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Nunukan Chicken: Genetic Characteristics, Phenotype and Utilization Sartika, Tike; Sulandari, Sri; Zein, M S A; Paryanti, Sri
Indonesian Bulletin of Animal and Veterinary Sciences Vol 16, No 4 (2006)
Publisher : Indonesian Animal Sciences Society

Nunukan chicken is a local chicken from East Kalimantan which spreads out in Tarakan and Nunukan Islands . The chicken has a specific buff color and Columbian type feather and also has very late feathering (VLF) trait . The Nunukan cocks and hens have no wing and tail primary feather; the tail feathers are short and fragile . The VLF trait is known to have association with a K gene on the Z chromosome. The chicken is efficient in protein metabolism . Sulfur amino acids (cystine and methionine) that needed for feather growth, could be utilized for meat and egg production . The egg production of Nunukan chicken was better than the Kampung chicken . The average of hen day, hen house and peak production of Nunukan chicken was 45 . 39.1 and 62%, respectively, while the Kampung chicken was 35 .9, 30 .9 and 48%, respectively . Based on genetic analysis, the external genotype characteristic of the Nunukan chicken is ii ce ss Idld pp. It means that the phenotype appearance of the Nunukan chicken was columbian and gold feathering type, yellow and white shank color and single comb type. This phenotype is similar to Merawang Chicken . The genetic introgression of the Nunukan chicken is affected by the Rhode Island Red with the genetic introgression value of 0.964 . Key words: Nunukan chicken, character, genetic; phenotype characteristics, utilization

Analysis of genetic relationship among Indonesian native chicken breeds based on 335 D-loop sequences Sulandari, Sri; Arifin Zein, M. Syamsul; Sartika, Tike
Indonesian Journal of Animal and Veterinary Sciences Vol 13, No 4 (2008)
Publisher : Indonesian Animal Sciences Society

The Mitochondrial DNA (mtDNA) D-loop segment was PCR amplified and subsequently sequenced for a total of 335 individuals from Indonesian native chicken. The individuals were drawn from sixteen populations of native chicken and three individuals of green jungle fowls (Gallus varius). Indonesian native chicken populations were: Pelung Sembawa, PL (n = 18), Pelung Cianjur, PLC (n = 29) and Arab Silver, ARS (n=30), Cemani, CM (n = 32), Gaok, GA (n = 7), Kedu Hitam, KDH (n = 11), Wareng, T & TW (n = 10), Cemani, CMP (n = 2), Kedu, KD (n=26), Kedu Putih, KDP (n = 15), Sentul Jatiwangi, STJ (n = 27), Ayam Kate, KT (n = 29), Ayam Sentul, STC (n = 15), Arab Golden, ARG (n = 26), Ayam Merawang, MR (n = 28), Kedu Putih Jatiwangi, KDPJ (n=6) and Kapas, KPS (n = 21). Green jungle fowls were: two individuals from Flores island (FL5 and FL57) and one individual (BD42) from Sumbawa island. The sequences of the first 530 nucleotides were used for analysis. Eighty two haplotypes were identified from 78 polymorphic sites for the 335 individuals. Seventy nine haplotypes were identified in native chicken from 57 polymorphic sites while three were of jungle fowls. Phylogenetic analysis indicates that Indonesian native chicken can be grouped into five clades (Clade I, II, IIIc, IIId and IV) of the previously identified seven clades (Clade I, II, IIIa, IIIb, IIIc, IIId and IV) in Asian domestic chicken. Haplotypes CM10 and CM32 fall to a different category while STC12 is also on its own. Interestingly STC12 clusters together with Gallus gallus gallus (GenBank accession No. SULANDARI et al. Analysis of genetic relationship among Indonesian native chicken breeds based on 335 D-loop sequences 296 AB007720). When CM10 (same as CM14), CM32 and STC12 were removed, 77 haplotypes of domestic chicken were identified from 53 polymorphic sites. All the green jungle fowls are clustered to one clade of their own. The clades of domestic chicken are: Clade I which has three haplotypes, Clade II has 52 haplotypes, Clade IIIc has one haplotype (represented by ARS30), Clade IIId has nine haplotypes while Clade IV has eleven haplotypes. The phylogenetic relationship between chicken populations has no link to the geographic locations. Analysis of molecular variance showed that the genetic variation within populations was 67.42% while 32.58% accounted for the genetic differentiation between populations. Key Words: Native Chiken, Green Jungle Fowls, D-Loop DNA Mitochondria, HV-1, Clade, Haplotype, Phylogenetic, Genetic Variation

Genetic diversity of Lombok chickens based on D-loop mitochondrial DNA sequences Arifin Zein, M. Syamsul; Sulandari, Sri
Indonesian Journal of Animal and Veterinary Sciences Vol 13, No 4 (2008)
Publisher : Indonesian Animal Sciences Society

Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Lombok chickens. A total of 45 individuals were sampled. The D-loop segment was PCR amplified and subsequently sequenced. The sequences of the 785 nucleotides were used for analysis. Twelve haplotypes were identified from 25 polymorphic sites with polymorphism between nucleotides 200 and 400 contributing to 80% of the variation. Fuâs Fs value was - 8.768 (all samples, P = 0), indicating high genetic diversity and population expansion, a conclusion supported by a neighborâ joining analysis of the haplotypes. Nucleotides diversity of the Lombok chicken were 0.00221 and haplotype diversity were 0.654 + 0.08. The dominant haplotype found among the Lombok chickens was haplotype B (62%) and genetic distances value ranged from 0.001 to 0.017. Â Â Key Words: Mtdna, D-Loop, Genetic Diversity, Haplotype, Lombok Chicken

Analisis Gen Cytochrome Oxydase-1 (CO1) untuk Konfirmasi Status Taksonomi Burung Srigunting Sumbawa (Dicrurus, Dicruridae) Astuti, Dwi; Ashari, Hidayat; Irham, Mohammad; Sulandari, Sri
ZOO INDONESIA Vol 26, No 1 (2017): Juli 2017
Publisher : Masyarakat Zoologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (620.941 KB)

Sekuen DNA dari gen cytochrome oxydase-1 (COI) diadopsi untuk membangun pengelompokan dan kekerabatan dari burung-burung srigunting (Dicrurus; Dicruridae). Tujuannya adalah untuk mengkonfirmasi apakah srigunting dari Sum-bawa merupakan spesies tersendiri atau merupakan bagian dari superspesies D. hottentotus. Sekuen DNA sepanjang 795-bp pada gen COI diambil dari delapan burung srigunting dari Sulawesi Tenggara (D. hottentotus leucops), enam srigunting dari T.N. Gn. Halimun, Jawa Barat (D. remifer), dan dua srigunting dari Sumbawa. Analisis Neighbor-joining (NJ) dilakukan untuk mengkonstruksi pohon filogeninya dengan mengkalkulasi semua substitusi basa (transisi dan trans-verse) pada software MEGA-5. Pohon NJ menunjukkan bahwa dua individu yang berasal dari Sumbawa jelas-jelas terpisah dari Dicrurus asal Sulawesi Tenggara (D. hottentotus) dengan didukung nilai bootstrap sebesar 100 % dan dipisahkan oleh nilai divergensi sekuen > 3,5%. Sedangkan D. remifer memisah jauh dari keduanya. Penelitian ini cenderung mendukung pendapat bahwa srigunting dari Sumbawa merupakan populasi yang berbeda dan tidak termasuk dalam grup D. hottentottus, tetapi termasuk dalam grup D. densus dari Nusa Tenggara dan kemungkinan besar adalah spesies monopiletik tersendiri sebagai D. bimaensis.

Kajian gen Amely Gajah Sumatra (Elephas maximus sumatranus) Zein, Moch Syamsul Arifin; Sulandari, Sri
JURNAL BIOLOGI INDONESIA Vol 12, No 1 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v12i1.2319

Sumatran elephants (Elephas maximus sumatranus) is endemic of Asian elephants in Indonesia, an endangered animal andlisted on Appendix I of CITES. Therefore, information on the status and distribution of the population of Sumatranelephants, including the distribution of genetic diversity is necessary to facilitate the development of adequate conservationand management strategies. The purpose of this research was to use Amely gene to trace paternal lineage of Sumatranelephants based on Y chromosome variation. A total of 22 blood samples of male Sumatran elephants were collected inSumatra (Way Kambas , Seblat, Bentayan, Sugihan, dan Bukit Serelo Lahat). We amplified intronic regions of the Ylinkedgene (Amely) using published primer sequences (Amely-R2 and Amely-F2) and sequenced. Sequences generatedfrom this study, aligned with reference sequences available in the GenBank, namely Elephas maximus (AY823325.1),Loxodonta Africana (AY 823320.1; AY 823321.1), Loxodonta cyclotis (AY823322.1; AY8233223.1, AY 823324.1).Neighbour Joining tree of Sumatran elephants was performed using MEGA version 5.2.2. The analysis results of 22-maleSumatran elephants, indicating that no diversity (no variation) of the Y chromosome obtained among the population ofSumatran elephants. Sumatran and Asian elephants have the same haplotypes. Further results confirmed that the savannaelephants (Loxodonta africana ) and the forest elephants (Loxodonta cyclotis ) formed two (2) separate clades, which showstwo different species. Results obtained in this study may help to design future conservation programs for the species.Keywords: Sumatran elephant, Amely gene, Y chromosome, Genbank, haplotype

COLLECTION OF MATERIAL DNA SAMPLES FROM BIRDS IN THE GUNUNG HALIMUN NATIONAL PARK (GHNP) FOR ESTABLISHING OF DNA BANK Sulandari, Sri; Astuti, Dwi; Kundarmasno, Agus; Marakarmah, Alwin; Wijamukti, Satrio
BERITA BIOLOGI Vol 5, No 6 (2001)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

This study was conducted to collect material DNA samples from birds in the Gunung Halimun National Park (GHNP) for establishing of DNA bank.Ciptarasa, Geger Hanjuang and Cikaniki village areas were chosen as sites for sample collections in the GHNP.In order to take the sample from birds, transect lines were established at each site where series of mist nets were operated.The captured birds, both live- and died-birds, were identified. For the living birds, blood and/or shed feathers were taken from the bird prior to releasing.In case of died birds, tissue and liver were collected. The collected samples were transported to genetic laboratory at Zoological Division,Researh Center for Biology (RCB)-LIPI (The Indonesian Institute of Science) and kept in 4Â°C. In this collection, a total of 411 collected samples were obtained, coming from 25 families and 79 species.The 19-endemic birds were found in GHNP.

Struktur Populasi Genetik Ayam Hutan Hijau Menggunakan Sekuen Hypervariable 1 D-Loop DNA Mitokondria Arifin Zein, M. Syamsul; Sulandari, Sri
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 13, No 3 (2008): October 2008
Publisher : Universitas Atma Jaya Yogyakarta

Thirty-three individuals from four populations of green junglefowl (Gallus varius) were collected throughout Indonesia: 14 from Central Java, 4 from Eastern Java, 3 from Sumbawa island and 12 from Flores island. The mitochondrial DNA D-loop the samples were analysed for sequence diversity. Twenty-five haplotypes with 28 polymorphic sites were identified within the first hypervariable-1 fragment (397 bp) of the D-loop. Fuâ€™s Fs value was -25.96 (all samples, P=0), indicating high genetic diversity and population expansion; a conclusion supported by a neighborâ€“joining analysis of the haplotypes. Though sample size per population varied between 3 and 14, the Fs values for the four populations, between -2.20 and -10.76, were all significant (P=0). Only one haplotype was shared between three populations (Central Java, Sumbawa island, and Flores island) by a total of seven individuals. Within populations, only three haplotypes were shared by three individuals. The remaining haplotypes were unique, indicating genetic differentiation between populations as confirmed by significant pairwise Fst values at P=0.05 in four out of the six population pairs (except two pairs of Central Java & Sumbawa island and Flores island & Sumbawa island). The diversity pattern observed at the mtDNA of the green junglefowl provides a baseline which may help to understand the recent population expansions of domesticated chickens from multiple centres of domestications. Our observations also suggest careful interpretation of the results of genetic characterization may be needed when applied to the management and conservation of species like the green junglefowl. As in other multiparous birds and mammals with a short reproductive interval, green junglefowl may have established distinct genetic entities in metapopulations across its geographic distribution.

DETECTION AND TRANSMISSION OF RICE STUNT VIRUS ON CIHERANG AND SITU BAGENDIT VARIETIES Helina, Selvi; Sulandari, Sri; Hartono, Sedyo; Trisyono, Andi
JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA Vol 18, No 2 (2018): SEPTEMBER, JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA
Publisher : Universitas Lampung

Detection and Transmission of rice stunt virus on Ciherang and Situ Bagendit Varieties. The explosion of brown planthoppers recently has caused reduction of rice production in Indonesia. Brown planthoppers do not only act as pest, but also transmit Rice grassy stunt virus (RGSV) and Rice ragged stunt virus (RRSV). Detection of the existence of the two viruses in rice plants and vector insects is important to be done to ensure that the virus is infected with the vector. The aim of this research is to detect the existence of virus in varieties of Ciherang and Situ Bagendit as a result of transmission in the laboratory and to find out the ability of brown planthoppers to transmit stunt virus to both of the varieties. This research was compiled using Completely Randomized Design (CRD) with 4 treatments, namely healthy rice plants of Ciherang and Situ Bagendit varieties, Ciherang and Situ Bagendit varieties which were infested by brown planthoppers each with 5 repetitions. The parameters observed were incubation period, symptoms, plant height, number of leaves and incidence of disease. The data on plant height, number of leaves and incidence of disease were analyzed using ANOVA and continued with the Least Significant Difference (LSD) test at the level of 5%. The results showed that Ciherang and Situ Bagendit varieties were only positively infected by Rice ragged stunt virus. The results of the rice transmission showed that Ciherang variety had a faster incubation period of 10 DAI while Situ Bagendit was 14 DAI, but the two varieties showed an inhibition of growth in plant height and number of leaves compared to healthy plants with each incidence of 51.3% and 46.3%.

KAJIAN GEN AMELY GAJAH SUMATRA (ELEPHAS MAXIMUS SUMATRANUS) Zein, Moch Syamsul Arifin; Sulandari, Sri
JURNAL BIOLOGI INDONESIA Vol 12, No 1 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v12i1.2319

Sumatran elephants (Elephas maximus sumatranus) is endemic of Asian elephants in Indonesia, an endangered animal andlisted on Appendix I of CITES. Therefore, information on the status and distribution of the population of Sumatranelephants, including the distribution of genetic diversity is necessary to facilitate the development of adequate conservationand management strategies. The purpose of this research was to use Amely gene to trace paternal lineage of Sumatranelephants based on Y chromosome variation. A total of 22 blood samples of male Sumatran elephants were collected inSumatra (Way Kambas , Seblat, Bentayan, Sugihan, dan Bukit Serelo Lahat). We amplified intronic regions of the Ylinkedgene (Amely) using published primer sequences (Amely-R2 and Amely-F2) and sequenced. Sequences generatedfrom this study, aligned with reference sequences available in the GenBank, namely Elephas maximus (AY823325.1),Loxodonta Africana (AY 823320.1; AY 823321.1), Loxodonta cyclotis (AY823322.1; AY8233223.1, AY 823324.1).Neighbour Joining tree of Sumatran elephants was performed using MEGA version 5.2.2. The analysis results of 22-maleSumatran elephants, indicating that no diversity (no variation) of the Y chromosome obtained among the population ofSumatran elephants. Sumatran and Asian elephants have the same haplotypes. Further results confirmed that the savannaelephants (Loxodonta africana ) and the forest elephants (Loxodonta cyclotis ) formed two (2) separate clades, which showstwo different species. Results obtained in this study may help to design future conservation programs for the species.Keywords: Sumatran elephant, Amely gene, Y chromosome, Genbank, haplotype

DETECTION AND IDENTIFICATION OF YELLOW MOSAIC STUNT DISEASE ON Petunia sp. USING NESTED PCR METHOD Astuti, Suryani Titi; Sulandari, Sri; Hartono, Sedyo; Somowiyarjo, Susamto
JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA Vol. 21 No. 1 (2021): MARCH, JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA
Publisher : Universitas Lampung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23960/jhptt.12156-62

Detection and identification of yellow mosaic stunt disease on Petunia sp. using nested PCR method. Yellow mosaic stuntdisease was found at some nurseries of Petunia in Sleman, Yogyakarta, also in Muntilan and Magelang Central Java. Thedisease was very important due to its ability reducing the quality and quantity of Petunia seedlings. The causal agent of thedisease may be carried over to imported seeds and necessary to identify as a basic information for developing controlstrategies. This research was done by mechanical transmission on indicator plants. The observation of the causal agents wasconducted using electron microscope with quick dipping method and the molecular detection was done using nested PCRwith TobRT up1-TobRT do2 as the external primers and TobN up3-TobN do4 as the internal primers. Mechanical inoculationshowed chlorosis symptoms that developed into local spot on Chenopodium amaranticolor as well as mosaic and veinbanding on Nicotiana benthamiana. The observation using electron microscope showed rod-shaped virus particles sizedapproximately 300 nm and by PCR method produced around 568 bp and 400 bp DNA band. Based on the sequence analysis,the disease was caused by Rehmania mosaic virus. This type of Tobamovirus has 96% similarity with ReMV-Japan. ReMV, aplant pathogen which was a member of Tobamovirus that has never been reported in Indonesia. This research was the firstreport of ReMV in Indonesia infecting Petunia as ornamental plant.

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