Kennedy, G. M.; Ogada, S. O.; Kuria, S. N.; Lichoti, J. K.; Ommeh, S. C.

This study aimed to investigate the signatures of selection in guineafowl and chicken genomes adapted to divergent climatic conditions across Africa, Asia, and Europe. We used whole genome sequence data of guineafowls and chicken from selected countries in these continents. To identify the signatures of selection, we employed three population genomics methods: FST, integrated Haplotype Score (iHS), and Cross-Population Extended Haplotype Homozygosity (XP-EHH). Our findings revealed enriched terms related to metabolic processes, response to stimulus, signaling, and developmental processes, all of which play a role in the stress response for both guineafowls and chickens. Several candidate genes such as CRYGN, BRAF, MAP3K2, ANGPT2, COL1A1, ATP13A4, and SLC66A1, were among the positively selected candidate genes. Most of the candidate genes selected and the significant pathways identified play various roles in stress response in these two poultry species. Examination of divergent populations has provided new insights into genes potentially under selection for tolerance to the populations indigenous environment, serving as a baseline for examining the genomic contributions to tolerance adaption. The knowledge gained from this research establishes a valuable foundation and guide for molecular breeding and conservation.