ABSTRACT
The phenotypic characterization, genetic variation and proteomic analysis of three main male chicken (Gallus gallus) breeds were investigated. These included hybrid red jungle fowl with the native chicken breed (KaiTor), white tail yellow chicken (WTYC) and commercial layer hen (HL). A phenetic analysis found that two major clades were observed in which the first two clades of Kai-Tor (clade A) and HL (clade B) were related. Meanwhile, WTYC was distinctly separated from the others. In terms of genetic diversity, three haplotypes were observed with 0.343 ± 0.097 of haplotypes diversity (Hd). The nucleotide diversity (Pi) of all samples was 0.00057 which conformed to low genetic diversity. In terms of protein characterization, two potential protein biomarkers were found in Kai-Tor serum samples namely 1) ATP-dependent RNA helicase DHX34 (DHX34; Accession number: XP_015128539.1) and 2) histone-lysine N-methyltransferase SETDB1 isoform X6 (SETDB1; Accession number: XP_015135538.1). Only one biomarker peptide was detected in HL (Cell division cycle 7-related protein kinase; CDC7; Accession number: XP_422347.5) as well as in WTYC (Bloom syndrome protein; BLM; Accession number: Q9I920).