Abstract
The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.
Highlights
Since Charles Darwin proposed a single ancestry of chicken from the red junglefowl, its status as either monophyletic or polyphyletic has been debated (Darwin, 1868; Beebe, 1918; Danforth, 1958; Morejohn, 1968; Fumihito et al, 1994)
The intermediate genomic variants generated for individual birds using the “HaplotypeCaller” from genome analysis toolkit (GATK) (Auwera et al, 2013) were used to jointly genotype all samples belonging to a population into a single variants file
We identified two candidates sweep regions that are shared between all domestic chicken and the red junglefowl
Summary
Since Charles Darwin proposed a single ancestry of chicken from the red junglefowl, its status as either monophyletic or polyphyletic has been debated (Darwin, 1868; Beebe, 1918; Danforth, 1958; Morejohn, 1968; Fumihito et al, 1994). A study on mitochondrial DNA suggests multiple centers of chicken domestication (Liu et al, 2006) from which chicken dispersed to different parts of the world through humans’ influence They entered North Africa, the Middle East and Sri Lanka from the Indian subcontinent, while maritime introductions, likely originating initially in South-East Asia, occurred along the coast of East Africa as well as Sri Lanka (Silva et al, 2009; GiffordGonzalez and Hanotte, 2011; Mwacharo et al, 2011). Following these migration events, natural and artificial selections have shaped the genome landscape of domestic chicken resulting in a wide spectrum of breeds and ecotypes
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