Population Genomics of Animal Domestication and Breed Development

Abstract

Domesticated animals have a rich and complex history, comprising several population-shaping events, which has resulted in an assortment of distinctive phenotypes and highly specialised breeds that meet a variety of human needs. The availability of whole genome sequences and single nucleotide polymorphism (SNP) arrays for the major domestic animal species allows for a thorough interrogation of the genomic landscape of breeds using population genomic approaches. In this chapter, we synthesise insights gained into the processes of domestication and breed development from the patterns of diversity mapped across domestic genomes, with particular focus on cattle (Bos taurus taurus and Bos taurus indicus), chicken (Gallus gallus domesticus), dog (Canis lupus familiaris), pig (Sus scrofa) and sheep (Ovis aries) breeds. First, we evaluate the current state of genome-wide diversity within domestic animals, a topic of importance considering concerns over the continuing erosion of genetic variation within breeds. Second, we review the growing catalogue of selective sweeps found for key phenotypic traits in domestic animals, illustrating that breeds have been intensively selected for a range of breed-defining traits (e.g. coat colour, horn morphology, ear carriage and body size) and production traits (e.g. milk production, muscular conformation, reproduction and meat quality). Finally, we discuss insights into the selection history of domestic animals and the genetic architecture of phenotypic traits and we address the future management of genetic diversity in domestic breeds.

The original version of this chapter was revised. In this revised version, Section 4.2, the caption of Figure 7 and some citations to the literature in the reference section have been updated.