The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken-a review

Chicken is a major source of protein for the increasing human population and is useful for research purposes. There are almost 1,600 distinct regional breeds of chicken across the globe, among which a large body of genetic and phenotypic variations has been accumulated due to extensive natural and arti-ficial selection. Moreover, natural selection is a crucial force for animal domestication. Several approaches have been adopted to detect selection signatures in dif-ferent breeds of chicken using whole genome sequencing (WGS) data including integrated haplotype score (iHS), cross-populated extend haplotype homozygosity test (XP-EHH), fixation index (FST), cross-popula-tion composite likelihood ratio (XP-CLR), nucleotide diversity (Pi), and others. In addition, gene enrichment analyses are utilized to determine KEGG pathways and gene ontology (GO) terms related to traits of interest in chicken. Herein, we review different studies that have adopted diverse approaches to detect selection signa-tures in different breeds of chicken. This review system-atically summarizes different findings on selection signatures and related candidate genes in chickens. Future studies could combine different selection signa-tures approaches to strengthen the quality of the results thereby providing more affirmative inference. This would further aid in deciphering the importance of selection in chicken conservation for the increasing human population.

Automated summary

Chicken is a valuable source of protein and the subject of research due to its genetic and phenotypic variations resulting from natural and artificial selection. Various approaches, including whole genome sequencing, have been used to detect selection signatures and identify candidate genes in different chicken breeds. In addition, gene enrichment analyses help determine pathways and gene ontology related to specific traits in chicken. This review summarizes different studies on selection signatures and provides suggestions for future research to strengthen the findings and understand the importance of selection in chicken conservation for the growing human population.