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

Nutritional values of wild rusa deer (Cervus timorensis) venison

Until 2002, the level of protein consumption from red meat origin by the Indonesian people was only 51.5% from the national target. The reasons for this condition were due to limited resources of domesticated animals and low income of many suburb people to buy red mead. One alternative in supplying the gap of protein consumption is by utilizing local prospective wildlife animals, such as deer. This species is widely distributed among the islands in Indonesia. In order to understand more on the quality of tropical rusa venison (Cervus timorensis), a study was conducted in Palu district, Southeast Sulawesi by collecting venison from hunters. The results showed there was no significant difference on cooking lost among the carcass parts (hind leg, front leg and saddle), with the range between 30.3 to 33.0%. There were also no significant differences on the gross energy, protein, ash, fat and phosphor values among the carcass parts. The contents of sodium , ferum and calcium were significantly different at p<0.05. In fatty acid contents, there was no interaction between the carcass parts and fatty acid groups, however among the fatty acid groups there was a significant difference (p<0.001) on the content. Palmitic and stearic acid had the highest contents (>9.5% DM), compared to other groups (<4.0% DM). In amino acid contents , it showed no interaction between the carcass parts to amino acid groups, however there was a significant difference among the amino acid groups. Glutamic acid had the highest level (15.74%DM), where as others were ranged between 2.7 to 7.6% DM. (Animal Production 7(1): 46-51 (2005) Keywords: Rusa deer, Cervus timorensis, venison, nutritional values

Influence of Non-fibrous Carbohydrate and Degradable Intake protein and Ruminal Fermentation ,Nutrien Digestion and performance of Local Sheep

The objective of current study was to evaluate the impact dietary non-fibrous carbohydrate ( NFC) and ruminally degradable intake protein (DIP) concentration have on ruminal fermentation , nutrient digestion and performance of local sheep. The animal had a mean of  liveweight 19.80 ±1.55 kg. four diets ,arranged in a 2x2 factorial ,were formulated to contain either 40 or 50 % NFC and 50 or 60 % of dietary crude protein as DIP .dietary DM contained 25 % Indonesian field grass and 75 % concentrate. Solvent –extracted or formaldehyd  2 % -treated soybean meal were used to alter DIP and corn or soybean hulls to alter NFC level. Percentage of  energy and NDF digestion was similar ( p<0,01) as DIP level decreased in the diets. The soybean hulls was fermentable and total VFA concentration in the rumen increased ( p<0.01), but N-NH3 concentration was decreased ( p<0.01) as DIP level decreased in the diets. Daily live weight gain ( 146.29±25.84 g) and body composition ( fat, water , protein and mineral) was similar ( p<0.05) among diets. The preponderance ruminal fermentation ,nutrient digestion and performance of local sheeps did not be improved by sincronization of energy and nitrogen release but may more likely be limited by either energy or nitrogen alone. (Animal Production 3(2): 53-61 (2001)Key Word : Carbohydrate, protein, rumen fermentation, nutrients digestion and performance