S. Sumadi
Faculty of Animal Science, Gadjah Mada University, Jl. Fauna No.3 Bulaksumur, Sleman, Yogyakarta 55281

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The Application of Polymerase Chain Reaction – Restriction Fragment Polymorphisms (PCR-RFLP) to Determine Genetic Diversity of Madura Cattle in Sapudi Island Hartatik, Tety; Volkandari, Slamet Diah; Sumadi, S.; Widodo, W.
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.7869

Abstract

The aim of this study was to determine genetic diversity of Madura cattle using Polymerase Chain Reaction – Restriction Fragment Length Polymorphisms (PCR-RFLP) analysis of the cytochrome b (cytb) gene. Samples used for the experiments were blood of 43 cattle that consist of 15 cattle obtained from Madura Island, 23 cattle from Sapudi Island, and 5 Limousin-Madura (Limura) cattle. A fragment of 464 base pair of cytb gene was amplifi ed by forward primer L14735 and reverse primer H15149. The PCR product was digested with TaqIand HinfI restriction enzymes to identify genetic patterns. Data of PCR-RFLP showed two haplotypes, that were A and B, in cattle obtained from both Madura Island and Sapudi Island. The frequencies of haplotype A and B of cattle from Sapudi Island were 69.57% and 30.47%, respectively. More diverse frequencies were observed in cattle obtained from Madura Island, where haplotype A and B were 86.67% and 13.33%, respectively. In this experiment, Limura cattle had only haplotype A. As a conclusion, PCR-RFLP of the cytb gene had been able to determine a genetic diversity of Madura cattle. Key words: Genetic diversity, Madura cattle, haplotype.
IDENTIFICATION OF MELANOCORTIN 1 RECEPTOR (MC1R) GENE BASED ON COAT COLOR OF BALI COWS OF KUPANG BY USINGTHE PCR-RFLP METHOD Tabun, A.C.; Hartatik, T.; Sumadi, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 38, No 2 (2013): (June)
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (150.517 KB) | DOI: 10.14710/jitaa.38.2.86-91

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The objective of this study was to identify the Melanocortin 1 Receptor (MC1R) gene in sorrel-,black- and white-Bali cows originated from Kupang-East Nusa Tenggara. Blood samples were takenfrom 46 cows consisted of of 17, 18 and 8 of sorrel, black and 8 heads, respectively, and 3 heads of bull.The PCR-RFLP method was performed to identify the gene. Amplification of PCR gene MC1R ofKupang's Bali Cattle (KBC) was 296 bp. The digestion by using MspI enzyme showed that there wereEE genotype (169, 136 bp) in Bali bull, sorrel and white cows. Two 2 genotypes, those were EE (169,136 bp) and Ee (296, 169, 136 bp) were found in black Bali cow. The frequency of E alele of KBC was0.99 (99%) and e alele was 0.01 (1%). MC1R gene in KBC was monomorphic and the it can be used asthe marker of the coat color in the population.
Polymorphism of the SNP g. 1180 C>T in leptin gene and its association with growth traits and linear body measurement in Kebumen Ongole Grade cattle Fathoni, A.; Maharani, D.; Aji, R. N.; Choiri, R.; Sumadi, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 44, No 2 (2019): June
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (296.751 KB) | DOI: 10.14710/jitaa.44.2.125-134

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The aim of this study was to identify the polymorphism of leptin gene and its association with growth traits in Kebumen Ongole Grade cattle. One hundred blood samples were collected for molecular analysis. Polymorphism of the leptin gene was analyzed using Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) with HpyCH4V restriction enzyme and DNA sequencing. Association analysis of the leptin gene with growth traits was analyzed by T-test. The results showed that SNP g. 1180 C>T was found in the population.The SNP changed amino acid from arginine to cysteine. The SNP was significantly associated with a high chest circumference at weaning age in animal having CC genotype (P<0.05). There were two identified alleles, namely C and T, with frequencies were 0.885 and 0.115,respectively. The genotype frequencies of CC, CT and TT were 0.78, 0.21 and 0.01, respectively. Allelic and genotypic distribution in the studied population were in Hardy-Weinbergequilibrium. Animals with CC genotype had a higher circumference at weaning age (WCC) than those with CT genotype. In conclusion, SNP g. 1180 C> T in the leptin gene is potential as genetic marker for growth traits in Kebumen Ongole Grade cattle.
PRODUCTIVITY COMPARISON BETWEEN BOER AND KACANG GOAT DAM Elieser, S.; Sumadi, S.; Budisatria, G.S.; Subandriyo, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 37, No 1 (2012): (March)
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (93.32 KB) | DOI: 10.14710/jitaa.37.1.15-21

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A study to evaluate the productivity of Boer and Kacang goats dam was carried out for 2 years atResearch Institute for Goat Production, Sungei Putih-North Sumatera. The materials used were goatsowned by the institute. The parameters observed were total birth and weaning weights of kid, litter size,parity of dam, pre-weaning mortality and kidding interval. The rate of reproduction and productivity ofthe dam were estimated using Amir and Knipscheer methods and were statistically analyzed usingGeneral Linear Model. The results showed that the total birth and weaning weight of Boer goats werehigher (P<0.05) than that of Kacang goats, while litter size of Boer goats were higher (P<0.05) than thatof Kacang goats. The pre-weaning mortality of Boer goat 15.1 ± 6.02% was lower than that ofKacang. The kidding interval of Boer goats was higher (P<0.05) than that of Kacang. Parity of dam hadsignificant effect on all production traits (P<0.05) except for pre-weaning mortality. Dam reproductionrate of Boer (1.81) was higher than that of Kacang (1.78), while productivity of Boer goat (37.12kg/head/year) was higher than that of Kacang (18.12). It can be concluded that the reproductivity ofBoer and Kacang goats were similar, however the productivity of Boer goat had better than Kacang.
Breeding value of sires based on offspring weaning weight as a recommendation for selecting Kebumen Ongole Grade cattle Sumadi, S.; Fathoni, A.; Maharani, D.; Ngadiyono, N.; Widayati, D. T.; Noviandi, C. T.; Khusnudin, M.
Journal of the Indonesian Tropical Animal Agriculture Vol 42, No 3 (2017): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (147.39 KB) | DOI: 10.14710/jitaa.42.3.160-166

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The objective of study was to estimate breeding value of sires of Kebumen Ongole grade cattle based on offsprings weaning weight. This research was carried out from August to December 2015 in Urut Sewu area, Kebumen. The calculation of genetic parameter estimation was heritability of weaning weight. The value of heritability was used to calculate the breeding value of sires based on offsprings weaning weight. Heritability was calculated using paternal half-sib correlation with the direct pattern variance analysis. Breeding Value (BV) of sire was calculated by absolute estimated breeding value. The materials used in this study included were data record during the last three years (2013-2015) consisted of 41 sires, 51 dams and 244 calves. Weaning weight data had been corrected based on age of dams, sex and weaning age of 120 days. The results showed that the heritability value of weaning weight was included in high category (0.36 ± 0.21). The highest BV was KJ.J608 (49.76) with a ratio of 231.45%. The results of this study were expected to be the basis recommendation for selecting sires in Kebumen.
Predicting the age and weight at puberty of Ongole Grade cattle using nonlinear mathematical model in Kebumen Farmer Association Maharani, D.; Amrullah, A. H. K.; Widayati, D. T.; Sumadi, S.; Fathoni, A.; Khusnudin, M.
Journal of the Indonesian Tropical Animal Agriculture Vol 42, No 4 (2017): December
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (295.497 KB) | DOI: 10.14710/jitaa.42.4.233-239

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This research is aimed to evaluate the nonlinear mathematical model in predicting the age and weight of Kebumen Ongole Grade (PO) cattle at puberty. The data used in this research was weight recordings of (768) PO cattle, ranging from calf (< 1 month) to adult (60 months), collected by Kebumen PO cattle Breeder Association (ASPOKEB) from 2013 to 2015. These cattle were reared by a group of farmers located in six sub-districts: Mirit, Lembu Purwo, Ambal, Puring, Petanahan, and Klirong in Kebumen district, Jawa Tengah Province. Brody, Bertalanfy, Logistic and Gompertz mathematical models were used to analyze the data. The analysis showed that the R2of the four models classify high in the category (R2 >0.70). Mature weight (A) of PO cattle predicted by Logistic (349 kg) and Gompertz (358 kg) were most appropriate. Out of the four models, the Logistic model was the most accurate in predicting the weight at puberty (174 kg) of PO cattle, but all observed cattle are still in the follicular phase.
Identification of MC4R gene and its association with body weight and body size in Kebumen Ongole Grade cattle Maharani, D.; Fathoni, A.; Sumadi, S.; Hartatik, T.; Khusnudin, M.
Journal of the Indonesian Tropical Animal Agriculture Vol 43, No 2 (2018): June
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (226.315 KB) | DOI: 10.14710/jitaa.43.2.87-93

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MC4R gene is known as an important candidate gene for the growth trait. The purpose of this research was to identify the MC4R gene in Kebumen Ongole grade cattle and examine its association with growth traits. Data of birth weight (BW), weaning weight (WW), birth body length (BBL), birth chest circumference (BCC), birth shoulder height (BSH), weaning body length (WBL), weaning chest circumference(WCC), weaning shoulder height (WSH) and average daily gain (ADG) were collected and used for analysis of MC4R gene. Sixty blood samples were collected for DNA isolation and PCR amplification. The single nucleotide polymorphisms (SNP) g.1133 C>G was used for genotyping by using PCR-RFLP methods. The frequenciy of G allele (0.59) was greater than C allele (0.41). The highest genotype frequencies have been detected in CG heterozygote animals (0.52) followed by GG (0.33) and CC (0.15) in homozygote animals. The results of Pearson ‘s Chi-square test indicated that the population was not deviate (P>0.05) from the Hardy-Weinberg equilibrium (HWE). The SNP g. 1133 C>G of MC4R gene indicated affecting high birth body length with GG genotype (P<0.05). In conclusion, the SNP g. 1133 C>G may can be a marker for birth body length of calf selection.
GROWTH HORMONE GENE GENOTYPING BY Msp I RESTRICTION ENZYME AND PCR-RFLP METHODS IN ACEH CATTLE BREED AT INDRAPURI DISTRICT OF ACEH PROVINCE Putra, W.P.B.; Hartatik, T.; Sumadi, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 38, No 4 (2013): (December)
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (126.987 KB) | DOI: 10.14710/jitaa.38.4.207-211

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The objective of this research was to identify growth hormone (GH) genes genotype in selectedAceh cattle at Indrapuri’s Breeding and Forage Centre (IBFC) of Aceh Cattle. Fourty one cattleconsisting of 21 male and 20 female cattle were used in this study. The genomic DNA was extractedfrom blood using Sambrook et al. (1989) methods. Polymerase Chain Reaction - Restriction FragmentLength Polymorphism (PCR-RFLP) and mehod of sequencing was used to detect MspI site on GH gene.Based on sequencing results, it can be concluded that all cattle were monomorphism. The frequency ofTT genotype were 1.00 and same as T allele frequency. The transition of C (cytosine) into T (thymine)on 1548 bp caused the lost of restriction site.
Melanocortin-4 Receptor (MC4R) gene polymorphism and its effect on growth traits in Madura cattle Prihandini, P. W.; Sumadi, S.; Suparta, G.; Maharani, D.
Journal of the Indonesian Tropical Animal Agriculture Vol 44, No 1 (2019): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (268.494 KB) | DOI: 10.14710/jitaa.44.1.38-46

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Melanocortin-4 receptor (MC4R) gene has an important role in the regulation of feed intake and energy balance control. The objective of this study was to identify the single nucleotide polymorphisms (SNPs) of MC4R gene and their association with growth traits in Madura cattle. A total of 198 calves were used in this study.Forward primer: 5’-GTCGGGCGTCTTGTTCATC-3’and reverse primer: 5’-GCTTGTGTTTAGCATCGCGT-3’ were used to amplify approximately 493 bp of MC4R gene. The results showed that two SNPs, g.1133C>G and g.1108C>T were identified by direct sequencing. The PCR-RFLP method was performed to genotype all individuals studied based on SNP g.1133C>G, and its SNP was significantly associated with shoulder height (SH) at yearling age (P<0.05). Animals with GG genotype had a higher SH (110.35±6.40cm) than those with CC (102.00±8.00 cm) and CG genotype (105.96±6.23 cm). The SNP g.1133 C>G changed amino acid from valine to leucine. In conclusion, the SNP g.1133C>G of the MC4R gene may be used as a marker-assisted selection for SH trait in Madura cattle.
Genotype analysis of partial growth hormone gene (GH891│MspI) in Pesisir cattle and Simmental-Pesisir crossbred cattle Hartatik, T.; Putra, D. E.; Volkandari, S. D.; Kanazawa, T.; Sumadi, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 43, No 1 (2018): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (247.337 KB) | DOI: 10.14710/jitaa.43.1.1-8

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Growth hormone gene that controls metabolism and body size of animals and polymorphism of the gene is known related to performance of livestock. Identification of gene polymorphisms was important to get early information to determine genetic markers associated with economically desirable traits. Genetic mapping is one of important characterizations in the selection process. Pesisir cattle is one of local cattle in Indonesia that are reared in West Sumatera and have become adaptive to local environment. The present study aimed to identify the genotype of Growth Hormone gene (GH891│MspI) of the Pesisir cattle and crossbred Simmental-Pesisir cattle (designated as SimPes) and relationship between growth performance (body weight and body size). The present study was conducted to 30 blood samples consisted of 15 Pesisir cattle and 15 SimPes cattle. Body weight and body size were measured at 12-18 months of age. The Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method was used in this research. The results showed that there exist three variant genotypes (MspI-/-, MspI+/-, MspI+/+) and that allele frequencies of MspI- and MspI+ were 53.3% and 46.7%, respectively. Non-significant effect has found between GH’s genotype and growth traits (Body measurement and body weight) in both of breed cattle. In conclusion, three variant genotypes (GH891│MspI) in Pesisir and SimPes (Simmental x Pesisir) cattle population were found and no significant effect on growth trait performance.