as genomic variants with negative potential are not counterweighted by an inflow of "good" genes from external populations. Over time, this leads to overall reduction of fitness in cattle and other . Sustainable agriculture and industry's ability to provide humans with higher quality, healthier and lower-cost farm products heavily relies on the knowledge of functional effects induced by either naturally occurring or technologically introduced mutations and our ability to eliminate harmful ones from future breeds.

Explore further: Crops hold harmful mutations that reduce productivity

More information: Elena Plekhanova et al, Prediction of deleterious mutations in coding regions of mammals with Transfer learning, Evolutionary Applications (2018). DOI: 10.1111/eva.12607

Related Stories

The advent of 'green' cattle

October 30, 2017

Implications of livestock farming on climate change should not be drawn from aggregate statistics, reveals a study based on a new method of carbon footprinting for pasture-based cattle production systems that can assess the ...

Infectious diseases A-Z: Antibiotics in farm animals

November 23, 2017

The World Health Organization is urging countries to restrict the use of antibiotics in food animal production. Food producers in many countries feed low-dose antibiotics to farm animals to encourage the animals to grow bigger ...

Gene editing mulled for improving livestock

February 21, 2017

Gene editing, which has raised ethical concerns due to its capacity to alter human DNA, is being considered in the United States as a tool for improving livestock, experts say.

Recommended for you

Pigs form a visual concept of human faces

August 17, 2018

Contrary to previous studies, pigs appear to have better visual discrimination abilities than had previously been assumed. Cognition researchers from the Messerli Research Institute showed in a new study that pigs not only ...

Are our wild animals growing old gracefully?

August 17, 2018

For most of us, the body's deterioration is an unavoidable part of getting older. This age-related decline, known as "senescence", can occur subtly and slowly for some individuals, while for others it happens much faster. ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.