GEroNIMO Hackathon: Spreading Ideas
We are a group of university students from all over the world that GEroNIMO Hackathon 2022 has brought together (two from Russia, one from Nigeria, one from Ghana, and one from Bangladesh). We were able to work together despite our varied backgrounds and areas of expertise to suggest a solution to issues in animal breeding. We were aware of how vast the field is and how much may be accomplished after receiving an introduction to contemporary issues and methods in selection and breeding. Listing all the improvements which can be done in animal production we came to the conclusion that we should focus not only on animals but also on the world which is changing right now. So, in our proposal, we proposed the notion of employing a multi-omics approach to identify biological markers linked to pig heat tolerance.
We know that genetics tells us next to nothing without the context of the environment. The crisis associated with environmental changes like global warming has detrimental effects on livestock production and welfare, whereas livestock production is an important sector of the global economy. Therefore, we need more tolerant and resilient pig breeding to continue the huge current contribution of pig breeding. Although the genetic mechanism underlying heat tolerance is not clear, the good news is, it is heritable in pigs.
Environmental issues are becoming more serious, but thankfully, biomolecular technologies are advancing, which can help humanity prepare for modern challenges. We discovered that, in light of all the developments in biological methodology, the -omics data generation are making a potential “good friend” for genome-wide association studies (GWAS).
Numerous attempts to identify loci responsible for various traits have shown that there are certain common problems. One of them is missing heritability, which we would like to face with epigenetics studies. Here we assume that some of the unexplained phenotypic variances can come from the epigenetic level instead of genetics. Another problem is the trade-off between false discovery and recovery rates. Almost all GWAS studies end up with a list of candidate quantitative trait loci which are disregarded only due to multiple test correction criteria. Here we suggest using other -omics data to validate and predict the role of putative alleles (loci) on heat tolerance in pigs.
We would like to start with a cohort of a thousand pigs grown in the same mild conditions during farrowing and six weeks after the weaning. In this cohort, we would like to skip the heat challenge due to a high variance of environmental factors (such as sow traits, the spread of post-weaning diarrhea, etc.), which would be challenging to account for in the association model. However, we would like to collect blood samples for genotyping and metabolomic profiling and muscle biopsy for RNA sequencing and epigenetic profiling.
In the second half of the trial, we would like to split the initial cohort into two groups: one group will be challenged and grown under increased temperature conditions and the second group will be a control group and will be grown under the mild condition as before. Having two groups will allow us to differentiate the heat shock effect from the effect of aging as well as markers for increased production traits in normal and challenging conditions. At the end of this period, we are going to collect the same samples as in the first period.
This idea made us win the contest. Winning the GEroNIMO Hackathon 2022 gave us multiple opportunities. We got the opportunity to present our proposal at the GEroNIMO annual meeting and awarded a grant to participate in one of the upcoming conferences (in 2022) related to animal breeding. We participated in the WCGALP 2022 in Rotterdam.
The hackathon and the conferences were eye-opening and offered ample networking opportunities. We experienced diverse viewpoints and lovely ideas from all other teams, and could meet and converse with the pioneers of different fields of Animal Sciences. We appreciate GEroNIMO for organizing the hackathon and providing us with opportunities to express and explore. We hope GEroNIMO will continue this fantastic enterprise and communicate ideas for the betterment of humankind.
But how can you quantify tolerance to heat in pigs? Our attitude is based on the benefit of breeding for heat tolerance, the final product. In this project, we are interested in the preservation of the current production rates in conditions of increased temperature. Thus, we wanted to find biological determinants for the high production trait in conditions of heat challenge. Mixing all components (methods and interest) we came to the following experimental design.