Novel Single Nucleotide Polymorphisms (SNPs) in Intron 2 and Exon 3 Regions of Leptin Gene in Sumba Ongole Cattle
الموضوعات :
1 - Research Center for Biotechnology, Indonesian Institute of Science, Jl. Raya Bogor Km. 46, Cibinong, Bogor 16911, West Java, Indonesia
2 - Biotechnology, Indonesian Institute of Science, Jl. Raya Bogor Km. 46, Cibinong, Bogor 16911, West Java, Indonesia
الکلمات المفتاحية: polymorphism, Leptin gene, Pasundan cattle, polymorphic informative content, SNPs,
ملخص المقالة :
The bovine leptin (LEP) gene was widely used as a candidate gene for molecular selection to improve productivity traits of cattle. This study was carried out to identify single nucleotide polymorphisms (SNPs) in the LEP gene of Sumba Ongole (SO, Bos indicus) cows using sequencing method. A total of 31 animals were used in this study for analyses. Research showed that total of 16 SNPs were detected in the LEP gene. Along 2025 bp of LEP gene sequence was analyzed in this study and consisted of intron 2 (1002 bp) and exon 3 (1023 bp). The polymorphic informative content (PIC) value was reached from 0.06 (low) to 0.37 (moderate). Total of 16 SNPs in LEP gene of SO cattle had moderate PIC value (0.25<PIC<0.50) and consisted of twelve SNPs in intron 2 and four SNPs in exon 3. The SNPs with moderate PIC value were detected in intron 2 (g.2325G/T; g.2423A/C; g.2448C/T; g.2456C/G; g.2466C/T; g.2778T/A; g.2857G/A) and exon 3 (g.3260T/C; g.3272T/C; g.3356C/T; g.3468G/A). The SNP of g.3468G/A as the novel SNP in LEP gene of SO cattle that not reported in other breeds of cattle. This SNP was changed the amino acid from glycine (GGG) to arginine (AGG). Two type of mutation were detected in the LEP gene of SO cattle and consisted of transversions (44%) and transitions (56%). It was concluded that the LEP gene in SO cattle was showed polymorphisme and potential for molecular selection in the breeding program through depth research.
Agung P.P., Anwar S., Wulandari A.S., Sudiro A., Said S. and Tappa B. (2015). The potency of Sumba Ongole (SO) cattle: A study of genetic characterization and carcass productivity. J. Indonesian Trop. Anim. Agric. 40, 71-78.
Agung P.P., Anwar S., Putra W.P.B., Zein M.S.A., Wulandari A.S., Said S. and Sudiro A. (2017). Association of growth hormone (GH) gene polymorphism with growth and carcass in Sumba Ongole (SO) cattle. J. Indonesian Trop. Anim. Agric. 42, 153-159.
Almeida S.E.M., Almeida E.A., Moraes J.F.C. and Weimer T.A. (2003). Molecular markers in the LEP gene and reproductive performance of beef cattle. J. Anim. Breed. Genet. 120, 106-113.
Bourdon R.M. (2000). Understanding Animal Breeding. Prentice Hall, New Jersey, USA.
Corva P.M., Macedo G.V.F., Soria L.A., Mazzucco J.P., Motter M., Villarreal E.R., Schor A., Mezzadra C.A., Melucci L.M. and Miquel M.C. (2009). Effect of leptin gene polymorphisms on growth, slaughter and meat quality traits of grazing Brangus steers. Genet. Mol. Res. 8, 105-116.
Falconer R.D. and Mackay T.F. (1996). Introduction of Quantitative Genetic. Prentice Hall, New Jersey, USA.
Fruhbeck G., Jebb S.A. and Prentice A.M. (1998). Leptin: physiology and pathophysiology. Clin. Physiol. 18, 399-419.
Giblin L., Stephen T.B., Breda M.K., Sinead M.W., Michael J.C. and Donagh P.B. (2010). Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires. BMC Genet. 11, 1-10.
Glaubitz J.C. (2004). Convert: A user friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. 4, 309-310.
Hardjosubroto W. (1994). Applied of Animal Breeding. Gramedia Widiasarana, Jakarta, Indonesia.
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.
Jecminkova K., Uwe M., Jitka K., Zuzana S., Ludmila Z., Miloslava S. and Ivan M. (2018). Association of leptin, toll-like receptor 4, and chemokine receptor of interleukin 8 C-X-C motif single nucleotide polymorphisms with fertilty traits in Czech Fleckvieh cattle. Asian Australasian J. Anim. Sci. 00, 1-8.
Jhala N.B., Rank D.N., Vataliya P.H., Joshi C.G., Bhong C.D., Mehta H.H. and Patil A.V. (2009). Cloning and sequencing of the leptin gene in Gir cattle and Mehsana buffalo. Buffalo Bull. 28, 29-33.
Kalinowski S.T., Mark L.T. and Tristan C.M. (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 1099-1106.
Kawaguchi F., Okura K., Oyama K., Mannen H. and Sasazaki S. (2016). Identification of leptin gene polymorphisms associated with carcass traits and fatty acid composition in Japanese Black cattle. Anim. Sci. J. 88, 433-438.
Liefers S.C., te Pas M.F.W., Veerkamp R.F., Chilliard Y., Delavaud C., Gerritsen R. and van der Lende T. (2002). Association of between leptin gene polymorphisms and production, live weight, energy balance, feed intake, and fertility in Holstein heifers. J. Dairy Sci. 85, 1633-1638.
Madeja Z., Adamowicz T., Chmurzynska A., Jankowski T., Melonek J., Switonski M. and Strabel T. (2004). Effect of leptin gene polymorphisms on breeding value for milk production traits. J. Dairy Sci. 87, 3925-3927.
Matteis G.D., Maria C.S., Francesco G., Francesca P., Fabio A., Gennaro C., Francesco N. and Bianca M. (2012). Association analyses ofsingle nucleotide polymorphisms in the leptin and leptin receptor genes on milk and morphological traits in Holstein cows. Open J. Anim. Sci. 2, 174-182.
Moussavi A.H., Ahouei M., Nassiry M.R. and Javadmanesh A. (2006). Association of leptin polymorphism with production, reproducion, and plasma glucose level in Iranian Holstein cows. Asian-Australasian J. Anim. Sci. 19, 627-631.
Nei M. and Kumar S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, Oxford, United Kingdom.
Oner Y., Onur Y., Hayrettin O., Nezih A.T.A., Gulnaz Y.M. and Abdulkadir K. (2017). Associations between GH, PRL, STAT5A, OPN, PIT-1, LEP and FGF2 polymorphisms and fertility in Holstein-Friesian heifers. Kafkas Univ. Vet. Fak. Derg. 23, 527-534.
Oprzadek J., Flisikowski K., Zwierzchowski L. and Dymnicki E. (2003). Polymorphisms at loci of leptin (LEP), Pit1 and STA-T5A and their association with growth, feed conversion, and carcass quality in Black-and-White bulls. Anim. Sci. Pap. Rep. 21, 135-145.
Orru L., Cifuni G.F., Piasentier E., Corazzin M., Bovolenta S. and Moioli B. (2011). Associations analyses of single nucleotide polymorphism in the LEP and SCD genes on the fatty acid of muscle fat in Simmental bulls. Meat Sci. 87, 344-348.
Pfister-Genskow M., Hayes H., Eggen A. and Bishop M.D. (1996). Chromosomal localization of the bovine obesity (OBS) gene. Mamm. Genome. 7, 398-399.
Pomp D., Zou T., Clutter A.C. and Barendse W. (1997). Mapping of leptin to bovine chromosome 4 by linkage analysis of a PCR-based polymorphism. J. Anim. Sci. 75, 1427-1435.
Putra W.P.B. and Indriastuti R. (2017). Leptin gene as potential gene for molecular selection on cattle in Indonesia. Wartazoa. 27, 105-116.
Putra W.P.B., Agung P.P. and Wulandari A.S. (2017). Profile of 3'flanking region of leptin gene in Sumba Ongole (SO) cattle. Bullet. Anim. Sci. 41, 371-378.
Putra W.P.B., Agung P.P. and Said S. (2018). Non-genetic factor and genetic parameter analysis for growth traits in Sumba Ongole (SO) cattle. J. Indonesian Trop. Anim. Agric. 43, 94-106.
Rasor C.C., Thomas M.G., Enns R.M., Salazar H.C., Zhang H.M., Williams G.L., Stanko R.L., Rendel R.J. and Rios J. (2002). Allelic and genotypic frequencies of the leptin gene Sau3AI restriction fragment length polymorphism and evaluation of its association with age at puberty in cattle in the Southwestern United States and Northern Mexico. Prof. Anim. Sci. 18, 141-146.
Said S., Agung P.P., Putra W.P.B., Anwar S., Wulandari A.S. and Sudiro A. (2016a). Selection of Sumba Ongole (SO) cattle based on breeding value and performance test. J. Indonesian Trop. Anim. Agric. 41, 175-187.
Said S., Agung P.P., Putra W.P.B., Anwar S., Wulandari A.S.W. and Sudiro A. (2016b). Estimation of most probable producing ability value for calf’s birth performance in Sumba Ongole cows. J. Indonesian Trop. Anim. Agric. 41, 53-60.
Shin S.C. and Chung E.R. (2007). Association of SNP marker in the leptin gene with carcass and meat quality traits in Korean cattle. Asian-Australasian J. Anim. Sci. 20, 1-6.
Tamura K., Stecher G., Peterson D., Filipski A. and Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725-2759.
Taniguchi Y., Itoh T., Yamada T. and Sasaki Y. (2002). Genomic structure and promoter analysis of the bovine leptin gene. IUBMB Life. 53, 131-135.
Yeh F.C. and Boyle T.J.B. (1997). Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian J. Bot. 129, 157-163.
