Identifying Molecular Signatures from Sex Chromosomes: A Case for Indigenous Chicken Based on the Analyses of the Z Chromosome

Domestications and selection have led to phenotypic variation in chicken and has left traceable signatures within their genome. Indigenous chicken has been shaped more by natural selection [1] imposed by the environmental conditions, parasites, diets and diseases. Several candidate genes that contribute to adaptation to harsh scavenging tropical conditions, for instance, those linked to response to endoplasmic reticulum stress and cell redox homeostasis (e.g. PDIA4 gene), suppression of viral infection and mediation of inflammatory responses (MAPK13), have been discovered [2]. Nevertheless, most of the detection of selection signatures is based on the genomic scans of autosomes, though chicken chromosome hosts both autosomes and allosomes. Allosome (sex chromosome) is more specialized than an autosome and plays a significant role in evolution [3]. Particularly, allosome has been suggested to be a good target for detection of signatures of selection because of its high gene density and undergoes more drift than autosomes [4]. In pigs, a selective scan of the X chromosome revealed genes contributing to immunity, reproduction and meat quality, in the potential regions affected by selections. In sheep, the X chromosome hosts several genes associated with tail fat deposition [5]. However, only a few genomic studies have scanned the allosome of the chicken. In this study, a Z-chromosome-wide genomic scan using F-statistics (Fst) method was performed to search for genomic selection signatures in chicken kept under low input production system compared to commercial layers. Identification of the regions affected by selection offers the opportunity of understanding the forces of historical selection, genes, and mutations underlying a phenotype difference between indigenous and commercial chicken.