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All Journal HAYATI Journal of Biosciences Jurnal Veteriner Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Jurnal Ilmu Ternak Veteriner WARTAZOA Indonesian Bulletin of Animal and Veterinary Sciences BERITA BIOLOGI Kebijakan: Jurnal Ilmu Administrasi Jurnal DIALEKTIKA : Jurnal Ilmu Sosial Journal of Community Research & Engagement (JCRE)
Sri Sulandari
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Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Economics, Econometrics & Finance Education Law, Crime, Criminology & Criminal Justice Social Sciences Veterinary

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Journal : HAYATI Journal of Biosciences

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Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences SRI SULANDARI; MOCH SYAMSUL ARIFIN ZEIN; TIKE SARTIKA
HAYATI Journal of Biosciences Vol. 15 No. 4 (2008): December 2008
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (520.93 KB) | DOI: 10.4308/hjb.15.4.145

Abstract

The Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Indonesian indigenous chickens. A total of 483 individuals belonging to 15 population breeds and 43 individuals belonging to 6 populations of jungle fowl (2 populations of Gallus gallus and 4 populations of Gallus varius) were sampled. The hypervariable I (HVI) segment of the D-loop was PCR amplified and subsequently sequenced. The sequences of the first 397 nucleotides were used for analysis. Sixty nine haplotypes were identified from 54 polymorphic sites with polymorphism between nucleotides 167 and 397 contributing to 94.5% of the sequence variation. Phylogenetic analysis indicates that Indonesian indigenous chickens can be grouped into five distinct 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 indigenous chickens. Fifty haplotypes belong to clade II, seven haplotypes are in clade IV, six are in clade IIId, three are in clade I and one haploype is in clade IIIc. There was no breed-specific clade. Analysis of Molecular Variance (AMOVA) based on partial D-loop sequences of Indonesian chicken indicates that 67.85% of the total sequence variation between haplotypes was present within the population and 32.15% between populations. One of the haplotypes (represented by PLC4) was shared by all populations, suggesting that these populations may share the same maternal ancestor. These results show a high mitochondrial D-loop diversity and indicate multiple maternal origins for Indonesian indigenous chickens. Key words: Indonesian indigenous chicken, mitochondrial DNA, D-loop, haplotype, phylogenetic analysis and clade
Detection and Host Range Study of Virus Associated with Pepper Yellow Leaf Curl Disease SRI SULANDARI; RUSMILAH SUSENO; SRI HENDRASTUTI HIDAYAT; JUMANTO HARJOSUDARMO; SOEMARTONO SOSROMARSONO
HAYATI Journal of Biosciences Vol. 13 No. 1 (2006): March 2006
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (45.61 KB) | DOI: 10.4308/hjb.13.1.1

Abstract

High incidence of Pepper yellow leaf curl virus (PepYLCV) was observed in Indonesia since early 2000. Disease incidence in Yogyakarta, Central and West Java reached 100% on Capsicum frutescens, but only 10-35% on C. annuum. As an exception, the disease incidence on C. annuum cv. TM 999 was in the range of 70-100%. The causal agent of the disease, PepYLCV, was detected by polymerase chain reaction. Viral specific DNA fragment of the size ~1600 bp and ~550 bp was amplified from infected plants using two pairs of geminivirus universal primers pAL1v1978/pAL1c715, and pAv494/pAc1048, respectively. The PepYLCV has an intermediate host range including plants belonging to the family of Solanaceae, Leguminosae, and Compositae. The species belonging to the families of Cucurbitaceae, Malvaceae, Chenopodiaceae, and Amaranthaceae were resistant to the virus. Physalis floridana, is very prospective as a propagation host for the geminivirus infecting pepper. Nicotiana spp., cucumber, watermelon, cotton, and Sida sp. could be used as a differential host. Besides, Capsicum frutescens cv. Cakra, tomato, N. benthamiana, N. glutinosa, and Ageratum conyzoides could be used as indicator plants for the geminivirus infecting pepper. Key words: Pepper yellow leaf curl virus, disease incidence, host range
Co-Authors Agus Kundarmasno Alwin Marakarmah Cece Sumantri Cokorda Putra Indrayana Dede, I Kadek Dede Junaedy Dwi ASTUTI Eka, I Gede Agus Eka Pradnyana Gede Wirata Harini Nurcahya Mariandayani i Wayan Astawa JUMANTO HARJOSUDARMO M S A Zein M. Syamsul Arifin Zein Moch Syamsul Arifin Zein Moch Syamsul Arifin Zein Ni Luh Putu Ening Permini Ni Nyoman Reseani Nyoman Suargita Putu Deva Pradnyana Mardiana Putera RUSMILAH SUSENO Satrio Wijamukti Soemartono Sosromarsono SRI HENDRASTUTI HIDAYAT Sri Paryanti TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN TIKE SARTIKA Tri Hayatining Pamungkas