With the development of high-throughput sequencing technology, genome sequencing of different species has increased sharply. A large amount of the available genomic data, together with the flaws in past approaches to characterizing the genetic diversity of species, pan-genomes have gradually become new reference coordinates for genomics research. However, the progress has been slower in eukaryotes than that in both bacteria and viruses due to the complexity of their genomes. This collection focuses on the recent progress on pan-genomes research in farm animals, so as to boost and lead its research in livestock and poultry. The articles in this collection are selected by the Editor-in-Chief from the publications inJournal of Animal Science and Biotechnology. All articles have undergone the journal's standard peer review and editorial processes outlined in itsSubmission Guidelines. Journal of Animal Science and Biotechnology is a leading open access journal publishing innovative research across agriculture, dairy and animal science.