Sequence analysis of exon 1 and intron 1 of growth hormone gene in six chicken genotypes raised in tropical environment

Abstract

Alpha % Growth hormone gene % Nigerian indigenous chicken % SNPs KR nema Chicken growth hormone (cGH) is a polypeptide hormone secreted by the pituitary gland which is responsible for several functions such as tissue growth and reproduction in chickens. This study was conducted to characterize six chicken genotypes using exon 1 and intron 1 regions of cGH gene sequences. One hundred and thirty-four (134) chickens comprising Normal feather (19), Naked neck (21), Frizzle feather (8), Arbor Acre (24), FUNAAB Alpha-1 (dihybrid) (31), and FUNAAlpha-2 (trihybrid) (31) were used for the study. Blood samples were collected from the birds into EDTA bottles for DNA extraction. The exon 1 and intron 1 regions of cGH were amplified using published primers. The product of the polymerase chain reaction was subjected to Sanger sequencing. DnaSP5 software was used to determine the diversity indices and MEGA6 software was used to determine the phylogenetic relationships among the six chicken genotypes and other chicken sequences. Fifteen (15) SNPs were identified in intron 1 and none in exon 1 of the cGH gene in all the six genotypes, and nine (9) of the SNPs occurred as transitions while others were transversions. The allele frequency ranged from 0.30 to 0.95 while the highest heterozygosity (0.66) was observed in mutation 410A>C in Naked neck genotype and lowest heterozygosity observed in Arbor Acre at SNP 330C>T. Polymorphic Information Content (PIC) was at the maximum in SNP 410A>C in Naked neck genotype with a value of 0.92. The exon 1 phylogeny tree revealed two clades where all the genotypes diverged. Intron 1 revealed two clades where Frizzle feather clustered with FUNAAB Alpha-1, Naked neck and FUNAAlpha-2 clustered together at one of the sub-clades in the second clade. Network analysis revealed Normal feather chicken as the major ancestor of all the genotypes. The study concluded that intron 1 of cGH is polymorphic in all the six chicken genotypes investigated, and this can be used as candidate gene for selection in growth-related traits.