DNA-Based Analysis of PIT1 Gene Variation Among Chicken Strains in Akwa Ibom State, Nigeria

Abstract

The study aimed to identify and characterise PIT1 gene variation across three chicken strains in Nigeria using DNA-based analysis. Blood samples were collected from three chicken strains: Broiler, Normal-feathered, and Frizzle-feathered. Blood samples were initially collected from 20 birds per genotype (60 in total); of these, 5 samples per strain (15 in total) yielded successful DNA amplification and were used for downstream sequencing and genetic diversity analyses. Bioinformatic analysis was performed using the gene sequences. PIT1 gene sequences were aligned and analysed; the results revealed that the Frizzle-feathered and Broiler chicken populations were closely related, whereas the Normal-feathered chicken population was genetically distinct from the other chicken populations. Regression analysis showed complete D' in both Broilers and Frizzle-feathered chickens (D' = 1), but the reported r2 value was lower in Broilers (0.6178) than in Frizzle-feathered chickens (1.0), indicating stronger allelic correlation in the Frizzle-feathered strain. Normal-feathered chickens showed the steepest negative LD-distance slopes, indicating more rapid LD decay within the fitted range; however, these regression slopes do not provide a direct estimate of recombination rate. Based on Table 1, Broilers showed the highest within-strain genetic diversity (H = 3, Hd = 1.0, NS = 3, K = 9.33, Pi = 0.0446), followed by Frizzle-feathered chickens (H = 2, Hd = 1.0, NS = 2, K = 3.33, Pi = 0.0145), whereas Normal-feathered chickens showed no detectable within-strain variation in the reported metrics (H = 0, Hd = 0.00, NS = 0, K = 0.00, Pi = 0.00). Moreover, the molecular marker (PIT1) used was highly polymorphic, informative, and suitable for the genetic characterisation of both Nigerian and exotic chicken populations. The marker results showed that Frizzle-feathered and Broiler chicken populations were closely related, whereas Normal-feathered chickens were genetically distant from Frizzle-feathered chickens. Normal-feathered chickens were genetically distinct from the other chicken populations in the phylogenetic analysis, but the study showed no detectable within-strain PIT1 diversity in the analysed Normal-feathered samples. The study revealed that the PIT1 gene, as a molecular marker, is useful for studying the evolutionary history and relationships among Normal-feathered, Frizzle-feathered, and Broiler chicken breeds and how evolutionary mutation has affected their genetic variation over time. Therefore, the PIT1 gene, as a molecular marker, should be used to study genetic variation and evolutionary relationships among chicken species, as it facilitates genetic improvement and conservation of chicken breeds.