863 genomes reveal the origin and domestication of chicken

Abstract

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data

“…They possess their own genetic structure in subgroups. In admixture result, game breeds and red jungle clustered as one group until K = 16, suggesting domestic breeds and wild populations have mutual introgression (Li et al, 2019;Wang et al, 2020). It is consistent with our NJ tree results that all breeds from the same population clustered, except that game breeds.…”

“…Red junglefowl, which is considered to be the ancestor of the domesticated chicken (Murray, 2016;Wang et al, 2020), showed no significant difference in the heterozygosity diversity between the Chinese local chicken breeds in our study. Malomane et al (2019) has reported similar observed heterozygosity in RJF compared with that of our study.…”

“…On chromosome 3, we showed that up to 40% of Beijing You chickens had a ROH between 69.38 and 70.93 Mb, retaining the gene ASCC3 which is also a candidate gene for silky feathers (Li et al, 2019). Besides, on chromosome 2, chromosome 3, and chromosome 13, we identified several potential candidate genes associated with egg production, eggshell quality and growth traits, such as GDF9, OPN, CDH9, CDH10, and KIF18A (Pines et al, 1995;Hincke et al, 2010;An et al, 2012;Lin et al, 2014;Wang et al, 2020). The ROH island results tended to provide useful information on genetic diversity and genetic foundation underpinning breed specific traits under different selection pressures.…”

Using whole-genome sequencing data for demographic and functional evaluations of small managed populations

“…The world-wide distribution of chicken is a fascinating example of a successful story of crossspecies relationship with human. Although chicken domestication has been a controversial topic for decades, a recent study published in Cell Research by Wang and colleagues (2020) seems to have taken the field a step forward in answering key questions on the geographic and temporal origins of chicken domestication [302]. Erasmus, Darwin's grandfather, was one of the first to suggest that the red junglefowl (Gallus gallus) was the wild ancestor of the domestic chicken.…”

“…However, with the advent of SNP arrays and next-generation sequencing technologies, chicken domestication was proposed to have occurred via multiple independent events in different areas of Asia between 7,000 and 10,000 AC [189,158] from at least two wild progenitors [94]. The 'multiple origins' hypothesis has recently been questioned by Wang et al (2020). In their study on 863 chicken genomes from a variety of domestic breeds and wild (sub)species, the authors showed that domestic chickens were initially derived from the wild red junglefowl subspecies G.g.…”