Genetic Characteristic of Indonesian Local Ducks Based on Single Nucleotide Polymorphism (SNP) Analysis in D-loop Region Mitochondria DNA

Abstract. The aim of the study was to know the genetic characteristic and polymorphysm of Indonesian local ducks including Magelang, Tegal, Mojosari, Bali and Alabio duck based on Single Nucleotide Polymorphism (SNP) analysis in D-loop region mtDNA. The long term aim was to set the spesific genetic marker based on SNP D-loop region mtDNA which could differentiate local ducks in Indonesia. In the future, it could be used as selection tool for local duck conservation, and refinement strategy as well as the improvement of genetic quality by utilizing the available native duck germplasm. There were 20 ducks for each duck population and were taken 3 ml of its blood as sample. DNA Isolation Kit high pure PCR template preparation (Geneaid) was uded for Genome DNA isolation.  Amplification with PCR technique used primer DL-AnasPF (L56) as forward and DL-AnasPR (H773) as reverse. Next, PCR product or amplicon were sequenced. Sequence result were analyzed with SNP technique and observed the similarity and difference of its nucleotide sequence between individual and population. The result of the study showed that genome DNA from local duck in Indonesia was successfully isolated. DNA fragment of 718 bp was amplified with primer pair of DL-AnasPF and DL-AnasPR. Nucleotide sequence was 469 nt and analyzed with SNP technique. It was compared with standard nucleotide sequence of Anas platyrhynchos (HM010684.1) in Gen Bank. The result of nucleotide sequence similarity percentage was 99.68±0.56%. Single Nucleotide Polymorphism D-loop region mtDNA Indonesian local duck was 0.32±0.56%.  Some SNP was found in Magelang duck C (Klawu blorok), F (Cemani black),  G (Gambiran), H (Jarakan kalung), I (Jowo plain) and K (Plain white) also Tegal duck 8, 1, 2, 5, 2, 8 and 2 SNP respectively. It could be concluded that polymorphic genetic characteristic similarity were existed in Indonesia local duck populations which was shown by its big standard deviation SNP in D-loop region mtDNA. Magelang duck with different feather color relatively more polymorphic to another local duck in Indonesia. Single Nucleotide Polymorphism which was achieved could be used as genetic marker that differentiate genetic characteristic of Indonesian local ducks.Key words:  genetic characteristic, local duck, Single Nucleotide Polymorphism (SNP), D-loop mtDNAAbstrak.  Penelitian ini bertujuan untuk mengetahui karakteristik genetik dan polimorfisme itik lokal Indonesia yaitu itik Magelang, Tegal, Mojosari, Bali dan Alabio berdasarkan analisis Single Nucleotide Polymorphism (SNP) daerah D-loop mtDNA. Tujuan jangka panjangnya adalah menetapkan marker atau penanda genetik berdasarkan SNP daerah D-loop mtDNA spesifik yang dapat membedakan itik-itik lokal yang ada di Indonesia. Selanjutnya digunakan sebagai  alat bantu seleksi untuk konservasi, pembibitan  dan pengembangbiakan itik lokal.  Populasi masing-masing jenis itik lokal yang digunakan sebanyak 20 ekor untuk diambil 3 ml sampel darahnya. Isolasi DNA genom menggunakan DNA Isolation Kithigh pure PCR template preparation (Geneaid). Amplifikasi dengan teknik PCR menggunakan pasangan primer DL-AnasPF (L56) sebagai forward dan DL-AnasPR (H773) sebagai reverse. Produk PCR atau amplikon yang diperoleh disekuensing. Hasil sekuensing dianalisis dengan teknik SNP dan diamati kesamaan dan perbedaan urutan nukleotida antar individu itik dan antar populasi.  Hasil penelitian menunjukkan bahwa DNA genom dari itik lokal di Indonesia berhasil diisolasi. Amplifikasi dengan teknik PCR berhasil memperoleh fragmen berukuran 718 bp. Urutan nukleotida hasil sekuensing sebesar 469 nt dianalisis dengan teknik SNP dan dibandingkan dengan urutan nukleotida standar dari itik Anas platyrhynchos (HM010684.1) yang ada di Gen Bank, diperoleh persentase kesamaan urutan nukleotid sebesar 99,68±0,56%. Single Nucleotide Polymorphism daerah D-loop mtDNA pada itik lokal di Indonesia sebesar 0,32±0,56%. Sejumlah SNP ditemukan pada itik Magelang C (Klawu blorok), F (Hitam cemani),  G (Gambiran), H (Jarakan kalung), I (Jowo polos) dan K (Putih polos) serta itik Tegal  masing-masing 8, 1, 2, 5, 2, 8 serta 2 SNP. Kesimpulan dari penelitian ini adalah terdapat karakteristik genetik yang polimorfik pada populasi itik lokal di Indonesia, ditunjukkan dengan adanya simpang baku SNP pada daerah D-loop mtDNA yang relatif besar. Itik Magelang dengan warna bulu yang berbeda relatif lebih polimorfik dibandingkan dengan itik lokal lainnya di Indonesia.  Single Nucleotide Polymorphism yang diperoleh dapat digunakan sebagai penanda genetik yang dapat membedakan karakteristik genetik yang dimiliki oleh itik lokal di Indonesia.Kata kunci:  karakteristik genetik, itik lokal, Single NucleotidePolymorphism (SNP),  D-loop mtDNA

Study of Socio Economic Profile of Small Holder Goat Farming in Gumelar Sub-District Banyumas Regency

Penelitian ini bertujuan untuk mengetahui profil sosial ekonomi usaha ternak kambing rakyat di daerah pedesaan Kecamatan Gumelar Kabupaten Banyumas. Pengumpulan data menggunakan metode survey pada tiga desa terpilih, kemudian 188 responden dipilih secara acak sebagai sampel. Data yang terkumpul dianalisis menggunakan analisis deskriptif. Hasil penelitian menunjukan bahwa tingkat pendapatan usaha ternak kambing sebesar Rp.349.184,71 per tahun, dengan tingkat efisiensi ekonomi sebesar 2,21. Jumlah pemilikan ternak kambing rata-rata sebesar 2,67 ST, dengan jumlah biaya pakan ternak per tahun rata-rata sebesar Rp.147.672,34. Umur peternak rata-rata 46,5 tahun, tingkat pendidikan peternak sebagian besar berpendidikan Sekolah Dasar dengan lama pendidikan formal rata-rata 5,78 tahun, dan tingkat pengalaman beternak kambing rata-rata 4,04 tahun. Sistem pemeliharaan ternak kambing yang digunakan yaitu sebagian besar menggunakan sistem pemeliharaan tradisional, sedangkan status pekerjaan peternak yaitu sebagian besar berstatus sebagai petani penggarap. (Animal Production 6(2): 61-67 (2004) Kata Kunci: Ternak Kambing Rakyat, Profil Sosial Ekonomi, Banyumas

Model of Small Holders Dairy Cattle Waste Pollution at Several Natural Physical and Economic Social Conditions: A Case Study in the Province of Central Java

Most of dairy farmings in Indonesia are managed in the forms of smallholder farmings that give more attention to productivity rather than ecological concerns. The purpose of this study was to make models of dairy cattle animal waste pollution on clean water quality and degree of smell at several regions with different natural physical and economic social conditions. This study also investigated the waste management that match with the characteristics, behavior, and the attitude of the farmers in each region.  System approach was used as the method of this study through model simulation with program of Powersim 2.5c. Model compiled based on to component situation of livestock, condition of environment and situation of farmer. Determination of regional sample of sub-province or town until chosen countryside conducted with multistage sampling without randomization (purposive sampling).  Based on the result of research can be concluded that (1) low natural physical region and low economic social condition to have endangering pollution level of environment, (2) the waste management for the region with high natural physical and high economic social of bio gas and composting accompanied by removing to excess of animal waste for regional with low natural physical and low economic social. (Animal Production 6(2): 68-75 (2004) Key Words: model, dairy  cattle, waste pollution

Profit Analysis of Small Holder Dairy Cattle Farm on Group and Individual System in Banyumas Regency

This research is aimed to study production, technical and the profit of group and individual system on smallholder dairy cattle farm. The research has been conducted in Banyumas Regency. Data collection was done by surveying about 80 farmers, Unit Output Price Cobb-Douglas Profit Function estimation employed Ordinary Leas Square (OLS) method. The different of variable from the result of profit estimation. Profit function analysis on group system showed that manpower pay, animal age, lactation period, lactation month and farmer education have a significant influence on the profit. Whereas, on individual system influence of manpower pay, animal age and lactation month were significant on the profit. Dummy variable showed that group system has more profit than individual system, it was because on group system; (1) has cheaper price on forage and concentrate cost, (2) has higher average of production result, and (3) has higher price of  milk per unit. (Animal Production 4(2): 94-100 (2002) Key words : Profit, Group and Individual System