GENET TIC POLYM IN MORPHISM INDONESI OF mt-DN IAN DOMES NA CYTOCH STIC CATT HROME B ( TLE (CYT B)

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Restriction Mapping of MC4R Gene on Bali Cattle (Bos sondaicus) as Genetic Marker for Breeding Program in Compared to Bos taurus and Bos indicus

MC4R is a gene that has potential effects on growth traits such as body weight and feed intake. The usage of single nucleotide polymorphism (SNPs) in melanocortin-4 receptor (MC4R) as selection markers could help achieve effectiveness in the breeding program. This study aimed to analyze the restriction mapping based on SNPs in the MC4R gene for Bali cattle (Bos sondaicus) compared to various breeds of cattle. Partial MC4R gene was amplified using a primer (F: 5’-ACC AAT GTC AGT GAG TCC CC- 3’ and R: 5’-CTT CAT GTT GGC GCC CTG-3’) with a polymerase chain reaction (PCR) method. Genotype and allele frequencies were calculated using Chi-Square test and analyzed with Hardy–Weinberg law. Restriction enzyme was analyzed using Nebcutter V.2 to see the association between SNPs and the recognition site of restriction enzyme. The result showed four SNPs g.554 T>C, g.634 G>T, g.673 C>T, and g.742 G>A were found in the exon region. SNP g.742 G>A was found as a heterozygote genotype and the rest are SNP g.554 T>C, g.634 G>T, and g.673 C>T were found as homozygote genotypes. All SNPs were synonymous which did not change the amino acid translated. Three restriction enzymes were identified as MmeI, TspRI, and BsrI which attach to SNPs g.554 T>C, g.634 G>T, and g. 742 G>A respectively.  SNPs found notably g. 742 G>A can be used as genetic markers associated with growth traits for further research on Bali cattle.

Identification of single nucleotide polymorphisms in GDF9 gene associated with litter size in Garut sheep

The growth differentiation factor 9 (GDF9) gene has been regarded as having major impacts on ovulation rate and litter size in sheep. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) of the GDF9 gene and their association with litter size in Garut sheep. For this purpose, a total of 60 ewes of Garut sheep were included in this study. Based on the sheep GDF9 reference sequences (Genbank Acc. No. AF078545.2), one pair of primers (5’-CTGCTGTTTAACCTGGATCGTG-3 5’-GGAGAGCCATACCGATGTCC-3 as forward and reverse, respectively) was used for PCR amplification. The results revealed that four SNPs (g.54C>T, g.60G>A, g.304G>A, and g.333G>A) were found in Garut sheep by direct sequencing. For SNP g.54C>T, the sheep exhibited the highest frequency of allele C and genotype CC. On the other hand, SNPs g.60G>A, g.304G>A, and g.333G>A showed a higher frequency of allele G than allele A, and the GG genotype was predominant in the population. SNP g.333G>A had a significant effect on litter size (p A may be useful as a genetic marker for litter size in Garut sheep

Single Nucleotide Polymorphism of Partial GDF9 Gene in Three Local Goat of Indonesia Compare with Several Goat in Asia

The GDF9 gene is a gene that affects the maturation of oocytes. GDF9 is expressed in oocytes and granulosa cell, it can stimulate granulose cell proliferation and regulate cumulus cell function from pre-ovulation to ovulation. The GDF9 gene is associated with an increase in the ovulation rate and litter size in animals. This study aims to determine the kinship relationship of local goats compared to goats in Asia on prolific traits and to determine the restriction mapping of the GDF9 gene in goats based on the different SNP locations. The local goat comes from the Bligon goat, Kacang goat and Kejobong goats which is compared to the GenBank data (EF446168, EU883989 and KY780296). GDF9 sequences were analyzed using BioEdit and sequencing results to identify Single Nucleotide Polymorphism (SNP) and using NEBCutter V2 to determine the restriction enzyme which recognized the sequence around SNP. The result shows that three variations of SNP were found in exon 2 (g.3615T>C, g.3760T>C and g.3855A>C). Identification of SNP position found 1 SNP position identified by restriction enzyme at g.3855A> C. The identified restriction enzyme is HpaII and MspI. The results of this study are expected to provide genetic information that will be used for further research on the relationship between GDF9 gene polymorphisms to animal prolific

Morphological diversity and genetic differentiation of PO cattle in smallholder farmers

PO cattle is one of  the local cattle with high genetic diversity. The aim of this research was to study genetic diversity of PO cattle in smallholder farmer  based on morfology and molecular markers. This research was conducted at breeding center in East Java and Central Java include Tuban, Lamongan and Blora regency, since June until December 2008.  PO bull used were of 18 months until 24 months of age and cow of 24 months until 36 months of age or at first calving as much as 30 head each location. The variables measured were body weight, body length, withers height, hip height, shoulder point width, chest girth, chest depth, canon bone circumference, head length and head width. Data were analyzed using descriptive statistic, average analysis between subpopulations, discriminant and canonical analysis and mahalanobis distance was done by SAS DISCRIM procedure. Whole blood were collected to get the data of polymorphism DNA microsatellite using technology of PCR and electrophoresis using 6 microsatellite loci. Variable measured were number and size of  alel, alel frequency, heterozygosity,genetic distance and fixation index (F-stat). Data were analyzed using analysis of Microsate Toolkit, GENEPOPV4, MSA (Microsatellite Analyser) and Mega 4. The result showed that Blora and Tuban subpopulation have genetic diversity which is relative lower  compared to that of Lamongan. The genetic distance which was close presented by Tuban and Blora subpopulation while Lamongan and Tuban subpopulation show far genetic distance. The result of canonical analyses showed  high correlation on shoulder point width, head width, body length, withers height and hip height variable so this five variable can be used as distinguishing variables among subpopulation. The result of molecular genetics analysis using microsatellite showed that highest frequency of alel presented by HEL9 locus at Tuban population so this loci have the high polymorfism. The genetic differentiation among subpopulation showed by differentiation FST value among six loci  indicating the increasing of inbreeding in  the three subpopulations. Key words: Morphological Diversity, Genetic Differentiation, PO Cattl

The Application of Polymerase Chain Reaction – Restriction Fragment Polymorphisms (PCR-RFLP) to Determine Genetic Diversity of Madura Cattle in Sapudi Island

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

Identifikasi Karakteristik Genetik Sapi Peranakan Ongole di Peternakan Rakyat (The Identification of Genetic Characteristic of Ongole Grade Cattle in Smallholder Farmers)

The aim of this research was to identity genetic characteristic of Ongole Grade cattle and to analyse the diversity of Ongole grade cattle in smallholder farmers. This research was conducted at breeding stock in East Java and Central Javainclude Tuban, Lamongan and Blora regencies, since June until December 2008. The animal use were PO cattle of 18 months until 24 months of age and cow of 24 months until 36 months of age or have once of calving as many 30 headfrom location, were used as sampling for the observation of genetic diversity which was based on quantitative and qualitative characteristic. Whole blood collection was conducted to get the data of polymorphism DNA microsatelliteby using technology of PCR and elektroforesis. Data and information were analysed in descriptive, explanatory and laboratoris. The result showed that Blora subpopulation had genetic distance which was close to Tuban subpopulationcompared to Lamongan. The result of molecular genetic analyses by using microsatellite showed that highest frequency alel was presented by HEL9 locus at Tuban population. Heterozigosity value at 3 subpopulation of PO cattle was verylow, representing an indication of leading to inbreeding cases.(Key words : Genetic characteristic, PO cattle, Smallholder farmers

Estimasi Parameter Genetik Sifat Pertumbuhan Kambing Boerawa di Kabupaten Tanggamus Propinsi Lampung (Genetic Parameters Estimation on Growth Traits of Boerawa Goat at Tanggamus Regency Lampung Province)

This research was conducted to estimate heritability, repeatability and genetic correlation values on growth traits of Boerawa goat at Sumber Rejeki farmer group at Campang Village, Gisting District and Karya Makmur I and Karya Makmur II farmer group at Wonoharjo and Sukoharjo Village, Sumber Rejo District, Tanggamus regency, Lampung province. Data consisted of production record and 238 Boerawa goat derived from 93 PE and 7 Boer buck.The research was started on October 30, 2009 up to January 30, 2010. The results indicated that heritability value of birth weight, weaning weight, yearling weigth, average of preweaning daily gain, and average of postweaning weightanalyzed by paternal half-sibs correlation were 0.80±0.40; 0.30±0.17; 0.80±0.04; 0.32±0.18 and 0.30±0.17, respectively. The repeatability values of birth weight, weaning weight and yearling weight analyzed based on tworecording per every dam were 0.42±0.07; 0.32±0.08; 0.30±0.08; 0.30±0.08 and 0.53±0.06. The genetic correlation values among birth weight and weaning weight, birth weight and yearling weight, weaning weight and yearling weight,average of preweaning weight and postweaning weight daily gain analyzed by paternal half-sibs correlation were 0.50±0.04; 0.44±0.08; 0.21±0.03 and 0.20±0.05, respectively. The result also indicated that the heritability andrepeatability values was high and the genetic correlation values were moderate to high.(Key words: Boerawa goat, Genetic parameter, Growth character

POLIMORFISME GEN GROWTH HORMONE (GH) PADA SAPI LIMURA (GROWTH HORMONE (GH) GENE POLYMORPHISM OF LIMURA CATTLE)

The research was conducted to identify Growth Hormone (GH) olymorphism of Limura cattle. The research was conducted in the smallholder at Lancar, Montok and Duko village, Larangan subdistrict in Pamekasan district, East Java Province and Animal Breeding Laboratory of Faculty of Animal Science, Gadjah Mada University in April 2012. Then research used 35 Limura calves and 10 Madura calves (as control). Blood samples for DNA molecular analysis, i.e. DNA isolation with SDS-PK modification method, DNA amplification with PCR method and genotyping with RFLP method. Identification of GH gene polymorphism was conducted by digesting the DNA fragment of 211 bp extended from the fourthintron region (49 bp) to fifth of exon (162 bp) by AluI enzyme. The result indicated that GH gene of Madura cattle was not polymorphic with frequencies of L allele 1.00 and V allele 0.00. The LL genotype of Madura cattle was 1.00. Frequencies ofL and V allele in Limura cattle were 0.91 and 0.09, respectively. Limura cattle indicated polymorphic with genotype LL 0.83and LV 0.17. As a results, GH gene polymorphism was found in Limura cattle with L allele frequencies higher than V allele. Limura cattles population were not deviated from Hardy-Weinberg quilibrium genetic condition.(Key words: Growth Hormone Gene, Limura Cattle, Polymorphism

Body Weight Gain and Carcass Quality of the Hybrid Chicken Derived from the Crossing between Female F1 Kampung Super and Male F1 Kampung-Broiler

This research was conducted to observe the body weight gain and carcass quality of the hybrid chicken derived from the crossing between female F1 Kampung Super and male F1 Kampung-Broiler. The weekly weight gain for seven weeks and carcass quality, including breast yield, protein content, lipid content, moisture, and pH were measured with each group consists of six individuals. The chickens were slaughtered for meat quality measurements on the 7th week. The results showed that the hybrid chickens’ weight at the 7th week (888.22±139.63) was higher than layer (467.06±85.7) and pelung (436.39±42.33). The hybrid chicken’s breast yield (3.20%) was significantly higher than pelung’s (1.66%). These characteristics of hybrid chicken breast muscle lead to the conclusion that hybrid chicken is a potential alternative meat-type chicken with local chicken meat characteristics and has relatively fast growth