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All Journal Jurnal Ilmu-Ilmu Peternakan (Indonesian Journal of Animal Science) Livestock and Animal Research
Muhammad Cahyadi
Department of Animal Science, Universitas Sebelas Maret
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Veterinary Other

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Keragaman genetik puyuh Jepang (Coturnix japonica) berdasarkan analisis sekuen DNA mitokondria gen Cytochrome-b Novisa Adimaka; Muhammad Rifki; Ratih Dewanti; Muhammad Cahyadi
Jurnal Ilmu-Ilmu Peternakan (Indonesian Journal of Animal Science) Vol 29, No 2 (2019): Agustus
Publisher : Faculty of Animal Science, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jiip.2019.029.02.05

Abstract

Coturnix japonica is a Japanese quail which is commonly raised in Indonesia. The aim of the study was to determine the genetic diversity of Japanese quail (Coturnix japonica) based on complete sequence of mitochondrial DNA Cytochrome b gene analysis. This study used 12 samples of quail blood collected from two different village breeding centres (VBC) representing black and brown plumage lines. Total DNA genome was isolated from whole blood by following the Wizard® Genomic DNA Purification Kit protocol (Promega, USA). The DNA amplification process in this study was carried out using novel forward and reverse primers using Primer3 software. Additionally, PCR products were sequenced and analysed using MEGA 6.0 and DNAsp v.5 softwares. A total of 21 sequences consists of 12 sequences of quail sample and 9 reference sequences obtained from NCBI website were analyzed to construct phylogenetic tree and to evaluate genetic diversity of Japanese quails. The sequence analysis showed that Japanese quail population in this study had kinship with Francolinus pintadeanus and Coturnix chinensis with an 81% bootstrap value. The genetic distance among Japanese quails was ranged from 0.000 to 0.003. In addition, the mean of genetic distance for Japanese quail was 0.002 and the mean of genetic distance for 21 samples was 0.067. Tajima D'test values were -1.35536 for Japanese quail population and -1.38090 for whole population used in this study. The conclusion of this study was the Japanese quail had low genetic diversity based on complete sequence of Mitochondrial DNA Cytochrome b gene analysis that mean Japanese quail had low level of evolution
Analysis of CSN2 variants in Friesian Holstein cows and their association with milk protein allergy and production traits Mohammad Ilham Dhiaurridho; Firmansyah Tristadika Prakosa; Firna Fauziatul Karimah; Salsabilla Ramadhana; Ine Febriantama; Thoriq Aldri Bramastya; Ahmad Pramono; Muhammad Cahyadi
Livestock and Animal Research Vol 20, No 1 (2022): Livestock and Animal Research
Publisher : Universitas Sebelas Maret

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (583.442 KB) | DOI: 10.20961/lar.v20i1.57596

Abstract

Objective: The objective of this study was to analyze CSN2 variants in Indonesian Friesian Holstein (FH) cow and their association with milk protein allergy and production traits.Methods: Genomic DNA was extracted from bloods of twelve Indonesian FH cow. Exon 7 of the CSN2 was amplified using novel primer pair to produce 683 bp amplicon. The primers were 5’-ACCCCAATTTCTTAACCAAACCA-3’ as a forward primer and 5’-CATCAGAAGTTAAACAGCACAGT-3’ as a reverse primer. The PCR products were analyzed to determine the nucleotide sequence of CSN2 using Bioedit version 7.2.5. Moreover, Hardy-Weinberg equilibrium (HWE) was calculated and one-way analysis of variance (ANOVA) was conducted to associate between CSN2 variants and milk production traits.Results: Two polymorphisms, c.350A>C and c.516G>C, were identified in the CSN2 exon 7. Base substitution from adenine (A) to cytosine (C) of c.350A>C changed amino acid codon from histidine (CAU) to proline (CCU), and base substitution guanine (G) to cytosine (C) of c.516G>C changed amino acid codon from arginine (AGG) to serine (AGC). The CC genotype frequency for c.350A>C SNP was 33% and they were able to produce A2 CSN2 variant which is favorable for preventing lactose intolerance. In addition, there were no association between c.350 A>C and c.516 G>C SNP of the CSN2 with milk production traits.Conclusions: In conclusion, A1 and A2 variants of CSN2 were identified in Indonesian FH population and they did not associate with milk production in Indonesian FH. 
Identification of the Membrane-Associated Transporter Protein (MATP) Gene Polymorphism as Candidate Mutation for Albinism in Japanese Quail Laksita Haniifah Pratiwi; Ratih Dewanti; Muhammad Cahyadi
Jurnal Ilmu-Ilmu Peternakan Vol. 33 No. 2 (2023): August 2023
Publisher : Faculty of Animal Science, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jiip.2023.033.02.09

Abstract

A pigmentation abnormality could be due to genetic mutation and trigger a disease related pigmentation deficiency such as albino which might be caused by mutation in membrane-associated transporter protein gene (MATP). The aim of this study was to identify polymorphism in the MATP exon 3 in Japanese quail. A total of nine Japanese quail consisting three brown plumage quail, three black plumage quail, and three albino quail were used in this study. Blood samples were used to extract the genomic Deoxyribonucleic acid (DNA) and used to amplify exon 3 regions of the MATP by polymerase chain reaction (PCR). The PCR products were then sequenced and analyzed. A total of 10 mutations were found, of which three mutations, g.4460G>A, g.4479G>A, and g.4514T>C, were within exon 3. These mutations were synonymous and non-synonymous. No specific mutation for albino was found in this study. In  summary those mutations did not specifically determine albinism in Japanese quail.
Co-Authors Ahmad Pramono Firmansyah Tristadika Prakosa Firna Fauziatul Karimah Ine Febriantama Laksita Haniifah Pratiwi Mohammad Ilham Dhiaurridho Muhammad Rifki Novisa Adimaka Ratih Dewanti Ratih Dewanti Salsabilla Ramadhana Thoriq Aldri Bramastya