Identification of SNPs and candidate genes associated with growth traits of Nigerian improved Indigenous chicken genotypes
Department of Animal Science, Faculty of Agriculture, University of Uyo, Akwa Ibom State, Nigeria.
Research Article
International Journal of Science and Technology Research Archive, 2026, 10(01), 086-100.
Article DOI: 10.53771/ijstra.2026.10.1.0010
Publication history:
Received on 09 January 2026; revised on 25 February 2026; accepted on 28 February 2026
Abstract:
For decades, genetic improvement based on measuring growth traits has been successfully applied in the production of meat-type chickens. A genome-wide association study using the chicken 60k SNP panel in 42 Nigerian indigenous chickens (NICs) derived from the crosses between Marshall and pure Nigerian chickens of 500 Chickens’ population at 8 weeks of age in T&R farm of FUNAAB, Nigeria to identify Single Nucleotide Polymorphisms on the chromosomes and genes associated with growth trait was carried out. BW was taken for 8 weeks. Blood samples were collected from 42 NICs from purebred and F2 upgrades to extract DNA, and PCR- RFLP technique was used for DNA amplification in which the Amplicons were sequenced. Molecular analysis using Molecular software packages and bioinformatics approach were used for the sequence analysis.The raw phenotypic data which comprises of the sex and body weight (>2 kg as 1 (case)) and <1 kg as 0 (control)) was analyzed using GenAbel of the R package software to carry out quality checks using some filtering techniques in NICs and their crosses. Selective sweep analysis was applied and ten SNPs were Identified on chromosomes with three candidate genes associated with body weight- (Peroxisome Proliferator-Activated Receptors (PPAR-201) gene, Breakpoint Cluster Region 201 (BCR-201) gene and Glycine Aminodino Transferase Mitochondrial (GATM) gene on Chromosomes 1, 15 and 10, respectively, were associated with body weight of NICs F2 resource population and (Glycine Aminodino Transferase Mitochondrial (GATM) gene) was a novel gene discovered. These findings made it easier to understand the traits of the good germplasm and their potentials for using the NICs.
Keywords:
Body Weight; Candidate Gene; Genome-Wide Association Study; Nigerian Indigenous Chickens; Single Nucleotide Polymorphism.
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