ABSTRACT
A lot of attention has been paid to the study of Insulin-like Growth factor 1 (IGF1) due to its function in stimulating systemic body growth and regulating cell growth and development. A bioinformatics study was carried out to investigate the Insulin-like Growth Factor 1 gene of turkey, chicken and quail. A total of 15 insulin-like growth factor 1 nucleotide sequence and their corresponding protein were obtained from the Genebank (a public domain protein database) and were analyzed using various software tools (Clustal W, MEGA 6, dnaSP, BLAST, phyre2, ExPASy GORIV and Rasmol software) to determine the percent identity and similarities in function of IGF 1 gene, genetic diversity, evolutionary relationship, protein structure prediction and physiochemical properties. The result obtained showed that percent identity and similarity of IGF1 gene in avians ranged from 86- 99% and were similar in function. Observed genetic diversity was high within each avian (1.000 in turkey, 0.900 in chicken and 0.900 in quail). However chicken had the highest haplotype number value (4), this showed that chicken has more variation than turkey and quail IGF1 gene sequence. Phylogenetic analysis showed that the IGF1 in gene sequence of avian were grouped into the same taxon, chicken and quail shared a most recent common ancestor and were closely related than the IGF1 gene of turkey. The secondary structure analyzed by GORIV (Garnier-Osguthorpe-Robson IV) software tool showed that the alpha helix structure of chicken, turkey and quail occupied (20.92%), (21.57%) and (20.92%) of the IGF1 gene sequences respectively. The results from the secondary and tertiary structure of IGF1 protein predictions showed that the IGF genes of avian are stable and properly formed. The physiochemical properties showed that chicken, turkey and quail IGF1protein had isoelectric potential (theoretical pI) of 9.25, estimated half-life of 30 hours. In conclusion, the high percent identity and similarity in function, high genetic diversity observed, a relative relatedness in the phylogentic study and high alpha helix in the protein structure of IGF1 gene seen in this study make the gene highly effective in improving growth, and regulating cellular activities.
CHAPTER ONE
1.1 INTRODUCTION
Insulin-like growth factors (IGF1) are naturally occurring protein capable of stimulating cellular growth, proliferation and differentiation. According to Hegarty et al. (2006), IGF1 are proteins which are important for regulating a variety of cellular processes. Insulin-like growth factor-1 is a mediator of many biological effects; it increases the absorption of glucose, stimulates myogenesis, inhibits cell cycle genes, increases the synthesis of lipids, and stimulates the production of progesterone in the synthesis of DNA, RNA and protein (Etherton, 2004). Due to these biological functions, IGF1 is being considered as a candidate gene for predicting growth and meat quality traits in the animal genetic development scheme (Andrade et al., 2008).
IGF1 is produced primarily by the liver as an endocrine hormone as well as in target tissues in a paracrine or autocrine manner (Kemp, 2007). Its production is stimulated by growth hormone and can be retarded by under-nutrition, growth insensitivity or lack of growth hormone receptors (Flier and Underhill, 2006). Growth hormone is made in the anterior pituitary gland and released into the blood stream and then stimulates the liver to produce IGF1 (Akinfenwa et al., 2011). Then IGF1 stimulates systemic body growth and has growth-promoting effects on almost every cell in the body system (Yilmaz et al., 2011). Deficiency of either growth hormone or IGF1 therefore results in diminished stature (Akinfenwa et al., 2011).
Different researchers have established a link between the concentration of the circulating IGF1 and growth trait in many livestock species and laboratory animals (Bertlett and Tom, 2005; Bunter et al., 2005; Hegarty et al., 2006).
Bioinformatics involves discovery, development and implementation of computational algorithms and software tools that facilitates an understanding of the biological processes with the goal to serve primarily agriculture and health care sectors with several spinoffs (Albert et al., 2011). In a developing country like Nigeria, bioinformatics has a key role to play in areas like agriculture where it can be used to analyze livestock genomic and proteomic data that can be very useful in making genetic improvements.
Computational analysis greatly helps in understanding the molecular basis of the biological function of proteins through the use of available information to understand the biological function of unknown proteins. Technical progress in computational methods offers the potential to make many improvements far faster and more efficient than would be possible by laboratory methods (Zimin et al., 2009). Bioinformatics is a branch of biological science which deals with the study of methods for storing, retrieving and analysis biological data, such as nucleic acid (Deoxyribonucleic acid/ribonucleic acids/ and protein sequences, structures, function, pathways and genetic interaction) (www.wikipeadia.com). Ribonucleic acids (RNA) and deoxyribonucleic acids (DNA) are the molecules that store the hereditary information about an organism. These macro-molecules have a fixed structure, which can be analysed by biologists with the help of bioinformatics tools and databases. A few popular data bases are gene Bank from NCBI (National Centre for Biotechnology Information), Swiss port from the Swiss institution of Bioinformatics and protein information Resources (PIR) (www.ncbi.nlm.nih.gov).
One of the major challenges of animal breeding is to understand the genetic basis of phenotypic diversity within and among species. Thousands of years of relative breeding of domestic animals has created a diversity of phenotypes among breeds that is only matched by that observed among species in nature. Selection of most livestock in Nigeria has been carried out with little or no knowledge of series of reactions at the molecular and cellular level. Selection has been on the effect of the gene rather than directly on the gene themselves (Akinbiyi, 2014). Traits are controlled by single or combination of many gene actions. The study of IGF1gene on avian using bioinformatics aim at enlightening the farmers and breeders more in understanding the importance of molecular components of genes in selection, especially in a developing country like Nigeria where molecular genetics and bioinformatics is still under study and not well documented.
According to Mahmoud et al. (2014), chicken IGF1have been seen to serve as better candidate gene for growth and other metabolic process (proliferation and cellular differentiation) when compared to most species. In this study, the role of IGF1in three avian species was identified and a comparison made to help researchers and farmers know which specie IGF1gene can best serve as a molecular maker and also as a growth promoter to improve production traits in farm animals. Toro et al., (2008) reported that molecular data on within and between breed genetic diversity are essential for effective management of farm animal genetic resources. FAO (2000) reported that genetic diversity in livestock allows farmers to select stocks or develop new breeds in response to environmental changes, threat of disease, new knowledge of human nutrition requirement, changing market conditions and societal needs.....
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