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Genetic characterization among Red Junglefowl (GS, Gallus  gallus spadiceus), Thai indigenous chicken (TIC, Gallus domesticus)  and commercial lines has been widely used for studies of genealogical origin,  genetic diversity, and effects of selection. We compared the efficiency of  genetic characterization of chicken populations that had been under different  intensities of selection using selective functional gene versus microsatellite marker  analyses. We genotyped 151 chickens from five populations: Red Junglefowl, TIC  and commercial lines (BR, broiler and WL, White Leghorn). Genetic structure  analyses using six loci of five functional genes - corresponding to heat  tolerance (heat shock protein 70, HSP70/C, HSP70/M), broodiness  (vasoactive intestinal peptide receptor-1, VIPR-1), egg  production-[24-bp indel (insertion or deletion) prolactin, 24bpPRL],  ovulation rate (growth hormone receptor, GHR), and growth (insulin-like  growth factor-1, IGF-1) - were compared with 18 microsatellite markers.  PCR-RFLP and allele specific PCR were used for functional gene typing. A  neighbor-joining tree from Nei's genetic distance was constructed to show  genetic relationships. A similar pattern was found with both functional genes  and microsatellites. Three groups consisting of BR, WL and TIC-GS-GG were  formed. A principal component plot based on individual similarity using Dice's  coefficient was also constructed to confirm the relationship. Different  patterns were found when using functional genes versus microsatellites. A  principal component plot with functional genes also gave three clusters  consisting of BR, WL and TIC-GS-GG. A principal component plot using  microsatellites gave four clusters, consisting of WL, GG, TIC, and BR-GS. Characterization  of BR and GS differs from previous studies. We concluded that genetic  characterization with appropriate functional genes is more accurate when  differences in genetic make-up among populations are known. Genetic  characterization using functional gene data was consistent in neighbor joining  and principal component plot analyses, while genetic characterization using  microsatellite data gave varied results depending on the analysis methodology.

genetics and molecular research

Genetic characterization of Red Junglefowl (Gallus gallus), Thai indigenous chicken (Gallus domesticus), and two commercial lines using selective functional genes compared to microsatellite markers