Homology modeling of single nuleotide polymorphisms in candidate genes controlling embryonic growth of buffalo

JEROME A; A K PANDEY; SUSHEEL KUMAR SARKAR

doi:10.56093/ijans.v85i6.49289

Authors

JEROME A Scientist, Division of Animal Physiology and Reproduction, ICAR-Indian Agricultural Statistics Research Institute, New Delhi
A K PANDEY Principal scientist, Division of Animal Genetics and Breeding, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana 125 001 India
SUSHEEL KUMAR SARKAR Scientist, ICAR-Indian Agricultural Statistics Research Institute, New Delhi

https://doi.org/10.56093/ijans.v85i6.49289

Keywords:

Buffalo, FGF2, Homology modeling, Pregnancy, STAT5A, UTMP

Abstract

Pregnancy involves interactions of numerous growth factors, proteins and hormones exerting their biological functions in cellular growth, migration, differentiation and signal transduction. FGF2, STAT5A and UTMP are important mediators of intra-cellular signals transduction and transcription functions during pregnancy. Mutations in these genes will eventually disrupt their biological functions leading to embryonic death. The present study was designed to analyze in silico the SNPs in buffalo FGF2, STAT5A and UTMP genes by homology modeling. In the present study genomic DNA was isolated from the blood of 75 adult female buffaloes which was subsequently used for the amplification of FGF2, STAT5A and UTMP gene specific regions. PCR products of 167 bp, 429 bp and 279 bp were obtained for specific FGF2, STAT5A and UTMP gene regions, respectively. Sequenced PCR products showed 96â€“97% similarity with bovine sequences on BLAST analysis for all the 3 gene segments. Sequence analysis showed 9, 3 and 9 distinct nucleotide differences in the regions of FGF2, STAT5A, UTMP genes, respectively. Furthermore, based on the nucleotide difference 3 variants for FGF2 and UTMP genes were deduced in comparison with the bovine sequence. Promotor region analysis of FGF2 and homology modeling of STAT5A and UTMP gene revealed modification in the protein structure arising due to the presence of nucleotide changes. In the present study single nucleotide polymorphism were deduced in FGF2, STAT5A and UTMP gene region of buffalo and homology modeling of the studied gene portions were carried out.

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References

Adamczak R, Poroll A and Meller J. 2004. Accurate prediction of solvent accessibility using neural networks based regression. Proteins 56: 753–67. DOI: https://doi.org/10.1002/prot.20176

Ahmed S S, Abdel eziz K B, Hassan N A and Mabrouk D M. 2011. Genetic polymorphism of some genes related to reproductive traits and their association with calving interval in Egyptian buffalo. Genomics and Quantitative Genetics 3: 1–8.

Agarwal S K, Singh S K and Rajkumar R. 2005. Reproductive disorders and their management in cattle and buffalo: A Review. Indian Journal of Animal Sciences 75 (7): 858–73.

Ashworth C J and Bazer F W. 1989. Changes in ovine conceptus and endometrial function following asynchronous embryo transfer or administration of progesterone. Biology of Reproduction 40: 425–29. DOI: https://doi.org/10.1095/biolreprod40.2.425

Ayalon N. 1978. A review of embryonic mortality in cattle. Journal of Reproduction and Fertility 54: 483–85. DOI: https://doi.org/10.1530/jrf.0.0540483

Barile V L. 2005. Reproductive efficiency in female buffaloes. A Borghese. Buffalo Production and Research. FAO, Rome:77– 108.

Base SAS® 93. 2011. Procedures Guide ISBN 978–1–60764– 895–6 SAS Institute Inc Cary, NC,USA.

Berglund B. 2008. Genetic improvement of dairy cow reproductive performance. Reproduction in Domestic Animals 43: 89–95. DOI: https://doi.org/10.1111/j.1439-0531.2008.01147.x

Demmers K J, Derecka K and Flint A. 2001. Trophoblast interferon and pregnancy. Reproduction 121: 41–49. DOI: https://doi.org/10.1530/rep.0.1210041

Falconer D S and Mackay T F C. 1996. Introduction to quantitative genetics, 4th edition Longman, Harlow, UK.

Garbayo J M, Green J, Manikkam M, Beckers J F, Kiesling D O, Ealy A D and Roberts R M. 2000. Caprine pregnancyassociated glycoproteins (PAGs): their cloning, expression and evolutionary relationship to other PAG. Molecular Reproduction Development 57: 311–22. DOI: https://doi.org/10.1002/1098-2795(200012)57:4<311::AID-MRD2>3.0.CO;2-F

Heinemeyer T, Wingender E, Reuter I, Hermjakob H, Kel A, Kel O, Ignatieva E, Ananko E, Podkolodnaya O, Kolpakov F, Podkolodny N and Kolchanov N. 1998. Databases on transcriptional regulation: TRANSFAC, TRRD, and COMPEL. Nucleic Acids Research 26: 364–70. DOI: https://doi.org/10.1093/nar/26.1.362

Kelley L A and Sternberg M J E. 2009. Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols 4: 363 –71. DOI: https://doi.org/10.1038/nprot.2009.2

Khatib H, Maltecca C, Monson R L, Schutzkus V, Wang X and Rutledge J J. 2008. The fibroblast growth factor 2 gene is associated with embryonic mortality in cattle. Journal of Animal Science 86: 2063–67. DOI: https://doi.org/10.2527/jas.2007-0791

Khatib H, Huang W, Wang X, Tran A H, Bindrim A B, Schutzkus V, Monson R L and Yandell B S. 2009. Single gene and gene interaction effects on fertilization and embryonic survival rates in cattle. Journal of Dairy Science 92: 2238–47. DOI: https://doi.org/10.3168/jds.2008-1767

Khatib H, Monson R L, Huang W, Khatib R, Schutzkus V, Khateeb H and Parrish J J. 2010. Validation of in vitro fertility genes in a Holstein bull population. Journal of Dairy Science 93: 2244– 49. DOI: https://doi.org/10.3168/jds.2009-2805

Michael D D, Alvarex I M, Ocón O M, Powell A M, Talbot N C, Johnson S E and Ealy A D. 2006. Fibroblast growth factor–2 is expressed by the bovine uterus and stimulates interferontau production in bovine trophectoderm. Endocrinology 147: 3571–79. DOI: https://doi.org/10.1210/en.2006-0234

Oikonomou G, Michailidis G, Kougioumtzis A, Avdi M and Banos G. 2011. Effect of polymorphisms at the STAT5A and FGF2 gene loci on reproduction, milk yield and lameness of Holstein cows. Research in Veterinary Science 91 (2): 235–39. DOI: https://doi.org/10.1016/j.rvsc.2011.01.009

Reese M G. 2001. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Computers and Chemistry 26 (1): 51–56. DOI: https://doi.org/10.1016/S0097-8485(01)00099-7

Schäfer-Somi S. 2003. Cytokines during early pregnancy of mammals: a review. Animal Reproduction Science 75 (1–2): 73–94. DOI: https://doi.org/10.1016/S0378-4320(02)00222-1

Szafranska B, Xie S, Green J and Roberts R M. 1995. Porcine Pregnancy-Associated Glycoproteins:new members of the aspartic proteinase gene family expressed in the trophectoderm. Biology of Reproduction 53: 21–28. DOI: https://doi.org/10.1095/biolreprod53.1.21

Thatcher W W, Guzeloglu A, Mattos R, Binelli M, Hansen T R and Pru J K. 2001.Uterine-conceptus interactions and reproductive failure in cattle. Theriogenology 56: 1435–50. DOI: https://doi.org/10.1016/S0093-691X(01)00645-8

Veerkamp R F and Beerda B. 2007.Genetics and genomics to improve fertility in high producing dairy cows. Theriogenology 68: 266–73. DOI: https://doi.org/10.1016/j.theriogenology.2007.04.034

Xie S, Low B G, Nagel R J, Kramer K K, Anthony R V, Zoli A P, Beckers J F and Roberts R M. 1991.Identification of the major pregnancy specific antigens of cattle and sheep asinactive members of the aspartic proteinase family. Proceeding of National Academy of Science, USA 88: 10247–51. DOI: https://doi.org/10.1073/pnas.88.22.10247

Xie S, Low B G, Nagel R J, Beckers J F and Roberts R M. 1994. A novel glycoprotein of the aspartic proteinase gene family expressed in bovine placental trophectoderm. Biology of Reproduction 51: 1145–53. DOI: https://doi.org/10.1095/biolreprod51.6.1145

Yeh F, Yang R C and Boyle T. 2000. POPGENE - for the analysis of genetic variation among and within populations using codominant and dominant markers, Win 95+ Version 132.