Third Backcross Generation Indonesian Indigenous Chicken Kampong Broiler-Type (Kambro) SOX5 Gene Polymorphism

The comb is an accessory organ on the head of chicken which is influenced by testosterone hormone and can be used as an indicator of chickens fertility. Comb shape is related to climate adaptation and associated with a dominant mutation in chicken chromosome 1. Therefore this research was aimed to study the association between Pea-comb shape and SOX5 gene polymorphism in the population of progenies (BC-III Kambro) derived from a crossbreed between females Pelung and males second backcross generation Kampong Broiler-Type (BC-II Kambro). Chicken (Gallus gallus) SOX5 gene was acquired from NCBI GenBank with the Ref. Seq. 418195. Primers used to amplify the SOX5 gene are (F):5-AGGTAGCCATGGTGACAAGC-3,(R):5-GATCTGTGAGGCAGCCAGTT-3. Progenies showed 100% Pea-comb shape, while parental generation composed of Pea-comb shape and Single-comb shape. PCR-RFLP and endonuclease restriction enzyme HindIII were unable to determine the genotype of the female parent with Pea-comb. The result of SOX5 gene polymorphism showed the comb shape uniformity between progenies and parental of Kambro backcross generation. This study concluded that the genotype of Pea-comb shape female Pelung was undetermined and there was no polymorphism of the SOX5 gene between pea and single comb. PCR-RFLP using endonuclease restriction enzyme HindIII produced both target products and non-target/artifact products. The sequencing procedure was required to provide nucleotide sequences.