Diversity of partial sequence leptin gene (Exon 3) in crossbred cattle compared to GenBank database
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Abstract. Ermawati D, Panjono, Bintara S, Hartatik T. 2022. Diversity of partial sequence leptin gene (Exon 3) in crossbred cattle compared to GenBank database. Biodiversitas 23: 5614-5620. Genetic marker method that is often used to select cattle is Single Polymorphism Nucleotide (SNP). Single Polymorphisms Nucleotide (SNP) has been found in various candidate genes, one of which is the leptin gene. Leptin is a gene that affects reproduction and cattle weight. Therefore, this research aims to identify SNP of the leptin gene (exon 3) in Crossbred cattle by comparison with GenBank data. A sample of Crossbred cattle was taken from Klaten in Central Java, Indonesia. Afterward, DNA sequencing results were analyzed with BioEdit to identify SNP. BioEdit software was used for DNA sequencing alignment part of intron 2, exon 3 and 3'UTR. The MEGA 11.1.1 program was used to analyze and edit the genetic distance and phylogenetic tree based on the SNP leptin gene. The result shows that nine variations of SNPs were found in exon 3. The phylogenetic tree shows that the Crossbred cattle, Bos taurus, Bos indicus, Hereford, Friesian Holstein and Bali, were in the same cluster. HindIII restriction enzyme can be recommended for genotyping Crossbred cattle using PCR RFLP. This research provides information on SNP in the leptin gene so that it can be used for further research on the association of the leptin gene to growth and reproduction.
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References
Amitani M, Asakawa A, Amitani H, Inui A. 2013. The role leptin in the control of insulin glucose axis. Front Neurosci 7: 51. DOI: 10.3389%2Ffnins.2013.00051.
Albakri MW, Hartatik T. 2021. Restriction mapping of melanocortin 4 receptor in Bos taurus and Bos indicus based on GenBank data. Res J Biotechnol 16 (1): 107-112. DOI: 10.22146/jtbb.67636.
Anugratama LE, Hartatik T. 2019. Short communication: Identification of leptin gene in crossbred beef cattle. Biodiversitas 21: 1. DOI: 10.13057/biodiv/d210129.
Atasoy D, Betley JN, Su HH, Sternson S. 2012. Deconstruction of a neural circuit for hunger. Nature 488: 172-177. DOI: 10.1038%2Fnature11270.
Awalia RS. 2022. Estimasi Parameter Genetik untuk Produksi Susu dan Sifat Reproduksi serta Identifikasi Gen Leptin pada Frishein Holstein di PT Ultra Peternakan Bandung. [Thesis]. Universitas Gadjah Mada, Yogyakarta. [Indonesian]
Bhowmik N, Ringwall KA, Dahlen CR, Swason KC, Clapper JA, Ward AK, Hulsman, Hanna LL. 2019. The role of leptin in reprosuctive charasteristic of commercial beef cows and heifer. Transl Anim Sci 3: 1764-1768. DOI: 10.1093/tas/txz083.
Cheng YH, Kuo CN, Lai CM. 2016. Effective natural PCR-RFLP primer desaign for SNP genotyping using teaching learning based optimalization with Elite Strategy. IEEE Trans Nanobiosci 15 (7): 657-665. DOI: 10.1109/TNB.2016.2597867.
Connoly S, Dona A, Hamblin D, D’Occhio MJ, Gonzales LA. 2020. Changes in the blood metabolome of Wagyu Crossbred steers with time in the feedlot and relationship with marbling. Nat Res 10: 18987. DOI: 10.1038/s41598-020-7610.
Criscuolo A. 2019. A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. Res Ideas Outcomes 5: e36178. DOI: 10.3897/rio.5.e36178.
D’occhio, Baruselli PS, Campanile G. 2019. Influence of nutrition, body condition, and metabolic status on reproduction in female beef cattle: A review. Theriogenology 125: 277-284. DOI: 10.1016/j.theriogenology.2018.110.
Hartatik T, Bintara S, Ismaya I, Panjono P, Widyobroto BP, Agus A, Budisatria IGS, Leroy P. 2020. Single nucleutide polymorphism of sex determining region Y gene coding sequences in Belgian Blue Bull and Wagyu Bull Crossbred Cattle. IOP Conf Ser Earth Environ Sci 478: 012020. DOI: 10.1088/1755- 1315/478/1/012020.
Hartatik T, Latifah, Yuliana R, Kustantinah A. 2019. Genotyping and chi-square analysis of 967 bp leptin gene in Bligon Goat. IOP Conf Ser Earth Environ Sci 478: 012019. DOI: 10.1088/1755-1315/478/1/012019.
Hayder O, Hasim, Mohammed BS, Al-Shuhaib. 2019. Exploring the potential and limitations of PCR-RFLP and PCR-SSCP for SNP detection. J Appl Biotechnol Rep 6 (4): 137-144. DOI: 10.29252/JABR.06.04.02.
Jecmicova K, Müller U, Kyselova J, Sztankoova Z, Zavadilova L, Stipkova M, Majzlik. 2018. Association of leptin, toll-like receptor 4, and chemokine receptor of interleukin 8 C-X-C motif single nucleotide polymorphisms with fertility traits in Czech Fleckvieh cattle. Asian-Australas J Anim Sci 31 (11): 1721-1728.
Kawaguchi F, Okura K, Oyama K, Mannen H, Sasazaki S. 2017. Identification of leptin gene polymorphisms associated with carcass traits and fatty acid composition in Japanese Black cattle. Anim Sci J 88: 433-438. DOI: 10.1111/asj.12672.
Khallaf AG, Geba KM, Osman AGM, Abouelfadl KY, Borrell YJ, Vasquez EG. 2017. SNP based PCR-RFLP, T-RFLP and FINS methodologies for the identification of commercial fish species in Egypt. Fish Res 185: 34-42. DOI: 10.1016/j.fishres.2016.09.031.
Kurlyana T. 2022. Estimasi Parameter Genetik Sifat Pertumbuhan dan Asosiasi Gen Leptin terhadap Sifat Pertumbuhan Sapi Bali di BPTU HPT Denpasar Bali. [Thesis]. Universitas Gadjah Mada, Yogyakarta. [Indonesian]
Kuswati K, Furqon A, Septian WA, Susilawati T. 2022. Polymorphism of leptin gene (Single Nucleotide Polymorphisms c.73T>C) and its association with body weight and body measurements in Madura cattle. Vet World 15 (3): 775-781. DOI: 10.1007/bf01731581.
Latifah L, Maharani D, Kustantinah A, Hartatik T. 2016. Association of melanorcotin 4 receptor gene polymorphism with growth traits in bligon goat. J Indones Trop Anim Agric 43 (4): 343-351. DOI: 10.14710/jitaa.43.4.343-351.
Lee PY, Costumbrado, Hsu CY, Kim YH. 2012. Agarose gel electrophoresis for the separation of DNA fragments. J Vis Exp 62: 3923. DOI: 10.3791/3923.
Lopez CH, Robles RCR, Godoy AV, Utrera AR, Ponce SIR, Padila EG. 2021. Relationships between seasonality, body characteristics and leptin at the beginning of puberty in Bos taurus taurus and Bos taurus indicus heifers in the Mexican tropics. Rev Mex Cienc Pecu 12 (4): 1025-1044. DOI: 10.22319/rmcp.v12i4.5796a.
Mahrous KF, Aboelenin MM, Rashed MA, Sallam MA, Rushdi HE. 2020. Detection of polyimorphism within leptin gene in egyptian river buffalo and predict its effects on different molecular levels. J Genet Eng Biotechnol 18 (1): 6. DOI: 10.1186/s43141-020-0020-5.
Mandefro A, Sisay T, Kim KS, Edaa Z, Konwarh R, Dadi H. 2021. Single Nucleutide Polymorphism of leptin gene in five ethiopian indigenous cattle breeds and the korean hanwoo breed. Trop Anim Health Prod 53 (2): 202. DOI: 10.1007/s11250-021-02642-1.
Nishimaki T, Sato K. 2019. An extension of the kimura two-parameter model to the natural evolutionary process. J Mol Evol 87 (1): 60-67. DOI: 10.1007/s00239-018-9885-1.
Park S, Ha J, Kim I, Kwon AG, Hwang JH, Park DH, Kang DG, Kim TW, Kim CW. 2015. Effects of LEP, GYS1, MYOD1, and MYF5 polymorphism on pig economic traits. Ann Anim Sci 15 (3): 629-640. DOI: 10.1515/aoas-2015-0022.
Perez-Montarelo D, Fernandez A, Folch JM, Pena RN, Ovilo C, Rodriguez C. 2012. Joint effect of porcine leptin and leptin receptor polymorphisms on productivity and quality traits. J Anim Genet 43 (6): 805-809. DOI: 10.1111/j.1365-2052.2012.02338.
Pramod RK, Velayutham D, Sajesh PK, Beena PS, Zachariah A, Chandramohan B, Sujith SS, Ganapathi P, Kumar BD, Lype S, Gupta S, Santhosh S, Thomas G. 2019. Complete mithogenome reveals genetic divergence and philogenetic relationship among indian cattle (Bos indicus) breed. Anim Biotechnol 30: 3. DOI: 10.1080/10495398.2018.1476376.
Priyadi DA, Panjono, Bintara S, Hartatik T. 2017. Genotype of brahman and brahman cross cattle based on SNP in Insulin-Like Growth Factor Binding Protein-3 (IGFBP-3) gene sequences. Biodiversitas 18 (2): 795-800. DOI: 10.13057/biodiv/d180255.
Romjali E. 2018. Program Pembibitan sapi potong lokal Indonesia. Wartazoa 28 (4): 190-210. DOI: 10.14334/wartazoa.v28i4.18. [Indonesian]
Rouf AA, Daryanto A, Fariyanti A. 2014. Daya saing usaha sapi potong di Indonesia: Pendekatan domestic resources cost. Wartazoa 24 (2): 97-107. DOI: 10.14334/wartazoa.v2412.1053.
Scheiner SM, Kosman E, Steven J, Presley, Wilig MR. 2017. The Component of biodiversity, with a particular focus on phylogenetic information. Ecol Evol 7 (16): 6444-6454. DOI: 10.1002/ece3.3199.
Sedykh TA, Kalashnikova LA, Gizatullin RS, Kosilov VI. 2020. Effects of leptin gene polymorphism on beef cattle performance. Russ Agric Sci 46 (6): 614- 618. DOI: 10.31857/S2500262720050130.
Uemoto YT, Nakano KH, Sato S. 2012. Effects of porcine leptin receptor gene polymorphisms on backfat thickness, fat area ratios by image analysis, and serum leptin concentrations in a Duroc purebred population. J Anim Sci 83 (5): 375-385. DOI: 10.1111/j.1740- 0929.2011.00963.
Wang L, Raza SHA, Gui L, Li S, Liu X, Yang X, Wang X, Zan L, Zhao C. 2022. Associations between UASMS2 polymorphism in leptin gene and growth, carcass and meat quality traits of cattle: A meta-analysis. J Anim Biotechnol 33 (2): 279-288. DOI: 10.1080/10495398.2020.1805327.
Yadav T, Magotra A, Kumar R. 2020. Evaluation of candidate genotype of leptin gene associated with fertility and production traits in Hardhenu (Bos taurus?×?Bos indicus) cattle. Reprod Dom Anim 12: 1698-1705. DOI: 10.1111/rda.13826.
Yadav T, Magotra A, Yogesh C, Bangar, Kumar R, Yadav AS, Gargh AR, Bahurupi P, Kumar P. 2021. Effects of BsaA I Genotyped Intronic SNP of leptin gene on production and reproduction traits in Indian dairy cattle. Anim Biotechnol 9: 1-7. DOI: 10.1080/10495398.2021.1955.
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