Genome wide analysis of growth and development genes in cattle (Bos taurus) and Buffalo (Bubalus bubalis)
DOI:
https://doi.org/10.33687/ricosbiol.03.01.0033Keywords:
Gene, GH, development, NCBI , growth, genes in cattle, genes in Buffalo, Bubalus bubalis, Bos taurusAbstract
Bos taurus and Bubalus bubalis have been major source of meat since about 10000 years. 50 genes associated with growth and development in Bos taurus and Bublus bubalis were analyzed integratedly by GWAS performing chromosomal mapping, gene structure, conserved motif analysis, gene expression, GO annotation analysis, protein-protein association and phylogenetic analysis, Main bio-informatics tools used were NCBI, Expasy, WebScipio, iTOL , heatmapper, string and MEGA 5. GH, TG and NEB were found as major genes of beef production by visulising expression by heatmapper, motif analysis by MEME and gene structure analysis using webScipio. All other genes were also linked differently with this trait. Each gene had unique structure and discrete role regarding growth.GH affects directly on growth and development. String results revealed that TG associates with other genes in complex networks to stimulate growth. Results of Motif analysis by using MEME and heatmapper showed that NEB has highly conserved domains associated with structural and functional role in skeletal muscle growth and development. Heatmapper analysis showed that CFL1 has role in growth and development of brain, lungs, spleen, colon and testis. ALDH2 showed overexpression in kidney and liver and ACTC1 in heart. Synteny analysis was performed to elucidate syntenic regions between Bt and Bb. Results showed that there is strong similarity and conserved regions. This is due to the strong evolutionary relationship of Bt and Bb. Phylogenetic analysis confirmed strong evolutionary relationship of Bos taurus and Bubalus bubalis. This comprehensive research could be used by animal scientists to understand growth pattern, association of genes and development of genetic markers to increase beef production to make Pakistan hub of halal food.
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Acosta, J., Carpio, Y., Borroto, I., González, O., & Estrada, M. P. (2005). Myostatin gene silenced by RNAi shows a zebrafish giant phenotype. Journal of biotechnology, 119(4), 324-331.
Amills, M., Jimenez, N., Villalba, D., Tor, M., Molina, E., Cubilo, D., ... & Estany, J. (2003). Identification of three single nucleotide polymorphisms in the chicken insulin-like growth factor 1 and 2 genes and their associations with growth and feeding traits. Poultry science, 82(10), 1485-1493.
Audic, S., & Claverie, J. M. (1997). The significance of digital gene expression profiles. Genome research, 7(10), 986-995.
Babicki, S., Arndt, D., Marcu, A., Liang, Y., Grant, J. R., Maciejewski, A., & Wishart, D. S. (2016). Heatmapper: web-enabled heat mapping for all. Nucleic acids research, 44(W1), W147-W153.
Bakhtiarizadeh, M. R., Salehi, A., & Rivera, R. M. (2018). Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing. PloS one, 13(2), e0193316.
Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B., & Lander, E. S. (2000). Human and mouse gene structure: comparative analysis and application to exon prediction. Genome research, 10(7), 950-958.
Belamkar, V., Selvaraj, M. G., Ayers, J. L., Payton, P. R., Puppala, N., & Burow, M. D. (2011). A first insight into population structure and linkage disequilibrium in the US peanut minicore collection. Genetica, 139(4), 411.
Biase, F. H., Rabel, C., Guillomot, M., Hue, I., Andropolis, K., Olmstead, C. A., ... & Lewin, H. A. (2016). Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium. Proceedings of the National Academy of Sciences, 113(51), 14492-14501.
Börchers, T., & Spener, F. (1994). Fatty acid binding proteins. Current topics in meters, 40, 261-294.
Brenner, S., Elgar, G., Sanford, R., Macrae, A., Venkatesh, B., & Aparicio, S. (1993). Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature, 366(6452), 265-268.
Caldas, Y. R., Renand, G., Ballester, M., Saintilan, R., & Rocha, D. (2016). Systems biology approach provides novel insights into gene networks controlling tenderness and meat quality traits across French beef breeds. In 35. Conference of the International Society for Animal Genetics (ISAG) (Vol. 94, p. np).
Cao, Y., Jia, H., Xing, M., Jin, R., Grierson, D., Gao, Z., ... & Li, X. (2021). Genome-wide analysis of MYB gene family in Chinese bayberry (Morella rubra) and identification of members regulating flavonoid biosynthesis. Frontiers in plant science, 12, 1244.
Carvalho, T. D. D., Siqueira, F., Torres Júnior, R. A. D. A., Medeiros, S. R. D., Feijó, G. L. D., Souza Junior, M. D. D., ... & Soares, C. O. (2012). Association of polymorphisms in the leptin and thyroglobulin genes with meat quality and carcass traits in beef cattle. Revista Brasileira de Zootecnia, 41, 2162-2168.
Chung, E. R., & Kim, W. T. (2005). Association of SNP marker in IGF-I and MYF5 candidate genes with growth traits in Korean cattle. Asian-australasian journal of animal sciences, 18(8), 1061-1065.
Cook, C. E., Lopez, R., Stroe, O., Cochrane, G., Brooksbank, C., Birney, E., & Apweiler, R. (2019). The European Bioinformatics Institute in 2018: tools, infrastructure and training. Nucleic acids research, 47(D1), D15-D22.
Cooper, D. N., Ball, E. V., & Krawczak, M. (1998). The human gene mutation database. Nucleic acids research, 26(1), 285-287.
Cunningham, E. P. (1989). The genetic improvement of cattle in developing countries. Theriogenology, 31(1), 17-28.
Curi, R. A., Chardulo, L. A. L., Mason, M. C., Arrigoni, M. D. B., Silveira, A. C., & De Oliveira, H. N. (2009). Effect of single nucleotide polymorphisms of CAPN1 and CAST genes on meat traits in Nellore beef cattle (Bos indicus) and in their crosses with Bos taurus. Animal genetics, 40(4), 456-462.
Davis, S. R., Spelman, R. J., & Littlejohn, M. D. (2017). Breeding heat tolerant dairy cattle: the case for introgression of the" slick" prolactin receptor variant into Bos taurus dairy breeds. Journal of Animal Science, 95(4), 1788-1800.
De Camargo, G. M. F., Aspilcueta-Borquis, R. R., Fortes, M. R. S., Porto-Neto, R., Cardoso, D. F., Santos, D. J. A., ... & Tonhati, H. (2015). Prospecting major genes in dairy buffaloes. BMC genomics, 16(1), 1-14.
Dezfulian, M. H., Soulliere, D. M., Dhaliwal, R. K., Sareen, M., & Crosby, W. L. (2012). The SKP1-like gene family of Arabidopsis exhibits a high degree of differential gene expression and gene product interaction during development. PloS one, 7(11), e50984.
Dunner, S., Sevane, N., Garcia, D., Levéziel, H., Williams, J. L., Mangin, B., ... & GeMQual Consortium. (2013). Genes involved in muscle lipid composition in 15 European Bos taurus breeds. Animal genetics, 44(5), 493-501.
Gan, Q. F., Zhang, L. P., Li, J. Y., Hou, G. Y., Gao, X., Ren, H. Y., ... & Xu, S. Z. (2008). Association analysis of thyroglobulin gene variants with carcass and meat quality traits in beef cattle. Journal of Applied Genetics, 49(3), 251-255.
Glatz, J. F. C., Vork, M. M., Cistola, D. P., & Van der Vusse, G. J. (1993). Cytoplasmic fatty acid binding protein: significance for intracellular transport of fatty acids and putative role on signal transduction pathways. Prostaglandins, leukotrienes and essential fatty acids, 48(1), 33
Gonzalez, T. L., Sun, T., Koeppel, A. F., Lee, B., Wang, E. T., Farber, C. R., ... & Pisarska, M. D. (2018). Sex differences in the late first trimester human placenta transcriptome. Biology of sex differences, 9(1), 1-23.
Gordo, D. G. M., Baldi, F., Lôbo, R. B., Filho, W. K., Sainz, R. D., & Albuquerque, L. G. D. (2012). Genetic association between body composition measured by ultrasound and visual scores in Brazilian Nelore cattle. Journal of Animal Science, 90(12), 4223-4229.
Greenhalgh, C. J., Rico-Bautista, E., Lorentzon, M., Thaus, A. L., Morgan, P. O., Willson, T. A., ... & Hilton, D. J. (2005). SOCS2 negatively regulates growth hormone action in vitro and in vivo. The Journal of clinical investigation, 115(2), 397-406.
Gui, L. S., Zhang, Y. R., Liu, G. Y., & Zan, L. S. (2015). Expression of the SIRT2 gene and its relationship with body size traits in Qinchuan cattle (Bos taurus). International journal of molecular sciences, 16(2), 2458-2471.
Hall, B. G. (2013). Building phylogenetic trees from molecular data with MEGA. Molecular biology and evolution, 30(5), 1229-1235.
Hansen, P. J. (2004). Physiological and cellular adaptations of zebu cattle to thermal stress. Animal reproduction science, 82, 349-360.
Hayes, B. J., Chamberlain, A. J., Maceachern, S., Savin, K., McPartlan, H., MacLeod, I., ... & Goddard, M. E. (2009). A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal genetics, 40(2), 176-184.
Herrington, J., Smit, L. S., Schwartz, J., & Carter-Su, C. (2000). The role of STAT proteins in growth hormone signaling. Oncogene, 19(21), 2585-2597.
Hocquette, J. F., Gondret, F., Baeza, E., Medale, F., Jurie, C., & Pethick, D. W. (2010).
Intramuscular fat content in meat-producing animals: development, genetic and nutritional control, and identification of putative markers. Animal, 4(2), 303-319.
Johansen, K. A., & Overturf, K. (2005). Quantitative expression analysis of genes affectingmuscle growth during development of rainbow trout (Oncorhynchus mykiss). Marine Biotechnology, 7(6), 576-587.
Kanis, E., De Greef, K. H., Hiemstra, A., & Van Arendonk, J. A. M. (2005). Breeding for societally important traits in pigs. Journal of animal science, 83(4), 948-957.
Kerr, T., Roalson, E. H., & Rodgers, B. D. (2005). Phylogenetic analysis of the myostatin gene sub‐family and the differential expression of a novel member in zebrafish. Evolution & development, 7(5), 390-400.
Kerr, T., Roalson, E. H., & Rodgers, B. D. (2005). Phylogenetic analysis of the myostatin gene sub‐family and the differential expression of a novel member in zebrafish. Evolution & development, 7(5), 390-400.
Kim, J. J., Farnir, F., Savell, J., & Taylor, J. F. (2003). Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle. Journal of Animal Science, 81(8), 1933-1942.
Kim, M., Choi, H., & Kim, Y. B. (2021). Therapeutic targets and biological mechanisms of action of curcumin against Zika virus: In silico and in vitro analyses. European Journal of Pharmacology, 904, 174144.
Korte, A., & Farlow, A. (2013). The advantages and limitations of trait analysis with GWAS: a review. Plant methods, 9(1), 1-9.
Li, M. H., Adamowicz, T., Switonski, M., Ammosov, I., Ivanova, Z., Kiselyova, T., ... & Kantanen, J. (2006). Analysis of population differentiation in North Eurasian cattle (Bos taurus) using single nucleotide polymorphisms in three genes associated with production traits. Animal Genetics, 37(4), 390-392.
Li, X., Ekerljung, M., Lundström, K., & Lundén, A. (2013). Association of polymorphisms at DGAT1, leptin, SCD1, CAPN1 and CAST genes with color, marbling and water holding capacity in meat from beef cattle populations in Sweden. Meat science, 94(2), 153-158.
Liu, Y., Duan, X., Liu, X., Guo, J., Wang, H., Li, Z., & Yang, J. (2014). Genetic variations in insulin-like growth factor binding protein acid labile subunit gene associated with growth traits in beef cattle (Bos taurus) in China. Gene, 540(2), 246-250.
Maccatrozzo, L., Bargelloni, L., Radaelli, G., Mascarello, F., & Patarnello, T. (2001). Characterization of the myostatin gene in the gilthead seabream (Sparus aurata): sequence, genomic structure, and expression pattern. Marine Biotechnology, 3(3), 224-230.
MacHug , R. T., Cunningham, P., & Bradley, D. G. (1998). Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Animal genetics, 29(5), 333-340.
Mackay, T. F. (2001). The genetic architecture of quantitative traits. Annual review of genetics, 35(1), 303-339.
Malheiros, J. M., Enriquez-Valencia, C. E., de Vasconcelos Silva, J. A. I., Curi, R. A., de Oliveira, H. N., de Albuquerque, L. G., & Chardulo, L. A. L. (2020). Carcass and meat quality of Nellore cattle (Bos taurus indicus) belonging to the breeding programs. Livestock Science, 242, 104277.
Mayr, E. (1954). Change of genetic environment and evolution.
Nadeem, A., Javed, M., Hassan, F. U., Luo, X., Khalid, R. B., & Liu, Q. (2020). Genomic identification, evolution and sequence analysis of the heat-shock protein gene family in buffalo. Genes, 11(11), 1388.
Nasser, A. K., Yusuf, M. E., & AL-Hassnawi, M. J. (2021). Thyroglobulin Gene Polymorphism in Fatty Acids for Back Area in Local and Imported Colombian Bull Calves. Annals of the Romanian Society for Cell Biology, 13987-13995.
Odronitz, F., Pillmann, H., Keller, O., Waack, S., & Kollmar, M. (2008). WebScipio: an online tool for the determination of gene structures using protein sequences. BMC genomics, 9(1), 1-13.
Park, S. J., Beak, S. H., Da Jin Sol Jung, S. Y., Kim, I. H. J., Piao, M. Y., Kang, H. J., ... & Baik, M. (2018). Genetic, management, and nutritional factors affecting intramuscular fat deposition in beef cattle—a review. Asian-Australasian journal of animal sciences, 31(7), 1043.
Rettenberger, G., Klett, C., Zechner, U., Kunz, J., Vogel, W., & Hameister, H. (1995). Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting. Genomics, 26(2), 372-378.
Rodgers, B. D., Roalson, E. H., & Thompson, C. (2008). Phylogenetic analysis of the insulin-like growth factor binding protein (IGFBP) and IGFBP-related protein gene families. General and comparative endocrinology, 155(1), 201-207.
Rump, R., Buhlmann, C., Borchers, T., & Spener, F. (1996). Differentiation-dependent expression of heart type fatty acid-binding protein in C2C12 muscle cells. European journal of cell biology, 69(2), 135-142.
Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution, 4(4), 406-425.
Shmelkov, S. V., Clair, R. S., Lyden, D., & Rafii, S. (2005). AC133/CD133/Prominin-1. The international journal of biochemistry & cell biology, 37(4), 715-719.
Silveira, L. G. G., Furlan, L. R., Curi, R. A., Ferraz, A. L. J., Alencar, M. M. D., Regitano, L. C., ... & Oliveira, H. N. D. (2008). Growth hormone 1 gene (GH1) polymorphisms as possible markers of the production potential of beef cattle using the Brazilian Canchim breed as a model. Genetics and Molecular Biology, 31(4), 874-879.
Sosnicki, A. A., & Newman, S. (2010). The support of meat value chains by genetic technologies. Meat Science, 86(1), 129-137.
Tadesse, M., Dessie, T., Tessema, G., Degefa, T., & Gojam, Y. (2006). Study on age at first calving, calving interval and breeding efficiency of Bos taurus, Bos indicus and their crosses in the highlands of Ethiopia. Ethiopian journal of animal production, 6(2), 1-16.
Tahara, K., Aso, H., Yamaguchi, T., Yamasaki, T., Takano, S., Rose, M. T., ... & Sugimoto, Y. (2004). Cloning and expression of type XII collagen isoforms during bovine adipogenesis. Differentiation, 72(4), 113-122.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution, 28(10), 2731-2739.
Tang, J., Shen, X., Ouyang, H., Luo, W., Huang, Y., Tian, Y., & Zhang, X. (2020). Transcriptome analysis of pituitary gland revealed candidate genes and gene networks regulating the growth and development in goose. Animal biotechnology, 1-11.
Thornton, P. K. (2010). Livestock production: recent trends, future prospects. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1554), 2853-2867.
Tian, J. H., Patel, N., Haupt, R., Zhou, H., Weston, S., Hammond, H., ... & Smith, G. (2021). SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice. Nature communications, 12(1), 1-14.
Vaughn, T. T., Pletscher, L. S., Peripato, A., King-ellison, K., Adams, E., Erikson, C., & Cheverud, J. M. (1999). Mapping quantitative trait loci for murine growth: a closer look at genetic architecture. Genetics Research, 74(3), 313-322.
Veerkamp, J. H., & Van Moerkerk, H. T. B. (1993). Fatty acid-binding protein and its relation to fatty acid oxidation. In Cellular Fatty Acid-Binding Proteins II (pp. 101-106). Springer, Boston, MA.
Voorrips, R. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of heredity, 93(1), 77-78.
Wang, Y. H., Bower, N. I., Reverter, A., Tan, S. H., De Jager, N., Wang, R., ... & Lehnert, S. A. (2009). Gene expression patterns during intramuscular fat development in cattle. Journal of Animal Science, 87(1), 119-130.
Warner, R. D., Greenwood, P. L., Pethick, D. W., & Ferguson, D. M. (2010). Genetic and environmental effects on meat quality. Meat science, 86(1), 171-183.
Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24(18).
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., ... & Yaschenko, E. (2007). Database resources of the national center for biotechnology information. Nucleic acids research, 36(suppl_1), D13-D21.
Wu, W., Fu, Y., Therkildsen, M., Li, X. M., & Dai, R. T. (2015). Molecular understanding of meat quality through application of proteomics. Food Reviews International, 31(1), 13-28.
Xia, L., Su, X., Shen, J., Meng, Q., Yan, J., Zhang, C., ... & Xu, M. (2018). ANLN functions as a key candidate gene in cervical cancer as determined by integrated bioinformatic analysis. Cancer management and research, 10, 663.
Zhang, Y. R., Gui, L. S., Li, Y. K., Jiang, B. J., Wang, H. C., Zhang, Y. Y., & Zan, L. S. (2015). Molecular characterization of bovine SMO gene and effects of its genetic variations on body size traits in Qinchuan cattle (Bos taurus). International journal of molecular sciences, 16(8), 16966-16980.
Zhang, Y., Laz, E. V., & Waxman, D. J. (2012). Dynamic, sex-differential STAT5 and BCL6 binding to sex-biased, growth hormone-regulated genes in adult mouse liver. Molecular and cellular biology, 32(4), 880-896.
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