Understanding genomic resources of indigenous chickens for the rapid improvement of their production efficiency

Abstract

After the domestication, tremendous chicken genetic resources have been developed across the world, and thus they have become both the most numerous farmed animals and the most widely preferred animal-sourced protein. To understand the history of domestication and establishment of different chicken breeds/ecotypes, large-scale whole genome sequencing initiatives based on a worldwide sampling of chickens and all wild Junglefowl species/subspecies have been established through intensive international collaboration involving scientists from more 20 countries in Asia (including Indonesia), Africa and Europe. These latest efforts suggest that domestic chickens were derived from the Red Junglefowl subspecies Gallus gallus spadiceus distributed in southwestern China, northern Thailand and Myanmar. From there, chickens were first transferred into Southeast and South Asia before they were subsequently taken to Europe and Africa. On their journeys out of the domestication center, chickens were further and continuously interbred with other Red Junglefowl subspecies and Junglefowl species, which have certainly facilitated their rapid adaptation and diversification in terms of unique adaptive, behavioral, and morphological attributes. These complex dispersal processes have enriched the genetic diversity of modern-day chickens relative to their ancestors after the initial bottleneck occurred along their domestication. This bottleneck led to the accumulation of deleterious mutations across the chicken genomes. Because most of such mutations are inherited in heterozygous states and masked as recessive alleles, the power of recent selective breeding to eradicate these genetic loads is questioned. It is therefore recommended to develop reliable genomic markers for monitoring the impact and efficiency of genetic improvement for indigenous chickens.