IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS ON CATTLE BREEDS IN INDONESIA USING BOVINE 50K

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dc.contributoren-US
dc.creatorLestari, Puji; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Indonesian Agency for Agricultural Research and Development Jalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia
dc.creatorRijzaani, Habib; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Indonesian Agency for Agricultural Research and Development Jalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia
dc.creatorSatyawan, Dani; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Indonesian Agency for Agricultural Research and Development Jalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia
dc.creatorAnggraeni, Anneke; Indonesian Research Institute for Animal Production Jalan Veteran III Ciawi, Bogor 16002, West Java, Indonesia
dc.creatorUtami, Dwinita Wikan; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Indonesian Agency for Agricultural Research and Development Jalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia
dc.creatorRosdianti, Ida; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Indonesian Agency for Agricultural Research and Development Jalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia
dc.creatorLutfi, Muchamad; Beef Cattle Research Station Jalan Pahlawan 2 Grati, Pasuruan 67184, East Java, Indonesia
dc.creatorTasma, I Made; Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development Indonesian Agency for Agricultural Research and Development Jalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia
dc.date2016-02-19
dc.date.accessioned2020-11-06T02:30:38Z
dc.date.available2020-11-06T02:30:38Z
dc.descriptionSingle nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.en-US
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dc.identifierhttp://ejurnal.litbang.pertanian.go.id/index.php/ijas/article/view/3161
dc.identifier10.21082/ijas.v16n2.2015.pp.59-70
dc.identifier.urihttps://repository.pertanian.go.id/handle/123456789/10499
dc.languageeng
dc.publisherIndonesian Agency for Agricultural Research and Developmenten-US
dc.relationhttp://ejurnal.litbang.pertanian.go.id/index.php/ijas/article/view/3161/2725
dc.rightsCopyright (c) 2015 Indonesian Journal of Agricultural Scienceen-US
dc.rightshttp://creativecommons.org/licenses/by-sa/4.0en-US
dc.sourceIndonesian Journal of Agricultural Science; Vol 16, No 2 (2015): October 2015; p.59-70en-US
dc.source2354-8509
dc.source1411-982X
dc.subjectBeef cattle; dairy cattle; Bovine 50K; SNP; Indonesiaen-US
dc.titleIDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS ON CATTLE BREEDS IN INDONESIA USING BOVINE 50Ken-US
dc.typeinfo:eu-repo/semantics/article
dc.typeinfo:eu-repo/semantics/publishedVersion
dc.typeen-US
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