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All Journal Jurnal Akuakultur Indonesia JURNAL SAINS DAN TEKNOLOGI INDONESIA JURNAL TEKNOLOGI LINGKUNGAN Jurnal Medik Veteriner Jurnal Rekayasa Lingkungan Jurnal Hidrosfir Indonesia Jurnal Teknologi Lingkungan Jurnal Bioteknologi & Biosains Indonesia (JBBI)
Ratu Siti Aliah
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Computer Science & IT Earth & Planetary Sciences Education Engineering Environmental Science Health Professions Veterinary

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MITOCHONDRIAL DNA DIVERSITY IN FOUR POPULATIONS OF INDONESIAN FRESHWATER GIANT PRAWN (Macrobrachium rosenbergii) Ratu Siti Aliah
Jurnal Bioteknologi dan Biosains Indonesia Vol. 9 No. 1 (2022)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Mitochondrial DNA has been widely applied to analyze fish genetic diversity, especially the cytochrome oxidase subunit I (COI) gene, which can be used as a marker of typical variation patterns, both intraspecific and interspecific crossbreeding. Haplotype diversity was observed in four populations of giant freshwater prawns (Macrobrachium rosenbergii) originating from Peureulak River in Aceh, Tabuk River in South Kalimantan, Bengawan Solo River in East Java, and the Siratu strain. Haplotype diversity was observed in the mitochondrial DNA COI gene of 1516 bp and restricted using 5 enzymes, namely AvaII, MspI, RsaI, HaeIII, and TaqI. The diversity of mtDNA COI haplotypes in the population of Peureulak River, Tabuk River, Bengawan Solo River, and Siratu were 0.8183, 0.6222, 0.7461, and 0.8044, respectively. The dendrogram of genetic distance showed that the Bengawan Solo River populations and the Siratu strain were in the same cluster, while Peureulak River and Tabuk River populations were in another group. The four populations can be used as genetic sources in crossbreeding activities based on haplotype data for each population, haplotype diversity, and genetic distance.
Genetic Characterization of Domesticated F1 Generation in Humpback Grouper (Cromileptes altivelis) Aliah, Ratu Siti; Wahidah, .; Sumantadinata, K.; Nugroho, Estu; Carman, O.
Jurnal Akuakultur Indonesia Vol. 5 No. 1 (2006): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (158.336 KB) | DOI: 10.19027/jai.5.87-96

Abstract

First generation (F1) of hatchery produced humpback grouper (Cromileptes altivelis) has been characterized genetically in order to serve the information of their status in related to their breeding strategy. PCR-RFLP method was used to detect the variation of mtDNA D-loop region of F1 population at BBPBL Lampung and BBAP Situbondo. The result of study showed that reducing of haplotype diversity had been arised from broodstock (0.8548) to F1 generation population (0.7473; 0.7273; and 0.6947, respectively).  Genetic divergence that had found between population BBPBL Lampung and BBAP Situbondo make it possible to do outbreeding in order to get its heterosis's effect. Keywords: mtDNA, haplotype diversity, genetic differentiation, Cromileptes altivelis   ABSTRAK Ikan kerapu tikus (Cromileptes altivelis) generasi pertama (F1) hasil domestikasi di hatchery telah dikarakterisasi secara genetik untuk menyediakan informasi status sehubungan dengan program pemuliaannya.  Metode PCR-RFLP digunakan untuk mendeteksi variasi sekuens D-loop mtDNA ikan kerapu tikus F1 yang diproduksi di BBPBL Lampung dan BBAP Situbondo.  Hasil penelitian menunjukkan bahwa telah terjadi penurunan keragaman haplotipe dari induk (0,8548) ke populasi generasi F1 (masing-masing 0,7473; 0,7273; dan 0,6947).  Adanya keragaman genetik antara populasi ikan kerapu tikus di BBPBL dan BBAP Situbondo memungkinkan dilakukannya outbreeding untuk mendapatkan efek heterosis. Kata kunci: mtDNA, keragaman haplotipe, diferensiasi genetik, Cromileptes altivelis
Genetic variability of the fifth generation of nile tilapia Oreochromis niloticus using microsatellite DNA markers Satriani, Gloria Ika; Soelistyowati, Dinar Tri; Hardianto, Dian; Aliah, Ratu Siti
Jurnal Akuakultur Indonesia Vol. 10 No. 2 (2011): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (263.481 KB) | DOI: 10.19027/jai.10.124-130

Abstract

ABSTRACTFifth generations of Nile tilapia from several strains have been produced by using selective breeding program in Main Centre for Freshwater Aquaculture Development (MCFAD) Sukabumi, West Java. This research was aimed to evaluate the impact of family selection program of some highly economic traits on its genetic variability using microsatellite DNA markers. The total of 180 specimens have been collected from fifth generation of nine reciprocal mating between three families selected from fourth generation of Nile tilapia and were screened for genetic variability at three microsatellite loci (UNH 123*, UNH 172*, UNH 216*). The results showed that the amount of genetic variability on fifth generations of Nile tilapia from three strains was ranged between 33 to 100% and the highest genetic distance relationship between families was 0.3875. This research approved that females and males issued from the family which have more amount of genetic variability and higher distance to others could be considered as genetic materials to produce the next generation.Keywords: microsatellite DNA, genotype, genetic variability, genetic distance, Oreochromis nilotiocus ABSTRAKBeberapa strain ikan nila generasi kelima telah dihasilkan dalam program pemuliaan di Main Centre untuk Freshwater Aquaculture Development (MCFAD) Sukabumi, Barat Jawa. Riset ini bertujuan untuk mengevaluasi pengaruh seleksi famili terhadap performa karakter ekonomis penting berdasarkan keragaman genetiknya menggunakan penanda microsatellite DNA. Spesimen dari 180 individu generasi kelima hasil persilangan resiprokal antara tiga famili generasi keempat dianalisis dengan penanda tiga microsatellite loci (UNH 123*, UNH 172*, UNH 216*). Hasil penelitian menunjukkan bahwa keragaman genetik ikan nila generasi kelima berkisar antara 33 sampai 100% dan hubungan kekerabatan genetik antar famili yang paling jauh adalah 0,3875. Individu betina dan jantan yang berasal dari famili dengan tingkat keragaman genetik dan kekerabatan yang lebih tinggi dapat dipertimbangkan sebagai sumber genetik berkualitas untuk menghasilkan generasi berikutnya.Kata kunci: microsatellite DNA, genotipe, keragaman genetik, jarak genetik, Oreochromis nilotiocus
Identification of sex linked molecular markers in Indonesian giant freshwater prawn Macrobrachium rosenbergii Megawati, Novi; Alimuddin; Aliah, Ratu Siti
Jurnal Akuakultur Indonesia Vol. 20 No. 1 (2021): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19027/jai.20.1.93-100

Abstract

Male giant freshwater prawn grows faster than its female. Therefore, male mono sex culture is one of the solutions to improve aquaculture production. The all-male population of giant freshwater prawns can be produced by mating the neo-females (sex-reversed males) with the normal males. This study was aimed to identify the molecular markers related to the giant freshwater prawn sex. Specific primers were designed based on female-specific AFLP marker sequences to distinguish male and female sex on the prawns. Three locations for obtaining the Indonesian prawns in this study were Aceh, Sukabumi, and Solo. Based on the PCR analysis with MrMKn primers, 30 samples of female prawns had 100 % occurred DNA bands, while no DNA bands were obtained in all-male prawns from Solo. Nevertheless, MrMKn primers still detected 10–16 % male prawns from Sukabumi and Aceh. This indicated that MrMKn primers could not yet distinguish the male prawns for all populations. Moreover, the results suggested that the three prawn samples were different based on female-specific gene sequence. The MrMKn primers have the opportunity to be used in the selection of the female ZZ (neo-female) prawns from Solo without progeny test, so that the determination of female ZZ candidates can be identified more quickly. However, the primer still needs to be redesigned to distinguish neo-female prawns from Sukabumi and Aceh. Keyword: giant freshwater prawn, mono sex, neo-female, sex markers ABSTRAK Udang galah jantan lebih cepat tumbuh dibandingkan dengan betinanya sehingga budidaya udang galah monoseks jantan menjadi salah satu solusi untuk meningkatkan produksi budidaya. Populasi monoseks jantan udang galah dapat dihasilkan dengan mengawinkan neofemales (sex-reversed males) dengan jantan normal. Sistem kromosom pada udang galah berbeda dengan ikan. Individu betina bersifat heterogametik (WZ) dan jantan homogametik (ZZ). Dalam perkembangannya, terdapat kendala dalam menentukan individu neofemale yang memiliki kromosom ZZ. Berdasarkan pendekatan sistem kromosom tersebut, maka dapat dijadikan acuan untuk membuat marka molekuler terkait kelamin udang galah. Penelitian ini bertujuan mengidentifikasi marka molekuler terkait jenis kelamin pada udang galah. Primer spesifik didesain berdasarkan sekuen female specific AFLP marker untuk membedakan kelamin jantan dan betina pada udang galah. Tiga sumber udang galah digunakan dalam penelitian ini, yaitu Aceh, Sukabumi, dan Solo. Berdasarkan hasil analisis PCR dengan primer MrKNn, dari 30 sampel pada kelompok udang galah betina diperoleh hasil 100% pita DNA muncul, dan tidak terdapat pita DNA pada semua udang galah jantan asal Solo. Namun demikian, primer MrMKn tersebut masih mendeteksi sebesar 10–16% pada udang galah asal Sukabumi dan Aceh. Hal ini menunjukkan bahwa primer MrMKn belum dapat membedakan udang galah jantan dari semua populasi. Selain itu, dapat dikatakan bahwa ketiga udang galah uji adalah berbeda, khususnya sekuen gen spesifik betina. Primer MrMKn berpeluang digunakan dalam proses seleksi udang galah betina ZZ (neofemale) asal Solo tanpa harus melalui uji progeni sehingga penentuan kandidat betina ZZ lebih cepat teridentifikasi. Akan tetapi, primer masih perlu didesain ulang untuk membedakan neofemale asal Sukabumi dan Aceh. Kata kunci: marka kelamin, monoseks, neo-female, udang galah
First Record of Anguillid Herpesvirus 1 Linked to a Mass Mortality Event in Shortfin Eel (Anguilla bicolor) in Indonesia Romadhona, Ekky Ilham; Widantara, Handang; Aslia, Aslia; Megawati, Novi; Ardiansyah, Arif Rahmat; Larassagita, Annisa Fitri; Dewi, Kiki Mariya; Farman, Aditia; Chaidir, Iding; Sujatmiko, Wisnu; Yaniharto, Dedy; Budiardi, Tatag; Aliah, Ratu Siti; Sutanti, Sutanti
Jurnal Medik Veteriner Vol. 8 No. 1 (2025): April
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jmv.vol8.iss1.2025.134-143

Abstract

Anguillid herpesvirus 1 (AngHV-1), a member of the Alloherpesviridae family, is known to cause high mortality in both wild and farmed eels. Notably, no cases of AngHV-1 infection in Indonesia until June 2023, when a significant mortality rate exceeding 75% among cultured glass eels was documented in Bogor, Indonesia. This study investigated the outbreak by collecting 30 diseased fish from multiple cultured tanks to examine clinical symptoms, histopathological changes, and viral presence through PCR targeting the viral DNA polymerase gene. Hemorrhagic lesions in the abdomen and anal regions were the primary clinical symptoms. Histopathological examination revealed hyperplasia, fusion, and epithelial lifting of the gill secondary lamellae. PCR, using 394 bp primer specific for AngHV-1, confirmed 100% infection among the collected samples, indicating rapid viral transmission within the rearing environment. Phylogenetic analysis of partial DNA polymerase amino acid sequences showed that Indonesian AngHV-1 isolate is genetically diverse and shares similarities with strains from China, Taiwan, Canada, and several European countries, suggesting the emergence of a novel strain. This study highlights the urgent need for enhanced biosecurity measures to curb AngHV-1 spread in the Indonesian eel aquaculture sector.
Evaluation of the Biophysical and Chemical Conditions of the Aquatic Environment During the Rainy Season to Mitigate the Ecological Disaster of Ciguatera Fish Poisoning (CFP) and Harmful Algal Bloom (HABs) in the Gili Matra Marine Tourism Park-Lombok: Evaluasi Kondisi Biofisikakimia Lingkungan Perairan Pada Musim Hujan Untuk Mitigasi Bencana Ekologi Ciguatera Fish Poisoning (CFP) dan Marak Alga Berbahaya (MAB) di Taman Wisata Perairan Gili Matra-Lombok Sachoemar, Suhendar Indrakusmaya; Rachman, Arief; Aliah, Ratu Siti; Megawati, Novi; Romadhona, Ekky Ilham; Meirinawati, Hanny; Prayogo, Teguh; Dewa, Riardi Pratista; Zamroni, Yuliadi; Ahyadi, Hilman; Fitriya, Nurul; Hamzah, Faisal; Garno, Yudhi Soetrisno; Susanto, Joko Prayitno; Riyadi, Agung; Haryanti; Ihsan, Iif Miftahul; Setiarti Sukotjo; Iskandar; Leonita, Shinta; Diswandi; Rahman; Muhami; Makosim, Syahril
Jurnal Teknologi Lingkungan Vol. 26 No. 2 (2025)
Publisher : BRIN Publishing (Penerbit BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jtl.2025.7213

Abstract

Abstrak Ciguatera Fish Poisoning (CFP) dan fenomena Marak Alga Berbahaya (MAB) yang disebabkan oleh dinoflagellata bentik beracun merupakan salah satu bencana ekologi atau lingkungan yang dapat mengancam kesehatan manusia di kawasan pesisir Indonesia, seperti di kawasan Taman Wisata Perairan (TWP) Gili Matra yang terdiri dari 3 pulau yaitu Gili Meno, Air, dan Trawangan. TWP Gili Matra merupakan pusat wisata bahari dan kawasan konservasi laut di kawasan Nusa Tenggara Barat yang diketahui mengalami tekanan akibat aktivitas manusia dari kegiatan pariwisata dan perikanan yang berdampak negatif kepada ekosistem pesisir, terutama terumbu karang. Kondisi tersebut dapat meningkatkan kelimpahan komunitas dinoflagellata bentik beracun yang berpotensi menyebabkan terjadinya CFP dan MAB di TWP Gili Matra. Untuk itu diperlukan upaya mitigasinya agar risiko bencana ekologi CFP dan MAB dikemudian hari yang selain dapat menyebabkan terjadinya kerusakan ekosistem perairan TWP Gili Matra, tetapi juga kerugian ekonomi yang cukup besar, tidak terjadi. Menurut perhitungan ekonomi para ahli, nilai ekonomi kegiatan pariwisata di TWP Gili Matra, mencapai 26,86 triliun rupiah per tahun.  Salah satu upaya mitigasi bencana ekologi CFP dan MAB adalah dengan mengetahui kondisi lingkungan perairan di TWP Gili Matra pada musim hujan. Berdasarkan hasil survei diketahui kondisi biofisikakimia lingkungan perairan pada musim hujan bulan Desember 2022 dan Maret 2024 dalam keadaan yang sangat baik dengan tingkat eutrofikasi sebagai indikator kualitas lingkungan perairan pada tingkat ultraoligotrofik dengan nilai skor TSI (Trophic State Index) 12,9-19,4 (<30) yang mengindikasikan bahwa kesuburan perairan sangat rendah, air jernih, konsentrasi oksigen terlarut tinggi sepanjang tahun dan mencapai zona hipolimnion.   Abstract Ciguatera Fish Poisoning (CFP) and the phenomenon of Harmful Algal Bloom (HABs) caused by toxic benthic dinoflagellates are one of the ecological or environmental disasters that can threaten human health in coastal areas of Indonesia, such as in the Gili Matra Aquatic Tourism Park (ATP) area which consists of three islands, namely Gili Meno, Air, and Trawangan. ATP Gili Matra is a center for marine tourism and conservation areas in the West Nusa Tenggara region which is known to be under pressure due to human activities from tourism and fisheries activities that have a negative impact on coastal ecosystems, especially coral reefs. This condition can increase the abundance of toxic benthic dinoflagellate communities that have the potential to cause CFP and HABs in ATP Gili Matra. For this reason, mitigation efforts are needed so the risk of CFP and HABs ecological disasters in the future which can not only cause damage to the ATP Gili Matra aquatic ecosystem, but also significant economic losses, does not occur. According to economic calculations by experts, the economic value of tourism activities in ATP Gili Matra reaches IDR 26.86 trillion per year. One of the efforts to mitigate the ecological disaster of CFP and HABs is to understand the condition of the aquatic environment in ATP Gili Matra during the rainy season. Based on the survey results, it is known that the biophysical and chemical conditions of the aquatic environment during the rainy season in December 2022 and March 2024 are in very good condition with the level of eutrophication as an indicator of the quality of the aquatic environment at the ultraoligotrophic level with a TSI (Trophic State Index) score of 12.9-19.4 (<30) which indicates that water fertility is very low, the water is clear, the concentration of dissolved oxygen is high throughout the year and reaches the hypolimnion zone.
Comparative Morphometric Analysis of a Salinity-Tolerant Nile Tilapia (Oreochromis niloticus) Local Strain (Salina) and Its Parental Strains Bawono, Yohanes Pamungkas; Dewi, Kiki Mariya; Romadhona, Ekky Ilham; Widantara, Handang; Sujatmiko, Wisnu; Aliah, Ratu Siti; Sutanti, Sutanti; Larassagita, Annisa Fitri; Firmansyah, Muhamad Kholik; Megawati, Novi; Aslia, Aslia; Ardiansyah, Arif Rahmat; Chaidir, Iding; Yaniharto, Dedy
Jurnal Medik Veteriner Vol. 8 No. 2 (2025): October
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jmv.vol8.iss2.2025.424-444

Abstract

This study focuses on the morphology of the Nile tilapia local strain (Salina), a salinity-tolerant tilapia hybrid strain developed by crossbreeding between female Nile tilapia Red NIFI with male Nile tilapia Sultana. The research aimed to analyse the morphometric characteristics of the Salina strain to understand species adaptation to suboptimal environmental conditions compared with the parental groups. A total of 60 Nile tilapia fish, ten female and ten male samples from each strain (Salina, Sultana, and red NIFI), were measured for their total length (TL), standard length (SL), head length (HL), body width (WID), dorsal fin length (DL), caudal fin length (CL), pectoral fin length (PL), caudal peduncle depth (CPD), eye diameter (ED), snout length (SNL), and body weight (BW). Each measurement parameter was then normalized by comparing it with the standard length (SL). The data were analysed using MS Excel 2019 and R v4.5.1 for all statistical analysis including MANOVA, Canonical Variance Analysis, Principal Component Analysis, and Hierarchical Clustering Analysis. Condition factor (K) and length-weight relationship (LWR) were calculated to investigate growth conditions and allometric growth patterns, respectively. Based on the findings, the six tilapia populations exhibit overlapping morphological traits, except for female Salina with slight differences in morphological variations. This implies its potential unique traits acquired from crossbreeding between two different strains. Meanwhile, male Salina showed morphometric traits closely aligned with its male parent, the Sultana strain. The condition factor across all populations indicates favourable growth conditions, although the negative allometric growth pattern suggests that length increases more rapidly than body weight, implying an adaptive trade-off in suboptimal environments.
Co-Authors . Wahidah Agung Riyadi Alimuddin Amarullah, M. Husni Amarullah, M. Husni Ardiansyah, Arif Rahmat Arief Rachman Aslia, Aslia Bawono, Yohanes Pamungkas Chaidir, Iding dedy yaniharto Dewi, Kiki Mariya Dian Hardianto Dinar Tri Soelistyowati Diswandi Estu Nugroho Faisal Hamzah Farman, Aditia Firmansyah, Muhamad Kholik Garno, Yudhi Soetrisno Gloria Ika Satriani Haryanti Hilman Ahyadi Ihsan, Iif Miftahul ISKANDAR Joko Prayitno Susanto K. Sumantadinata Larassagita, Annisa Fitri Makosim, Syahril Megawati, Novi Meirinawati, Hanny Muhami Nurul Fitriya O. Carman Rahman Riardi Pratista Dewa, Riardi Pratista Romadhona, Ekky Ilham Sachoemar, Suhendar I. Sachoemar, Suhendar I. Sachoemar, Suhendar Indrakusmaya Setiarti Sukotjo Shinta Leonita Suhendar I Sachoemar Sujatmiko, Wisnu sutanti sutanti Tatag Budiardi Teguh Prayogo Widantara, Handang Yuliadi Zamroni