What is it about?
There are many gaps in the genome map; in these gaps, the function of genes is not known (or unannotated). Global efforts are trying to fill these gaps, so many groups around the world provide functional annotations of animal genomes, such as the Functional Annotation of ANimal Genomes (FAANG) consortium. While lots of annotations are now provided (gaps in the genome maps are filled), how to use such information is unknown. For example, which type of annotations can tell useful genes relevant to traits of economic importance or respond to climate change? We developed a new method that effectively uses the annotation information from global consortia, called Functional-And-Evolutionary Multi-trait Importance (FAEMI) score. This score combines information from various types of annotations with the potential impact of underlying genes on important cattle traits. We then tested the usefulness of the FAEMI score in new data on heat tolerance traits. We found FAEMI score can effectively translate the values of various types of annotations into practical use - for example, they can help identify important genes of high economic importance such as milk yield volume, fertility and survival of cows. We also found FAEMI score can help in the selection of cattle tolerant to heat stress. We provide proof-of-concept evidence that FAEMI score can help identify important genes related to beef cattle meat quality - something a bit surprising, as we did not use data from beef cattle to estimate the FAEMI score. We achieved these results by analysing a large amount of cattle data, including millions of genome-wide markers in more than 100K cattle, and millions of annotation data from the public domains.
Featured Image
Photo by alex° on Unsplash
Why is it important?
Importantly, we show that the global efforts in the basic research of generating a large amount of data to fill the cattle genome map have practical values - they can be effectively used in the way discovered by us (FAEMI score) to improve important traits of cattle. Secondly, the FAEMI score can indicate which types of annotations are more effective at identifying important genes, thereby informing future annotation experiments. Thirdly, the fact that the FAEMI score can inform better breeding decisions for heat tolerance in cows means we can use fundamental genetic information to help farmers breed more resilient cows in a hotter world.
Perspectives
FAEMI score demonstrates the practical use of basic genomic research (filling the genome gap), helps identify important genes related to traits with high economic importance, and assists in breeding resilient cows in a hotter world. Scientifically, we would like to further refine the list of important genes related to traits with high economic importance and heat tolerance. For application, useful information from the FAEMI score will also be passed to the dairy industry to help develop more accurate Australian breeding values of heat tolerance, which will help farmers to selectively breed resilient cows in the changing environment.
Ruidong Xiang
Agriculture Victoria Research
Read the Original
This page is a summary of: Integrating extensive functional annotations and multiomics of cattle enhances climate resilience prediction and mapping, Proceedings of the National Academy of Sciences, November 2025, Proceedings of the National Academy of Sciences,
DOI: 10.1073/pnas.2514736122.
You can read the full text:
Resources
Contributors
The following have contributed to this page
