Molecular and Bioinformatics Analysis of Allelic Diversity in IGFBP2 Gene Promoter in Indigenous Makuee and Lori-Bakhtiari Sheep Breeds
Subject Areas : Camelع. ولیپور کوتنایی 1 , ا. فرهادی 2 , س.ح. حافظیان 3 , م. قلیزاده 4
1 - Department of Animal Science, Faculty of Animal Science and Fishery, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
2 - Department of Animal Science, Faculty of Animal Science and Fishery, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
3 - Department of Animal Science, Faculty of Animal Science and Fishery, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
4 - Department of Animal Science, Faculty of Animal Science and Fishery, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
Keywords: promoter, sequencing, Lori-Bakhtiari sheep, Makuee sheep, <i>IGFBP gene</i>,
Abstract :
The aim of this study was to perform molecular and bioinformatics analysis of IGFBP2 gene promoter in association with some economic traits in indigenous Makuee (MS) and Lori-Bakhtiari (LB) breeds. DNA was extracted from blood samples of 120 MS and 200 LB and a 297 bp fragment from the upstream sequences of studied gene was amplified and genotyped by single-strand conformational polymorphism (SSCP) technique. Two genotypes of AB and BB were seen in MS and LB breeds. Then one sample from each genotype was send to sequencing. After obtaining the sequencing result, the sequences homology was performed on the National Center for Biological Information NCBI server by basic local alignment search tool (BLAST) program. The alignment of the obtained sequences and their comparison with reference sequences from the Gene Bank were done using CLUSTALW multiple alignment tool of BioEdit software. In addition, the DNASIS MAX software was used to identify DNA motifs. The bioinformatics analysis revealed differences in sequences of IGFBP2 between observed genotypes. Ten motifs in promoter sequence of IGFBP2 genes were seen, so that the CAP_site motif was most abundant in both fragments motif. Statistical analysis using general linear method model (GLM) procedure of SAS software showed significant (P<0.05) association of IGFBP2 with thigh round (TR) trait in Makuee sheep. Further studies in other indigenous sheep breeds and investigation of other genetic regions along with regulatory sites seem to be necessary.
Adam C.L., Gadd T.S., Findlay P.A. and Wathes D.C. (2004). IGF-I stimulation of luteinizinghormone secretion, IGF-binding proteins (IGFBPs) and expression of mRNAs for IGFs, IGFreceptors and IGFBPs in the ovine pituitary gland. J. Endocrinol. 166, 247-254.
Baxter R.C. (1990). Circulating levels and molecular distribution of the acid-labile (α) subunit of the high molecular weight insulin-like growth factor-binding protein complex. J. Clin. Endocrinol. Metab. 70(5), 1347-1353.
Blum W.F., Jenne E.W., Reppin F., Kietzmann K., Ranke M.B. and Bierich J.R. (1989). Insulin-like growth factor I (IGF-I)- binding protein complex is a better mitogen than free IGF-I. Endocrinology. 125(2), 766-772.
Busby S. and Ebright R.H. (2001). Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293(2), 199-213.
D’haeseleer P. (2006). What are DNA sequence motifs? Nat. Biotechnol. 24, 423-425.
Fenwick M.A., Liewellyn S., Fitzpatrick R., Kenny D.A., Murphy J.J., Patton J. and Wathes D.C. (2008). Negative energy balance in dairy cows in associated with specific changes in IGF-binding protein expression in the oviduct. Reproduction. 135, 63-75.
Hall T.A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98.
Holly J. (2004). Physiology of the IGF system. Novartis Found Symp. 262, 19-26.
Hu V., Oh Y. and Rosenfeld R.G. (1999). The insulin-like growth factor binding protein (IGFBP) superfamily. Endocrinol. Rev. 20, 761-787.
Jones J.I. and Clemmons D.R. (1995). Insulin-like growth factors and their binding proteins biological actions. Endocrinol. Rev. 16, 3-34.
Karimzadeh S., Farhadi A. and Tanha T. (2016). Introduction and Evaluation of Livestock Breeds (Iran and World). Parto Vaghe Publication, Tehran, Iran.
Kostecka Z. and Blahovec J. (2002). Animal insulin-like growth factor binding proteins and their biological functions. Vet. Med. 47, 75-84.
Kumar P., Choudhary V., Padma B., MishraA., Bhattacharya T.K., Bhushan B. and Sharma A. (2004). Bubaline insulin-like growth factor binding protein-3 (IGFBP-3) gene polymorphism and its comparison with cattle. Buffalo J. 20, 183-192.
Lawson C.L., Swigon D., Murakami K.S., Darst S.A., Berman H.M. and Ebright R.H. (2004). Catabolite activator protein: DNA binding and transcription activation. Curr. Opin. Struct. Biol. 14, 10-20.
Lee M.M., Nie Q.H., Peng X., Zhang D.X. and Zhang X.Q. (2005). Single nucleotide polymorphisms of the chicken insulin-like factor binding protein 2 genes associated with chicken growth and carcass traits. Poult. Sci. 84, 1191-1198.
Miller S.A., Dykes D.D. and Polesky H.F. (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16(3), 1215-1221.
Monget P., Manniaux D., Pisselet C. and Durand, P. (1993). Changes in insulin-like growthfactor-I (IGF-I), IGF-II and their binding proteins during growth and atresia of ovine ovarian follicles. Endocrinology. 132, 1438-1446.
Nagao K., AmanYaman M., Murai A., Saki T., Saito N., Okumura J. and Kita K. (2001). Insulin administration suppresses an increase in insulin-like growth factor binding protein-2 gene expression stimulated by fasting in the chicken. Br. Poult. Sci. 42, 501-504.
Orita M., Iwahana H., Kanazawa H., Hayashi K. and Sekiya T. (1989). Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA. 86(8), 2766-2770.
Ostecka Z.K. and Lahovec J.B. (2002). Animal insulin-like growth factor binding proteins and their biological functions. Vet. Med. Czech. 47(2), 75-84.
SAS Institute. (2004). SAS®/STAT Software, Release 9.1. SAS Institute, Inc., Cary, NC. USA.
Shannon C.E. and Weaver W. (1949). The Mathematical Theory of Communication. University of Illinois Press, Illinois, Urbana.
Sharma A., Dutt G., Silvalingam J., Singh M.K., Pathodiya O., Khadda B.S. and Dixit S.P. (2013). Novel SNPs in IGF1, GHR and IGFBP3 genes reveal significant association with growth traits in Indian goat breeds. Small Rumin. Res. 115, 7-14.
Yeh F.C., Yang R.C., Boyle T.B.J., Ye Z.H. and Mao J.X. (1997). POPGENE, the user-friendly shareware for population genetic analysis. Ph D. Thesis. University of Alberta, Alberta, Canada.
Yu M., Shimonka S., Shimosaki S. and Ling N. (1989). An insulin-like growth factor-binding protein in ovarian follicular fluid blocks follicle-stimulating hormone-stimulated steroid production by ovarian granulosa cells. Endocrinology. 125, 912-916.
Zapf J. (1997). Total and free IGF serum levels. European J. Endocrinol. 136(2), 146-147.