Journal of Animal Breeding and Genomics (J Anim Breed Genom)
B. O. AKINBAMI1 AND A. A. TOYE1,2*
1Quantitative, Molecular and Functional Genetics Group, Department of Animal Production, Faculty of Agriculture, University of Ilorin, Kwara State, Nigeria.
2Institute for Molecular Science and Biotechnology, University of Ilorin, Kwara State, Nigeria.
Correspondence to Ayokunle Afolabi Toye , E-mail: ayo.toye@btinternet.com
Volume 3, Number 3, Pages 83-94, September 2019.
Journal of Animal Breeding and Genomics 2019, 3(3), 83-94. https://doi.org/10.12972/jabng.20190010
Received on 16 September, 2019, Revised on 20 September, 2019, Accepted on 20 September, 2019, Published on September 30, 2019.
Copyright © 2019 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).
A candidate gene for growth determination (Adipocyte Fatty Acid Binding Protein (A-FABP/FABP4) was examined for polymorphisms which can serve as markers of its differential functional status and role in differential growth performance between genetically slow growing indigenous chickens (Fulani Ecotype, and Yoruba Ecotype Nigeria Local Chicken, FE-NLC and Y-NLC) and fast growing exotic commercial chicken (Hubbard broiler) breeds. Primers for amplification of each exon of the predicted primary transcript of A-FABP of Red Jungle Fowl and the 50 base sequences immediately preceding and following each exon were designed, synthesised and used to amplify their target region in Hubbard and FE-NLC genomic DNA by use of the Polymerase Chain Reaction (PCR). PCR products were sequenced using ABI 3500XL Genetic Analyzer (Applied Biosystems). Exon sequences were subjected to multiple sequence alignment (MultAlin software). Phylogeny trees were constructed using Phylogeny.fr. Multiple sequence alignment (MSA) of Hubbard broiler and FE-NLC FABP4 exon 3 DNA sequences against FABP4 exon 3 of the Red Jungle Fowl primary transcript (ENSGALT00000025427.3 nt 1746 -1847) and flanking intron DNA revealed the existence of a purine to purine Single Nucleotide Polymorphism (SNP) in position 1765 (position 266 of the mature transcript predicted from NM_204290; position 20 of exon 3) of the primary transcript. The Red Jungle Fowl and Fulani Ecotype chicken carried an Adenine (A) base and Hubbard broiler carried Guanine (G), at the polymorphic site which led to an Asparagine to Serine change at an evolutionarily conserved region of codon 7 of exon 3 of the gene. Phylogenetic analysis of the predicted peptide sequence of exons using the order aves (within superorder Palaeognathae) as in-group and eutherian and non-eutherian mammals as out-group revealed that exon 3 of Hubbard broiler was the most recently emerged in the examined group of bird. The location of the FABP4 polymorphism within the coding portion of the gene (exon) and specifically its location within an evolutionarily conserved codon, coupled with its non-synonymous nature suggest that the broiler variant may affect function of the encoded protein and the mutation might contribute to differential fat deposition and early growth rate in Hubbard Broilers relative to NLC chickens carrying the consensus/ancestral variant.
Fatty Acid Binding Protein, molecular marker, phylogeny, Single nucleotide polymorphism, Fulani ecotype chicken.
This Single Nucleotide Polymorphism (SNP) c 266 A >G should be used as a marker for studying effect of FABP4 on growth and performance in chickens. Association studies should be conducted in a cohort (Hubbard broiler, Fulani ecotype, unimproved Yoruba ecotype and improved Yoruba ecotype) in which alleles are segregating. The present study should be repeated to ensure sequencing of all exons of both (FABP4) gene for Hubbard broiler, Fulani ecotype and Yoruba ecotype so as to examine the consequence of variation in as-yet-unsequenced portions of the gene.