Analisis Genetik Gen KiSS1 pada Kambing Berdasarkan Sekuen DNA GenBank
Keywords:
Gen KiSS1, kambing, identifikasi SNP, perubahan asam amino, Phylogenetic tree.
Abstract
Gen KiSS1 merupakan kandidat gen yang berpengaruh pada sifat reproduksi kambing. Tujuan penelitian ini untuk identifikasi SNP, perubahan asam amino dan phylogenetic tree kambing berdasarkan data sekuen DNA gen KiSS1 GenBank. Dua puluh sekuen DNA gen KiSS1 yang terdiri dari 17 kambing dan 3 domba yang diambil dari data GenBank NCBI. Data sekuen DNA KiSS1 disejajarkan menggunakan BioEdit untuk mengetahui lokasi SNP dan perubahan asam amino. Phylogenetic tree dibuat menggunakan fitur di NCBI. Berdasarkan hasil penjajaran sekuen DNA gen KiSS1 pada 2 kelompok daerah sekuen, terdapat 22 SNP yang terdiri dari 7 SNP di 5’UTR, 13 SNP di Intron 1 dan 2 SNP di ekson 2. Dua SNP yang ditemukan pada ekson bersifat silent mutation. Phylogenetic tree menunjukkan bahwa gen KiSS1 kambing berkumpul pada satu branch kemudian diikuti dengan gen KiSS1 domba pada branch yang berbeda. Hasil penelitian ini dapat digunakan sebagai informasi dasar untuk melakukan studi lanjutan yaitu studi asosiasi SNP gen KiSS1 dengan sifat reproduksi pada kambing.
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References
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An, X., T. Ma, J. Hou, F. Fang, P. Han, Y. Yan, H. Zhao, Y. Song, J. Wang & B. Cao. 2013a. Association analysis between variants in KISS1 gene and litter size in goats. BMC Genet. 14:63.
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El-Tarabany, M.S., A.W. Zaglool, A.A. El-Tarabany & A. Awad. 2017. Association analysis of polymorphism in KiSS1 gene with reproductive traits in goats. Anim. Reprod. Sci. 180:92–99.
Hall, T., I. Biosciences & C. Carlsbad. 2011. BioEdit: an important software for molecular biology. GERF Bull Biosci 2:60–61.
Han, Y., X. Peng, W. Si, G. Liu, Y. Han, X. Jiang, R. Na, L. Yang, J. Wu & E. Guangxin. 2020. Local expressions and function of Kiss1/GPR54 in goats’ testes. Gene 738:144488.
Hartatik, T., Latifah, R. Yuliana & A. Kustantinah. 2020. Genotyping and Chi-Square Analysis of 967 bp Leptin Gene in Bligon Goat. Page 12019 in IOP Conference Series: Earth and Environmental Science. IOP Publishing.
Hou, J.X., X.P. An, J.G. Wang, Y.X. Song, Y.H. Cui, Y.F. Wang, Q.J. Chen & B.Y. Cao. 2011. New genetic polymorphisms of KiSS-1 gene and their association with litter size in goats. Small Rumin. Res. 96:106–110.
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Li, D., W. Yu & M. Liu. 2009. Regulation of KiSS1 gene expression. Peptides 30:130–138.
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Maitra, A., R. Sharma, S. Ahlawat, M.S. Tantia, M. Roy & V. Prakash. 2014. Association analysis of polymorphisms in caprine KiSS1 gene with reproductive traits. Anim. Reprod. Sci. 151:71–77.
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NCBI. 2020a. KiSS-1 Metastasis Suppressor [ Capra Hircus (Goat) ]. Accessed. https://www.ncbi.nlm.nih.gov/gene/100860861.
NCBI. 2020b. Capra Hircus Breed San Clemente Chromosome 16, ASM170441v1, Whole Genome Shotgun Sequence. Accessed. https://www.ncbi.nlm.nih.gov/nuccore/NC_030823.1?report=genbank&from=1340188&to=1343186&strand=true.
Pruitt, K.D., T. Tatusova & D.R. Maglott. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61–D65.
Raza, K. 2012. Application of data mining in bioinformatics. arXiv Prepr. arXiv1205.1125.
Sahoo, S.S., C. Mishra, R. Kaushik, P.K. Rout, M.K. Singh, S. Bhusan & M.S. Dige. 2019. Association of a SNP in KISS 1 gene with reproductive traits in goats. Biol. Rhythm Res. 1–12.
Sankhyan, V., Y.P. Thakur & P.K. Dogra. 2019. Association of kisspeptin gene (KISS1) with litter size in migratory Gaddi goats in western Himalayan state of Himachal Pradesh. Indian J. Anim. Sci. 89:1352–1355.
UGM. 2010. Pengenalan National Centre for Biotechnology Information (NCBI). Accessed. http://dhiantika.staff.ugm.ac.id/files/2010/11/BUKU-PETUNJUK-DRYLAB-BIOSEL-2010.pdf.
Widodo & Miftahhunnafisah. 2012. Pengenalan NCBI untuk analisis DNA, protein dan senyawa kimia.
Williams, R.J. 1981. Restriction Endonu-cleases. Gene Amplif. Anal. 1:157.
An, X., T. Ma, J. Hou, F. Fang, P. Han, Y. Yan, H. Zhao, Y. Song, J. Wang & B. Cao. 2013a. Association analysis between variants in KISS1 gene and litter size in goats. BMC Genet. 14:63.
An, X.P., P. Han, J.X. Hou, H.B. Zhao, Y. Yan, T. Ma, F. Fang, F.X. Meng, Y.X. Song & J.G. Wang. 2013b. Molecular cloning and characterization of KISS1 promoter and effect of KISS1 gene mutations on litter size in the goat. Genet. Mol. Res 12:4308–4316.
Barrett, T., S.E. Wilhite, P. Ledoux, C. Evangelista, I.F. Kim, M. Tomashevsky, K.A. Marshall, K.H. Phillippy, P.M. Sherman & M. Holko. 2012. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res. 41:D991–D995.
Cao, G.L., M.X. Chu, L. Fang, R. Di, T. Feng & N. Li. 2010. Analysis on DNA sequence of KiSS-1 gene and its association with litter size in goats. Mol. Biol. Rep. 37:3921–3929.
El-Tarabany, M.S., A.W. Zaglool, A.A. El-Tarabany & A. Awad. 2017. Association analysis of polymorphism in KiSS1 gene with reproductive traits in goats. Anim. Reprod. Sci. 180:92–99.
Hall, T., I. Biosciences & C. Carlsbad. 2011. BioEdit: an important software for molecular biology. GERF Bull Biosci 2:60–61.
Han, Y., X. Peng, W. Si, G. Liu, Y. Han, X. Jiang, R. Na, L. Yang, J. Wu & E. Guangxin. 2020. Local expressions and function of Kiss1/GPR54 in goats’ testes. Gene 738:144488.
Hartatik, T., Latifah, R. Yuliana & A. Kustantinah. 2020. Genotyping and Chi-Square Analysis of 967 bp Leptin Gene in Bligon Goat. Page 12019 in IOP Conference Series: Earth and Environmental Science. IOP Publishing.
Hou, J.X., X.P. An, J.G. Wang, Y.X. Song, Y.H. Cui, Y.F. Wang, Q.J. Chen & B.Y. Cao. 2011. New genetic polymorphisms of KiSS-1 gene and their association with litter size in goats. Small Rumin. Res. 96:106–110.
Jenuth, J.P. 2000. The NCBI. Springer.
Latifah, D. Maharani, Kustantinah & T. Hartatik. 2019. Comparison Study of Melanocortin 4 Receptor in Cattle, Buffalo, Sheep and Goat Based on Genbank Data. Page in Proceedings - 2018 1st International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering, BioMIC 2018.
Latifah, D.A. Priyadi, D. Maharani, Kustantinah & T. Hartatik. 2017. Genetic analysis using partial sequencing of melanocortin 4 receptor (MC4R) gene in Bligon goat. Media Peternak. 40:71–77. doi:10.5398/medpet.2017.40.2.71.
Li, D., W. Yu & M. Liu. 2009. Regulation of KiSS1 gene expression. Peptides 30:130–138.
Maglott, D., J. Ostell, K.D. Pruitt & T. Tatusova. 2005. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 33:D54–D58.
Maitra, A., R. Sharma, S. Ahlawat, M.S. Tantia, M. Roy & V. Prakash. 2014. Association analysis of polymorphisms in caprine KiSS1 gene with reproductive traits. Anim. Reprod. Sci. 151:71–77.
Mekuriaw, G., J.M. Mwacharo, T. Dessie, O. Mwai, A. Djikeng, S. Osama, G. Gebreyesus, A. Kidane, S. Abegaz & K. Tesfaye. 2017. Polymorphism analysis of kisspeptin (KISS1) gene and its association with litter size in Ethiopian indigenous goat populations. African J. Biotechnol. 16:1254–1264.
NCBI. 2020a. KiSS-1 Metastasis Suppressor [ Capra Hircus (Goat) ]. Accessed. https://www.ncbi.nlm.nih.gov/gene/100860861.
NCBI. 2020b. Capra Hircus Breed San Clemente Chromosome 16, ASM170441v1, Whole Genome Shotgun Sequence. Accessed. https://www.ncbi.nlm.nih.gov/nuccore/NC_030823.1?report=genbank&from=1340188&to=1343186&strand=true.
Pruitt, K.D., T. Tatusova & D.R. Maglott. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61–D65.
Raza, K. 2012. Application of data mining in bioinformatics. arXiv Prepr. arXiv1205.1125.
Sahoo, S.S., C. Mishra, R. Kaushik, P.K. Rout, M.K. Singh, S. Bhusan & M.S. Dige. 2019. Association of a SNP in KISS 1 gene with reproductive traits in goats. Biol. Rhythm Res. 1–12.
Sankhyan, V., Y.P. Thakur & P.K. Dogra. 2019. Association of kisspeptin gene (KISS1) with litter size in migratory Gaddi goats in western Himalayan state of Himachal Pradesh. Indian J. Anim. Sci. 89:1352–1355.
UGM. 2010. Pengenalan National Centre for Biotechnology Information (NCBI). Accessed. http://dhiantika.staff.ugm.ac.id/files/2010/11/BUKU-PETUNJUK-DRYLAB-BIOSEL-2010.pdf.
Widodo & Miftahhunnafisah. 2012. Pengenalan NCBI untuk analisis DNA, protein dan senyawa kimia.
Williams, R.J. 1981. Restriction Endonu-cleases. Gene Amplif. Anal. 1:157.
Published
2020-11-12
Section
Articles
