Zeitschriftenartikel: „Indonesian Primers“

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Arsyad, Mirza Arsiaty, Siti Halimah Larekeng, I. Iswanto, Muhammad Restu, Yuni Fitri Cahyaningsih und Michely Jauwdy Stevic. „Genetic Diversity Hopea celebica an Indonesian endemic species by ISSR Marker“. Agrotech Journal 7, Nr. 1 (29.07.2022): 7–17. http://dx.doi.org/10.31327/atj.v7i1.1737.

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Indonesia is a mega-diversity country with numerous endemic plants distributed throughout its regions. An Indonesias’ island with the unique and the highest endemic plant species due to being located in the Wallace area is Sulawesi Island. Hopea celebica, an endemic species to Sulawesi Island, is currently categorized as endangered by IUCN. Here, we selected the ISSR primers suitable for the genetic study of H. celebica from Luwu and Konawe provenances and investigated their genetic diversity. Ten ISSR primers were employed in primer screening, and fifty H. celebicaindividuals were genetically analyzed for their genetic diversity. The selected ISSR primers for genetic diversity analysis were UBC 810, UBC 813, UBC 814, UBC 820, UBC 822, UBC 823, and UBC 827. The evaluated H. celebica individuals have high genetic diversity, and this information will be beneficial for designing H. celebica breeding and conservation strategies

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Saadah, Imas Rita, Shinta Hartanto, Juniarti P. Sahat und Rinda Kirana. „Selection of potato molecular markers of Granola L. variety“. IOP Conference Series: Earth and Environmental Science 1172, Nr. 1 (01.05.2023): 012020. http://dx.doi.org/10.1088/1755-1315/1172/1/012020.

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Abstract Granola L. is one of potato variety that is very popular in Indonesia and is currently difficult to replace by other varieties. One of the efforts to maintain the genetic purity of the Granola L. variety can be done through biotechnology technique using molecular markers. This research aimed to obtain molecular markers for the Granola L variety. The selection of molecular markers was carried out at the Molecular Biology Laboratory and screenhouse of Indonesian Vegetable Research Institute (IVEGRI) from March to October 2020. The treatments consisted of DNA of Granola L variety from Source Seed Management Unit (UPBS) - IVEGRI, 8 DNA genotypes/germplasm collections which were assumed to be Granola or has a Granola background (Granola BPBK, GM-05, G2, G8, G-771, G-772, GC21, Papita), and 2 DNA genotypes that do not have Granola background (non-Granola) namely Spudi and Amabil varieties. The molecular markers used in this study were 17 SSR primers (Simple Sequence Repeats) from Indonesian Agricultural Genome Center. The results showed that 11 primers were monomorphic and 6 primers were polymorphic. These polymorphic primers still cannot specifically distinguish between Granola L. and non-Granola L. varieties. There is one primer that can distinguish Granola and non-Granola in terms of the band size formed. Further research is needed to find molecular markers that can distinguish Granola L from varieties/genotypes/germplasm collections that are assumed to be Granola L. or having the Granola L. genetic background.

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Devy, Lukita, Indah Anita-Sari, Tengku Imam Saputra, Agung Wahyu Susilo, Ade Wachjar und Sobir. „Identification of Molecular Marker Based on MYB Transcription Factor for the Selection of Indonesian Fine Cacao (Theobroma cacao L.)“. Pelita Perkebunan (a Coffee and Cocoa Research Journal) 34, Nr. 2 (31.08.2018): 59–68. http://dx.doi.org/10.22302/iccri.jur.pelitaperkebunan.v34i2.314.

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Indonesia is the third largest cacao (Theobroma cacao L.) producer in the world and also well-known for its fine cacao varieties (Java fine-flavor cacao). Indonesian fine cacao breeding program will be accelerated by early detection of its specific trait through the use of molecular marker. One of the traits thatcould differentiate fine and bulk cacao, in this case Criollo and Forastero, respectively, is the pod color. Previous research reported that MYB transcription factor gene regulated cacao pod color and was able to differentiate Criollo from Forastero. The gene involved in the control of plant-specific processes including primary and secondary metabolism, cell fate and identity, developmental processes and responses to biotic and abiotic stresses. This research aimed to identify the diversity of Indonesian fine and bulk cacao based on MYB nucleotide sequence fragments. Identification of the MYB nucleotide sequence was conducted by DNA isolation from cacao leaves and specific primer design based on two cacao MYB transcription factor ene accessions. These primers were used to evaluate the diversity of three Indonesian fine cacao (DRC 16, PNT 16, and ICCRI 01) and two bulk cacao (PA 191 and ICCRI 03) clones. The cluster analysis showed that this specific primer is similar to other MYB gene accessions in Malvaceae family (Theobroma, Herrania, Gossypium). It is also able to differentiate bulk and fine cacao in accordance to their pedigree. The primer developed in this study could be used for further analysis of Indonesian fine cacao molecular marker.

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Megawati, Novi, Alimuddin und Ratu Siti Aliah. „Identification of sex linked molecular markers in Indonesian giant freshwater prawn Macrobrachium rosenbergii“. Jurnal Akuakultur Indonesia 20, Nr. 1 (23.06.2021): 93–100. http://dx.doi.org/10.19027/jai.20.1.93-100.

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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

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Darli Kyaw Zaw, Nwet, Putu Angga Wiradana, Sin War Naw, Aondohemba Samuel Nege, Mochammad Amin Alamsjah, Rizhar Eman Karunia Akbar und Fahror Rosi. „First Report on Molecular Identification of Caulerpa Green Algae from Mandangin Island Indonesia Using Partial 18SrRNA Genes“. Journal of Aquaculture and Fish Health 9, Nr. 3 (28.08.2020): 252. http://dx.doi.org/10.20473/jafh.v9i3.19255.

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Caulerpa is one of the seaweed that grows naturally in Indonesian waters such as those in Mandangin Island. This study aimed to identify Caulerpa sp. based on molecular analysis using certain genetic markers. This research is expected to provide information on the identification of macroalgae from Indonesia waters, especially Mandangin Island, Madura with the use of molecular analysis based on 18SrRNA primers. The two green seaweed samples from the Caulerpa genus in this study were successfully analyzed using 18SrRNA primers. The BLAST results of samples 1and 2 are related to Caulerpa taxifolia 18SrRNA, but in the phylogenetic tree result, Sample 1 was more closely related to Caulerpa sertularioides f. longipes. 18SrRNA primers have been used for molecular identification of green seaweed from Mandangin for the first time and this shows that barcode markers can be used for molecular identification of seaweed, specifically Caulerpa in the waters of Mandangin Island, Indonesia.

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Suprapto, Rommy, I. Gusti Ngurah Permana, Haryanti, Ahmad Muzaki, Gunawan, Sari Budi Moria Sembiring und Imron. „Genetic variation of Barramundi (Lates calcarifer Bloch) from Indonesian and Australian populations using Simple Sequence Repeats (SSR)“. E3S Web of Conferences 442 (2023): 02033. http://dx.doi.org/10.1051/e3sconf/202344202033.

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Genetic profiles of broodstock are crucial to enhance a successful selective breeding program in barramundi aquaculture. However, there is currently a lack of information on the genetic variation of the barramundi broodstock population. The study aimed to examine DNA microsatellite characteristics of barramundi from two different wild populations, i.e., Indonesian and Australian waters. In this study, a total of 30 fish were sampled and analyzed from the two localities using six microsatellite primers (LcaM21F, LcaM27F, LcaM32, LcaM35F, LcaM36, and LcaM37). The observation on body weight of 9 months old barramundi showed that broodstock from Australia and Indonesia were 820.25 g and 786.59 g, respectively. Generally, private alleles and the heterozygosity numbers of the Indonesian population were higher than the Australian population. The present study suggests a different genetic profile between the Australian and Indonesian barramundi populations.

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Nabila, Tsania Taskia, Ata Rofita Wasiati, Afif Pranaya Jati und Annisa Khumaira. „The design of Indonesian SARS-CoV-2 primers based on phylogenomic analysis of their clades“. Indonesian Journal of Biotechnology 27, Nr. 1 (29.03.2022): 19. http://dx.doi.org/10.22146/ijbiotech.66854.

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Molecular detection needs to be augmented for COVID‐19 detection in Indonesia using the PCR method with primer‐based gene analysis. This is necessary because the RNA of the SARS‐CoV‐2 virus, the causative infectious agent of the pandemic, has been mutated. Therefore, this study aimed to develop a primer design for determining SARS‐CoV‐2 clades in Indonesia using phylogenomic analysis. Data were obtained from 38 GISAID (Global Initiative on Sharing All Influenza Data) viruses and the relationships were analyzed using maximum likelihood (ML) phylogenomic analysis with a substitution model of generalized time‐reversible (GTR) to construct the tree topology. The results showed that the five types of SARS‐CoVs‐2 clades in Indonesia were L, G, GH, GR, and O. It also indicated that the GH region had the highest rate of clade at 50%, with the S clade affecting its formation. Furthermore, the genome sequences of the GH type used to design its primer were based on three genes, namely RdRp, S, and N. The RdRp and N genes were found to be conserved and hardy mutants, while the S gene occurred repeatedly. Several previous studies have stated that the designed primers produced missense mutations compared to another in silico. Therefore, three sets of primers were achieved from the GC contents and clamps, Tm range, and structural secondary indicator standards.

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Imron, Imron, Agung Asrori, Khotibul Umam, Otong Zenal Arifin und Dessy Nurul Astuti. „Cross-Species Amplification and Variability of Microsatellite DNA Markers in Domesticated Indonesian Mahseer; A Case Study with Tor soro, Tor douronensis and their Interspecific Hybrids“. HAYATI Journal of Biosciences 29, Nr. 3 (25.03.2022): 409–16. http://dx.doi.org/10.4308/hjb.29.3.409-416.

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Indonesian mahseer (Tor spp.) are freshwater species of high economic, cultural, and conservatory values. Owing to their high values and environmental degradation, the population of Tor fish gradually decreased, and domestication efforts have been made to conserve the population. This study was aimed to assess the cross-species amplification and microsatellite genetic diversity in Indonesian mahseer Tor soro (SS), Tor douronensis (DD), and their interspecific hybrids using primers developed for Tor putitora. Eleven primer sets were used to test for amplifiability and screen genetic diversity in 40 progenies derived from those three groups. Results showed that seven primer sets (64%) successfully amplified loci. Genetic screening using the three most consistently amplifying primers showed that the number of alleles in the three populations was low, ranging from 2 to 5 alleles. The observed heterozygosity (HO) was high ranging from 0.650 to 0.789, and the fixation index (FIS) was negative, indicating heterozygosity excess. In line with other parameters, the P-values of the HW parameter of several loci-population combinations were significantly departed from equilibrium (P <0.05). A few private alleles were observed in parental line DD and the hybrids. Overall, the cross-species primers developed from T. putitora were able to amplify loci in T. soro, T. douronensis and their hybrids and genetic diversity in the hybrid population was slightly higher than those in parental lines. Possible factors driving the phenomena and practical implications of these findings on the conservation measures are discussed.

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Dewi, Yasinta, und Hari Purwanto. „Major Royal Jelly Protein 2 (mrjp2) Gene Detection in Apis dorsata Fabricius, 1793, Apis dorsata binghami Cockerell, 1906, Apis florea Fabricius, 1787, and Apis nigrocincta Smith, 1860“. Journal of Tropical Biodiversity and Biotechnology 9, Nr. 2 (05.04.2024): 85987. http://dx.doi.org/10.22146/jtbb.85987.

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Indonesian people’s interest in honey, the product from honey bees, is quite high. It caused many cases of honey fraud such as mislabelling the entomological origin of honey. The Major Royal Jelly Protein 2 (mrjp2) gene, which encodes MRJP, can be used to determine the entomological origin of honey. The mrjp2 gene, for example, can be detected in honey from A. mellifera and A. cerana using species-specific primers for A. mellifera (MF-MR) and A. cerana (CF-CR). This study aims to detect the mrjp2 gene in several honey bee species native to Indonesia, namely A. dorsata, A. dorsata binghami, A. florea, A. nigrocincta, A. mellifera, and A. cerana as well as analyse the feasibility of MF-MR and CF-CR primers in determining the entomological origin of honey. The results showed that the MF-MR primers can amplify the DNA of A. dorsata binghami, A. florea, and A. mellifera, while CF-CR primers can amplify the DNA of both A. nigrocincta and A. cerana. The amplicons were subsequently sequenced. The phylogenetic tree and the genetic distance showed that there were differences and variation between each species of honey bee samples with the honey bee database. The data obtained from this research indicated that both primers could not determine the entomological origin of honey directly up to species level. The species level determination will only be possible using sequences information. However, in certain situations, the MF-MR and CF-CR primers were able to differentiate the honey bee species by including the information of the geographical origin of honey sample and the distribution area of each species of honey bees in Indonesia.

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Hidayati, Dewi Noor, Eko Agus Srihanto, Tri Untari, Michael Haryadi Wibowo, Koichi Akiyama und Widya Asmara. „The establishment of PCR amplification, cloning, and sequencing of bovine herpesvirus 1 (BHV-1) glycoprotein D gene isolated in Indonesia“. Indonesian Journal of Biotechnology 24, Nr. 1 (18.06.2019): 34. http://dx.doi.org/10.22146/ijbiotech.44298.

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Considering the increasing incidence of infectious bovine rhinotracheitis (IBR) in Indonesia, it was necessary to conduct a more in-depth study of bovine herpesvirus-1 (BHV-1) as the causative agent of IBR disease. Previous research reports indicate that the BHV-1 subtypes found in Indonesia are subtype 1.1. Currently, IBR field case detection in Indonesia still uses the serological method (ELISA), which has the potential to give false positive results and cannot explain the virus subtype. Other detection methods, such as viral isolation, take longer and require adequate resources. This study aimed to determine the BHV-1 subtypes of Indonesian isolates using molecular techniques. Nested PCR using two pairs of primers was successfully used to amplify the glycoprotein D (gD) gene. The gD gene fragment was cloned into the pGEM-T plasmid. Analysis of the gD gene sequence was subsequently carried out to determine the BHV-1 character of the Indonesian isolates. The results indicated that the isolates were different from the previous isolates, and had similarities (100%) with subtype 1.2 strain SP1777 and SM023.

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Laurent, Danny, Nesti F. Sianipar, Chelen _, Listiarini _ und Ariandana Wantho. „Analysis of Genetic Diversity of Indonesia Rodent Tuber (Typhonium flagelliforme Lodd.) Cultivars Based on RAPD Marker“. KnE Life Sciences 2, Nr. 1 (20.09.2015): 139. http://dx.doi.org/10.18502/kls.v2i1.133.

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Rodent tuber (Typhonium flagelliforme Lodd.) is a plant from Araceae family. The plant has high medical potential as anti-cancer agent. The information regarding Indonesian rodent tuber’s genetic diversity is not available yet. Genetic information is very important for the development of rodent tuber as medicinal plant. In this research, genetic diversity and genetic distance of three Indonesian rodent tuber’s cultivars, from Bogor, Pekalongan, and Medan, were analyzed by using RAPD molecular markers. The data obtained was analyzed by NTsys software. Out of 16 primers used in the study, the 12 primers were found to be polymorphic. There were 83 bands of DNA obtained and 31 of them were polymorphic. Dendogram analysis of the three rodent tuber cultivars showed that these cultivars were clustered into two clusters. The first cluster consists of rodent tuber Bogor and Medan. The second cluster consists of rodent tuber Pekalongan. The coefficient of similarity ranged from 0.81 to 0.87. The highest coefficient of similarity was 0.87, which was detected between rodent tuber Pekalongan and Medan. The lowest coefficient of similarity was 0.81, which was detected between rodent tuber Bogor and Pekalongan. Among these three cultivars of rodent tuber, cultivar Bogor was exclusively different. Keywords: Indonesia-rodent tuber, genetic diversity, RAPD-marker

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Widayanti, Rini, Ken Ayik Kusumaastuti, Joana Martha Novi, Fadila Khairuna Adani, Catrine Relia Patrecia Gultom, Ayuning Devina Prastiti, Herjuno Ari Nugroho und Suhendra Pakpahan. „Genetic variation and phylogenetic analysis of Indonesian indigenous catfish (baung fish) based on mitochondrial 12S rRNA gene“. March-2021 14, Nr. 3 (24.03.2021): 751–57. http://dx.doi.org/10.14202/vetworld.2021.751-757.

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Background and Aim: Baung fish is an essential commodity in Indonesia; however, few studies have explored the genetic diversity of Indonesian catfish. Thus, this study aimed to analyze the genetic variation and phylogenetic relationships among Indonesian catfish based on the mitochondrial 12S ribosomal RNA (rRNA) gene. Materials and Methods: In total, 28 catfish were collected from nine rivers in seven provinces and from the Indian Ocean. Catfish genomes were obtained from epaxial and hepaxial muscle samples. The mitochondrial 12S rRNA gene was amplified by polymerase chain reaction using a pair of primers (Baung12SF and Baung12SR). The 12S rRNA sequences were analyzed using MEGA X to determine genetic variation and phylogenetic relationships. Results: In total, 178 variation sites in the 12S rRNA gene were substituted among Indonesian catfish. The genetic distance between all Indonesian catfish samples was 0.1-16.0%. The closest genetic distance was between MP and PM catfish, whereas the farthest genetic distances were between BF and EM and PD and EM. For the entire population, based on mean diversity calculations, the number of base substitutions per site was 0.08. Conclusion: Indonesian catfish were divided into four clades based on the 12S rRNA gene. The catfish MP, KR, PM, MS, BB, and KS were grouped with Hemibagrus nemurus, the catfish EM was grouped with Mystus vittatus, the catfish BSBJ was grouped with Pangasius pangasius, and the catfish PD and BF were grouped with Netuma thalassina.

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Hafzari, Rini, Tia Setiawati, Budi Irawan und Joko Kusmoro. „Evaluation of RAPD markers for molecular identification of five bamboo genera from Indonesia“. Folia Forestalia Polonica 61, Nr. 4 (01.12.2019): 255–66. http://dx.doi.org/10.2478/ffp-2019-0025.

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Abstract Conservation of bamboos for future exploitation as fuel, fibre and as an ingredient for cosmetics depends on knowledge of its natural genetic variation. The study of molecular genetic diversity in bamboos will provide important information for its conservation. This article reports on the genetic diversity in 25 species representing five genera of bamboos found in Indonesia using Random Amplified Polymorphic DNA (RAPD) molecular markers. Out of 40 primers, 24 primers produced 1107 total bands and 86.21% of polymorphic bands across the 25 species. Sixteen bands were uniquely found in one species only and their presence or absence helped to define nine bamboo species. RAPD band sizes ranged from 162 to 2247 base pairs. A dendrogram based on the similarity coefficient of Dice divided the bamboo species into three big clusters. In conclusion, RAPD can capture the diversity among five different bamboo genera and has a great potential to be used in the study of genetic diversity in Indonesian bamboos.

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Slamet, Slamet, Nonon Saribanon, Saptowo Jumali Pardal, Tatang Mitra Setia, Wening Enggarini und Reflinur Reflinur. „Determination of The Parents Based on Molecular Analysis for Soybean Lines Development“. JURNAL SAINS NATURAL 12, Nr. 3 (30.07.2022): 112. http://dx.doi.org/10.31938/jsn.v12i3.391.

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Soybean is the third most important food commodity in Indonesia, which is a cheap source of protein and rich in different nutritional contents for humans. This study aimed to analyze the four genotypes of the crossing parents using SSR primers and select one SSR polymorphic primer to confirm the F1 generation alleles compared to their parents. The research was conducted in the laboratory and greenhouse of the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD). The research activities included a polymorphic primers survey, population formation, and confirmation of crossing populations using one polymorphic primer. A total of 20 SSR primers were used to amplify the DNA of the four crossing parents (Biosoy 1, Biosoy 2, Demas, and Tanggamus). The results of the polymorphic SSR survey showed that 6 SSR primers could distinguish the combination of Biosoy 2 vs Demas parents, then 7 SSR primers could distinguish the combination of Biosoy 1 vs Tanggamus and Biosoy 2 vs Tanggamus parents. Satt 406 polymorphic primer was chosen to analyze F1 hybrid lines of three crossings. Based on phenotypic observation, two individuals were suspected to be hybrid lines. Molecular analysis using Satt 406 showed that alleles from male parents were not found in 16 F1 individuals from the three crossings. Selection using molecular markers such as Satt 406 polymorphic SSR can help breeders screen heterozygous populations in F1 generations to check successful crossings.Keywords: biosoy 1; biosoy 2; Demas; Tanggamus; Al tolerance; SSR markers ABSTRAKPenentuan Tetua Berbasis Analisis Molekuler Untuk Pembentukan Galur KedelaiKedelai merupakan komoditas pangan penting ketiga di Indonesia yang dimanfaatkan sebagai sumber protein yang murah dan kaya berbagai kandungan gizi bagi manusia. Tujuan penelitian ini adalah untuk untuk menganalisis 4 genotip tetua persilangan menggunakan primer SSR dan memilih satu primer polimorfik SSR untuk mengonfirmasi alel-alel generasi F1 dibandingkan dengan para tetuanya. Penelitian dilakukan di laboratorium dan rumah kaca Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian (BB Biogen). Kegiatan penelitian terdiri dari survei primer polimorfik, pembentukan populasi, dan konfirmasi populasi persilangan menggunakan satu primer polimorfik. Sebanyak 20 primer SSR digunakan untuk mengamplifikasi DNA dari empat tetua persilangan kedelai (Biosoy 1, Biosoy 2, Demas, dan Tanggamus). Hasil survei polimorfisme SSR menunjukkan bahwa 6 primer SSR dapat membedakan kombinasi tetua Biosoy 2 vs Demas, serta 7 primer SSR dapat membedakan Biosoy 1 vs Tanggamus dan Biosoy 2 vs Tanggamus. Primer polimorfik Satt 406 terpilih untuk menganalisis hibrida F1 dari tiga persilangan. Berdasarkan hasil pengamatan fenotipik, diperoleh 2 nomor individu F1 yang diduga sebagai generasi hibrida. Analisis molekuler menggunakan Satt 406 menunjukkan bahwa alel-alel dari tetua jantan tidak ditemukan pada 16 nomor tanaman dari 3 populasi persilangan. Seleksi menggunakan marka molekuler seperti SSR polimorfik Satt 406 membantu pemulia dalam menskrining populasi heterozigot pada generasi F1 untuk mengetahui keberhasilan persilangan.Kata kunci: biosoy 1, biosoy 2, Demas, Tanggamus, toleransi Al, marka SSR

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Artanto, Yohanes Kristiawan, Slamet Budi Prayitno, Sarjito Sarjito, Desrina Desrina und Alfabetian Harjuna Condro Haditomo. „Molecular Characteristics of Indonesian Isolate Enterocytozoon hepatopenaei Based on Sequence Analysis of 18S rRNA Genes“. Omni-Akuatika 15, Nr. 1 (03.07.2019): 93. http://dx.doi.org/10.20884/1.oa.2019.15.1.694.

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ABSTRACT Enterocytozoon hepatopenaei (EHP) infection have been reported as an obstacle of whiteleg shrimp (Penaeus vannamei) culture in Indonesia. However, understanding of the molecular characteristics of EHP species in Indonesia is not widely known. The aims of this study were to determine the identity and characters of DNA, and their phylogeny of EHP species from several different locations in Indonesia with specific references to 18S rRNA gene. The EHPs were collected from cultured P.vannamei from Lampung, Pangandaran, Sidoarjo, Banyuwangi, Probolinggo, Blitar, Makassar, and Lombok. Thirteen (13) samples were randomly selected to explore their gene characters through 18S rRNA gene sequencing. The primers used were EHP_F and EHP_1R. Parameter observed were DNA sequencing, nucleotide sequence homology with related available genes in the Gen Bank database, multiple sequence alignment, and reconstruction of genetic relationship trees. DNA sequence homology analysis showed that all samples had 99.89-100% similarity to Indian Enterocytozoon hepatopenaei (Accession Number MH259890.1 and MH260592.1). The alignment results illustrated that all EHP sequences of Indonesian isolates were 100% identical each other. The phylogenetic tree topology provided information that all sample accessions were in the same clade and spread evenly. The conclusion were that the Indonesian EHP species were identical (100%) and it could be said that they were genetically homogeneous. Keywords: Enterocytozoon hepatopenaei, 18S rRNA gene, Indonesia.

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Putra, Ivan Permana, Mada Triandala Sibero, Saipul Sihotang, Lilis Supratman, Rudy Hermawan und Oktan Dwi Nurhayat. „An Introduction to Indonesian Wild Shiitake“. HAYATI Journal of Biosciences 30, Nr. 6 (21.08.2023): 1132–38. http://dx.doi.org/10.4308/hjb.30.6.1132-1138.

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Pegler suggested that shiitake comprises three morphological species: Lentinula edodes (continental and northeast Asia), L. lateritia (tropical Asia and Australasia), and L. novae-zelandiae (New Zealand). The current study reported for the first time the occurrence of L. lateritia (Berk.) Pegler in Indonesia. During a fungus foray in Kerinci (Jambi, Sumatra, Indonesia) in 2022 and 2023 by the Indonesian mushroom hunter community, some basidiomata of Lentinula were obtained. At a glance, our specimens resembled L. edodes. The current study aims to justify the taxonomical position of our specimens based on morphological and molecular data. The fresh basidiomata were used for morphological and molecular analyses. The molecular work was done using ITS 4/5 Primers for phylogenetic analysis of rDNA-ITS region. Morphologically, the uniformly reddish brown, smooth, and glabrous of pileus confirmed our specimens as L. lateritia. In addition, the absence of a range of colors and squamules pileus distinguished L. lateritia BO24628 form L. edodes, while the formation of florets cheilocystidia in L. madagasikarensis was the distinctive character of our specimens. The BLAST result revealed that our specimen has high similarity (99-100%) with L. lateritia and L. edodes as the top hits. The phylogenetic tree (RAxML) nested our specimens in the L. lateria clade and is closely related to one specimen from Papua New Guenia (PNG) (BS 98%). In addition, L. lateritia BO24628 has a sister clade of the specimen from PNG and Australia. Moreover, we provide the herbarium collection of wild L. lateritia in Indonesia.

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Prihandini, P. W., A. P. Z. N. L. Sari, Y. N. Anggraeni, S. Irmawanti und B. Tiesnamurti. „The ATP1A1 Gene Polymorphisms in Indonesian Beef Cattle“. IOP Conference Series: Earth and Environmental Science 1114, Nr. 1 (01.12.2022): 012076. http://dx.doi.org/10.1088/1755-1315/1114/1/012076.

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Abstract In this research, the direct sequencing method was used to identify the polymorphism and genetic diversity of the ATP1A1 gene in Indonesian beef cattle. The study used five breeds of local beef cattle with a total of 60 DNA samples (POGASI = 20, Jabres = 10, Bali = 10, Galekan = 10, and Madura = 10). The amplification of the ATP1A1 gene was using one set of primers (F = 5′- AGG GGT AGC CAG AGT TCC TA – 3′ and R = 5′ – CCC AAA GGT CAC GTG CTT TT – 3′). The result showed 6 SNPs in the APT1A1 gene, namely SNPs g.17293G/A, g.17356C/T, g.17359G/A, g.17541A/G, g.17585 A/G, and g. 17682C/T. Three SNPs were located in coding sequence nine, and the other SNPs were in intron 9 of the ATP1A1 gene. Based on the total population, the Chi-square test indicated that only two polymorphic loci (.17585 A/G and g. 17682C/T) fitted Hardy-Weinberg equilibrium (χ2<5.99). In conclusion, the polymorphic loci of the ATP1A1 gene can be used for genetic diversity and further association study to anti-heat stress traits of Indonesian beef cattle.

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Prihatini, Riry, Tri Budiyanti und Noflindawati Noflindawati. „GENETIC VARIABILITY OF INDONESIAN PAPAYA ACCESSIONS AS REVEALED BY RANDOM AMPLIFIED POLYMORPHIC DNA AND MORPHOLOGICAL CHARACTERIZATION“. Indonesian Journal of Agricultural Science 20, Nr. 1 (15.06.2019): 1. http://dx.doi.org/10.21082/ijas.v20n1.2019.p1-8.

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Diverse papaya (Carica sp.) accessions are found in many regions in Indonesia, but their genetic diversity have not yet been studied. Random Amplified Polymorphic DNA (RAPD) is a simple yet accurate method that can be used to examine the genetic diversity of papaya. The study aimed to examine the genetic diversity of Indonesian papaya accessions using RAPD markers and morphological characters. The RAPD was applied on 23 papaya accessions using 30 primers. The appearing bands were further analyzed with the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principal Component Analysis (PCA). The molecular results were then compared to the fruit morphological data, including fruit shape, size, flesh color, texture, and flavor. The RAPD analysis revealed that the 23 papaya accessions clustered into six main clades with Dice-Sorensen coefficient similarity ranged from 0.71 to 0.98. The first group consisted of 11 accessions, including both the hybrids and local accessions. The second group consisted of eight accessions especially six Indonesian hybrids, a Mexican Hybrid and a Hawaiian hybrid. The other four groups had a single member namely Sicincin Panjang, Lokal Sumani, Cariso, and Carica. The molecular grouping, however, did not align with the fruit character grouping. Overall, it was implied that the Indonesian papaya accessions were genetically narrow, of which some accessions were closely related to Hawaiian and Mexican accessions. These results can be used as a reference on papaya crossbreeding program in Indonesia.

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Pambuko, Galih, Rebecca Vanessa und Sigit Prastowo. „Amplification of CHD-1 gene fragment in Z and W sex chromosomes of Cemani chicken using a different set of PCR primers“. IOP Conference Series: Earth and Environmental Science 1208, Nr. 1 (01.07.2023): 012058. http://dx.doi.org/10.1088/1755-1315/1208/1/012058.

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Abstract Cemani chicken is a local breed of Indonesian chicken known for its mystical appearance. Selecting sex earlier is essential for the breeding program to determine the population structure. Instead of using phenotype, sexing in birds can be done molecularly by employing the variation of the CHD-1 gene, which belongs to the Z chromosome. Five primers (pair), namely AVP2 and AVP8; CHD1F and CHD1R; AV1237L and AV1272H; CHDZ and CHDW, then AV2550F and AV2718R, were employed to amplify the CHD-1 gene in PCR reaction followed with electrophoresis analysis. Cemani chicken blood was collected from the Bracial vein, followed by DNA extraction. Two primers set, CHD1F and CHD1R, and AV2550F and AV2718R, were able to amplify the CHD-1 gene and distinguish the difference between male (ZZ) vs. female (ZW) chromosome by showing two clear DNA bands in the female source sample and one band in the male sample. Meanwhile, the AVP2 and AVP8, AV1237L, and AV1272H, only show one clear band in both female and male source samples, and no bands resulted from using CHDZ and CHDW primer. Two sets of primers were able to amplify the CHD-1 gene fragment using PCR and amplified for further molecular sex determination in Cemani chicken.

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ARISTYA, GANIES RIZA, RINA SRI KASIAMDARI, RACHMI SETYONINGRUM und BENING LARASATI. „Genetic variations of strawberry cultivars of Fragaria x ananassa and Fragaria vesca based on RAPD“. Biodiversitas Journal of Biological Diversity 20, Nr. 3 (02.03.2019): 770–75. http://dx.doi.org/10.13057/biodiv/d200322.

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Abstract. Aristya GR, Kasiamdari RS, Setyoningrum R, Larasati B. 2019. Genetic variations of strawberry cultivars of Fragaria x ananassa and Fragaria vesca based on RAPD. Biodiversitas 20: 770-775. In Indonesia, the increasing market demand for strawberries (Fragaria spp.) is not comparable to increased strawberry productivity. One of the efforts made to increase strawberry productivity with superior quality is plant breeding. The purpose of this research was to determine the genetic variation, lineage, and similarity index in some strawberry cultivars using molecular markers of Random Amplified Polymorphic DNA (RAPD). Eleven strawberry cultivar samples were taken from Indonesian Citrus and Subtropical Fruits Research Institute (Balitjestro), Batu City, East Java, Indonesia and Strawberry Agritourism in Banyuroto Village, Magelang District, Central Java, Indonesia. DNA isolation using modified CTAB buffer method. DNA amplification using PCR-RAPD method with 5 primers, namely UBC-516, UBC-594, OPA 10, OPA 16, and OPG 11. Strawberry lineage dendrogram construction was analyzed with clustering of Unweight Pair-Group Using Arithmetic Average (UPGMA) software Multi-Variate Statistical Average (MVSP). The research results showed that the 5 RAPD primers used in 11 strawberry cultivars produced 30 polymorphic DNA bands and 20 monomorphic DNA bands so it can be concluded that the genetic variation among 11 strawberry cultivars can be detected using RAPD molecular markers. The lineage of 11 strawberry cultivars that have the highest similarity index is found in Earlibrite and Rosalinda II cultivars of 98.85%.

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Wibowo, Sarwo Edi, Muhammad Anwar Djaelani und Hermin Pancasakti Kusumaningrum. „Pelacakan Gen Sitokrom Oksidase Sub Unit I (COI) DNA Mitokondria Itik Tegal (Anas domesticus) Menggunakan Primer Universal“. Bioma : Berkala Ilmiah Biologi 15, Nr. 1 (11.06.2013): 20. http://dx.doi.org/10.14710/bioma.15.1.20-26.

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Currently local ducks are generally quite difficult to find in a big farm in Inonesia, including Tegal ducks. Tegal ducks is one of the genetic resources native to Indonesia with it’s advantages in terms of high and large egg production. Conservation and development of local ducks have strived to maintain our existence of Indonesian livestock germplasm. If such information is not superior to native species exist, the opportunity to increase his lead further also getting smaller. Tracking the mitochondrial COI gene DNA of Tegal ducks may underlie the process of an organism's genetic characterization. Information about Tegal duck mitochondrial DNA has not been done. The information obtained can be used for optimization of duck products native to Indonesia both in physiological aspects, phylogeny and genetic engineering. The research method used in this research is tracking COI gene data from Gen Bank with the programs Clustal X and Genedoc. Tracking then continued using universal primers HCO and LCO. The results of the data followed up with the isolation and amplification of COI gene mitochondrial DNA as well as the optimization of PCR conditions. The results showed mitochondrial DNA COI gene Tegal ducks were amplified with primer LCO obtain DNA fragments of length less than 250 bp. Kata kunci: duck’s from Tegal, COI gene, mitochondrial DNA

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Prihatini, Riry, Noflindawati , und Tri Budiyanti. „Application of RAPD Markers on Sex Determination of Papaya (Carica papaya)“. Comm. Horticulturae Journal 1, Nr. 1 (04.10.2019): 1. http://dx.doi.org/10.29244/chj.1.1.1-5.

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Molecular sex determination of five varieties of Indonesian papaya were investigated using RAPD (Random Amplified Polymorphism DNA) markers. Overall, 12 of 14 primers produced polymorphic bands on either several or all tested varieties. The OPC04 and RAPD2 markers could be used determined sex types on all varieties, whereas others primers are only on certain varieties. The Tangkai Ungu variety can be differentiate by markers: OPA11, OPA14, OPC14, RAPD2, RAPD3, and RAPD5; the Lokal Sumani can be determine using markers: OPA01, OPA11, OPA14, OPC01, OPC04, RAPD2, RAPD3, RAPD5, and RAPD6; the Merah Delima could be determined using OPC04, OPN09, RAPD2, and RAPD5; the Dampit could be determined using OPC01, OPC04, RAPD2, and RAPD6; whereas the Sicincing Panjang could be determined using OPA04, OPA11, OPA14, OPC04, RAPD2, and RAPD3.

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DARYONO, BUDI SETIADI, APRILIA SUFI SUBIASTUTI, ARVITA FATMADANNI und DIAN SARTIKA. „Phenotypic and genetic stability of new Indonesian melon cultivar (Cucumis melo L. ‘Melonia’) based on ISSR markers“. Biodiversitas Journal of Biological Diversity 20, Nr. 4 (23.03.2019): 1069–75. http://dx.doi.org/10.13057/biodiv/d200419.

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Abstract. Daryono BS, Subiastuti AS, Fatmadanni A, Sartika D. 2019. Phenotypic and genetic stability of new Indonesian melon cultivar (Cucumis melo L. ‘Melonia’) based on ISSR markers. Biodiversitas 20: 1069-1075. Cucumis melo L. ‘Melonia’ was new Indonesian melon cultivars produced by segregation of Meloni cultivar. The Meloni cultivar has a yellowish-skinned color, orange flesh fruit, and sweet taste. The stability of phenotype and genotype characters of this new cultivars were assessed using 27 morphological traits and 4 ISSR primers, respectively. Phenotype characters in F2 and F3 populations have been stable on 25 of 27 morphological traits used, except in weight of seed cavity and color of skin fruit. The 4 ISSR markers were produced 41 fragments, contained 28 monomorphic DNA bands and 13 polymorphic DNA bands. All of DNA bands were scored and used for genetic similarity analysis using MVSP 3.1A Program. The highest genetic variation was produced by UBC-808 primer with a polymorphic percentage of 38.46%. All of ‘Melonia’ populations were clustered together with 100% similarity percentage. Compared to other cultivars, ‘Melonia’ had high similarity with ‘Meloni’ in 87.8%, meanwhile, ‘Melonia’ and Meloni cultivars had relationship with Melona at a similarity value of 70.7%.

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Rumiyati, Rumiyati, Rien Arini, Purwanto Purwanto und Abdul Rohman. „The employment of real-time polymerase chain reaction for analysis of canine meat in meatball products for halal authentication analysis“. Journal of Advanced Veterinary and Animal Research 11, Nr. 2 (2024): 247. http://dx.doi.org/10.5455/javar.2024.k770.

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Objective: Meatballs are a popular meat-based food consumed widely in Indonesian society. However, the issue of unethical substitution of halal meatballs with non-halal meats, particularly pork and canine meat (CM), has emerged. The existence of non-halal meats, including CM, in food products is prohibited in Islam, necessitating the development of reliable analytical techniques for their identification. In this study, we designed species-specific primers (SSPs) targeting the D-loop region of mitochondrial DNA for CM meatball product identification. Materials and Methods: The study was commenced by creating specific primers for canine DNA using Integrated DNA Technologies software and subsequently performing DNA isolation. The designed primers were then subjected to comprehensive evaluation using RT-PCR, including spec¬ification, linearity, limit of detection, efficiency, and repeatability. Results: The results indicated that the primer D-Loop 443 (forward: 5¢-GGG ACA TCT CGA TGG ACTA ATG-3’, reverse: 5’-GCG GTC ATA GAT GAG TGA TAG C-3’) designed and validated in silico using primer-basic local alignment search tool nucleotide (BLAST) program from NCBI accurately identified canine DNA when the optimal annealing temperature was set at 57.5oC. The real-time PCR technique utilizing the D-loop 443 primer exhibited the ability to amplify canine DNA down to a minimum quantity of 100 pg, with an efficiency value of 91.8%, a correlation coefficient (R) of 0.990, and a precision value (RSD) of 0.30%. Conclusion: The SSP-based RT-PCR method developed is a versatile and efficient tool for detect¬ing CM in meatballs. Its implementation helps maintain consumer trust and addresses concerns regarding the substitution of halal meats with non-halal alternatives.

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Suharjo, Radix, I. Gede Swibawa, Joko Prasetyo, Yuyun Fitriana, Yanuar Danaatmadja, Ari Budiawan, Sean Roberts, Nanin Noorhajati, Muhammad Amad und Marco Thines. „Peronosclerospora australiensis is a synonym of P. maydis, which is widespread on Sumatra, and distinct from the most prevalent Java maize downy mildew pathogen“. Mycological Progress 19, Nr. 11 (November 2020): 1309–15. http://dx.doi.org/10.1007/s11557-020-01628-x.

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Abstract This study was performed to identify Peronosclerospora species found in Indonesia based on sequence analysis of the cox2 gene. In addition, sequence data in total, 26 isolates of Peronosclerospora were investigated in this study. They were obtained from 7 provinces in Indonesia, namely Lampung, Jawa Timur, Jawa Barat, Sumatera Utara, Jawa Tengah, Yogyakarta, and Sulawesi Selatan. Sequence analysis of cox2 and phylogenetic inference were performed on all the 26 isolates. A set of primers developed in this study, PCOX2F and PCOX2R, was used for PCR amplification. Phylogenetic analyses showed that all the Indonesian isolates were divided into two groups. Group I contained 13 isolates; 9 isolates obtained from Lampung, 3 isolates from Sumatera Utara, and 1 isolate from Jawa Barat. Group II consisted of 13 isolates; 7 isolates from Jawa Timur, 2 isolates from Jawa Tengah, 1 isolate from Yogyakarta, and 3 isolates from Sulawesi Selatan. All the members of group I clustered with the ex-type sequence of P. australiensis. Meanwhile, all members of Group II formed the sister clade of isolates obtained from Timor-Leste and may represent P. maydis.

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Imron, Imron, Dadan Sunandar, Rini Susilowati, Rommy Suprapto und Ikhsan Khasani. „RANDOMLY AMPLIFIED POLYMORPHIC DNA (RAPD) FINGERPRINTING OF SIX INDONESIAN POPULATIONS OF GIANT FRESHWATER PRAWN, Macrobrachium rosenbergii“. Indonesian Aquaculture Journal 4, Nr. 2 (31.12.2009): 93. http://dx.doi.org/10.15578/iaj.4.2.2009.93-100.

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Indonesia is rich of giant fresh water prawn (GFP) germ plasms. Best utilization of these resources for the purpose of either aquaculture development or conservation of genetic resources requires some information on the structure and levels of their genetic diversity. This study was aimed to characterize those GFP genetic resources by applying RAPD genetic markers. Six Indonesian populations of GFP from Asahan, Barito, Ciasem, Ogan, GImacro and Papua were collected and analyzed for their genetic variation using five RAPD primers. The results showed the diversity within the populations, as revealed by the level of polymorphism, ranged from 29% to 76% while genetic divergence between populations as shown by genetic distance ranged from 0.04 to 0.50. In terms of genetic divergence, two genetically distinct groups of GFP, namely the Papua GFP in one group and the remaining five GFP populations in the other, were identified. The results also showed the presence of specific population markers that are useful for genetic identification of GFP populations. Implication of these finding with regard to breed development is discussed.

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Abdullah, Asadatun, Mala Nurilmala und Kinanti Permata Sitaresmi. „DNA Mini-Barcodes as A Molecular Marker for Various Hairtail Fish Products Traceability“. Jurnal Pengolahan Hasil Perikanan Indonesia 22, Nr. 1 (30.04.2019): 33. http://dx.doi.org/10.17844/jphpi.v22i1.25874.

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Hairtail fishery is an important fishery commodity with high economic value as export commodity. Authentication based on DNA mini-barcodes can be applied to overcome seafood fraud and to support Indonesian traceability system. This study was aimed to design species-specific primers of DNA minibarcodes and authentication of various processed hairtail fish products such as smoked, baked, fried, canned, and boiled. Analytical method applied PCR-based of cytochrome c oxidase 1 (COI) full length and mini-barcodes. Mini-barcode primer specific for hairtail (Trichiurus lepturus) successfully amplified DNA of processed hairtail fish. The BLAST analysis showed the samples were identified as Trichiurus sp. and T. lepturus with homology level of 91% to 100%. Phylogenetic analysis showed the processed sample (LC dan LD) were in the same group with T. lepturus.

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Yulianti, Farida, C. Martasari, NFN Karsinah und Tangguh Hartanto. „Variasi Genetik Jeruk Keprok SoE (Citrus reticulata Blanco) Hasil Radiasi Sinar Gamma Menggunakan Penanda ISSR“. Buletin Plasma Nutfah 16, Nr. 2 (10.10.2016): 134. http://dx.doi.org/10.21082/blpn.v16n2.2010.p134-139.

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Genetic Variation of Keprok SoE Mandarin (Citrus reticulata Blanco) Resulted from Gamma Iradiation Based on ISSR Markers. SoE mandarin is one of the best mandarin from Indonesia which has been chosen as one of mandarin for import substitution. The citrus quality could be improved through breeding program, one of this program was mutation breeding using gamma rays irradiation. The research was aimed to obtain information of SoE mandarin genetic variation derived from gamma rays irradiation using ISSR marker. The research was conducted at Breeding and Tissue Culture Laboratory of Indonesian Citrus and Subtropical Research Institute (ICISFRI) from May to September 2008. Five ISSR primers were used to amplify DNA samples. Matrix data was counted and dendrogram of samples was established using UPGMA and SAHN methods. The resulst showed that 3 of the primers indicated polymorphism. About 22 locus were amplified from 3 primers, 9 (40.9%) locus showed polymorphism. The genetic similarity of SoE mandarin derived from gamma rays irradiation were 73-100%. AbstrakJeruk keprok SoE merupakan salah satu jeruk keprok unggulan Indonesia untuk mensubstitusi jeruk impor. Kualitas jeruk dapat ditingkatkan melalui program pemuliaan, salah satunya adalah melalui pemuliaan mutasi dengan menggunakan sinar gamma. Tujuan penelitian ini adalah untuk mendapatkan informasi tentang variasi genetik jeruk keprok SoE hasil radiasi sinar gamma menggunakan penanda ISSR. Penelitian dilaksanakan di Laboratorium Pemuliaan dan Kultur Jaringan, Balai Penelitian Tanaman Jeruk dan Buah Subtropika (Balitjestro) pada bulan Mei-September 2008. Lima penanda ISSR digunakan untuk mengamplifikasi sampel DNA. Pengelompokan tanaman di dalam dendrogram dihitung menurut UPGMA menggunakan metode SAHN. Hasil penelitian menunjukkan bahwa tiga penanda mengindikasikan adanya polimorfisme. Dari 22 lokus yang terbentuk dari tiga penanda, sembilan lokus (40,9%) menunjukkan polimorfisme. Tingkat kesamaan genetik jeruk keprok SoE hasil radiasi sinar gamma berkisar antara 73-100%.

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Hidayatun, Nurul, Chaerani Chaerani und Dwinita Wikan Utami. „Sidik Jari DNA 88 Plasma Nutfah Ubi Jalar di Indonesia Berdasarkan Delapan Penanda SSR“. Jurnal AgroBiogen 7, Nr. 2 (01.10.2011): 119. http://dx.doi.org/10.21082/jbio.v7n2.2011.p119-127.

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DNA Fingerprinting of Indonesian 88 Sweet Potato Germplasm Based on Eight SSR Markers. Nurul Hidayatun, Chaerani, and Dwinita W. Utami. Indonesia possesses a great number of sweet potato varieties. Understanding the diversity and distribution of this genetic resource is essential for its management and future use. The objective of this study was to elaborate the molecular character as DNA finger print of Indonesian sweet potato germplasm. Eight fluorescent labeled SSR primers were used to amplify DNA of 88 sweet potato accessions consisting of improved varieties and landraces collected from 7 islands in Indonesia. The amplified products were detected using capillary electrophoresis method in CEQ Genetic Analysis System machine. A total of 135 alleles ranging from 8 to 36 alleles per locus with an average of 17 alleles were generated. Each accession had a unique microsatellite finger print marked by specific combination of 11 to 22 alleles in 8 SSR loci. Dendrogram generated by UPGMA based on simple matching coefficients produced 4 nonspecific groups at 80% similarity. The groups revealed the possibilities that the accessions were distributed from similar genetic resources.

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Sulaeman, Sulaeman, Andi Parenrengi, Emma Suryati und Rosmiati Rosmiati. „GENETIC, COLORATION, AND GROWTH PERFORMANCE OF TWO DIFFERENT VARIETIES OF Kappaphycus alvarezii“. Indonesian Aquaculture Journal 2, Nr. 1 (30.06.2007): 23. http://dx.doi.org/10.15578/iaj.2.1.2007.23-26.

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Two different colors (green and brown) of Kappaphycus alvarezii have been farmed in Indonesian waters for many years. This study aimed at comparing two ‘varieties’, i.e. green and brown, both genetically and morphologically. Samples for DNA analysis were collected from a farmer in Pinrang Regency, South Sulawesi. Five universal primers i.e. Ca-01, Ca-02, P-40, P-50, and DALRP were selected to obtain DNA genetic markers in differentiating the green and brown varieties. To compare coloration patterns during cultivation and the growth performance of both varieties, a field experiment was performed in a seaweed farming area in Pinrang Regency, during dry season of August-September 2004. The result of genetic assessment showed that the five selected primers revealed different RAPD banding pattern for both varieties. P-50 and DALRP primers demonstrated the greatest amplification in differentiating RAPD fragment between green and brown varieties. Fragment 900 bp and 1.300 bp were consistently generated in the green variety but were not amplified in the brown variety. The result of the field study confirmed that the coloration pattern of green and brown varieties was fixed; no interchange in color occurred during one crop cultivation.

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Cahyaningsih, Ria, Lindsey Jane Compton, Sri Rahayu, Joana Magos Brehm und Nigel Maxted. „DNA Barcoding Medicinal Plant Species from Indonesia“. Plants 11, Nr. 10 (21.05.2022): 1375. http://dx.doi.org/10.3390/plants11101375.

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Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use.

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Sooai, Christiane Marlene, Elsa Herdiana M und Supargiyono Supargiyono. „OPTIMAL CONDITION FOR MULTIPLEX POLYMERASE CHAIN REACTION (PCR) IN DETECTING ASCARIS LUMBRICOIDES, TRICHURIS TRICHIURA, AND NECATOR AMERICANUS IN PRESERVED STOOL“. Berkala Ilmiah Kedokteran Duta Wacana 5, Nr. 1 (19.08.2020): 34. http://dx.doi.org/10.21460/bikdw.v5i1.171.

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Background: Multiplex PCR examination is one of the molecular examination methodologies applied to detect soil-transmitted helminth (STH) infection. Optimization of the multiplex PCR method is a complex process, but it is necessary to obtain both a correct detection process and a satisfactory DNA product. Objective: To determine whether multiplex PCR can be optimized to diagnose STH from Indonesian isolates, and to find the optimal method for detection of A. lumbricoides, T. trichiura, and N. americanus infections in stool that have been stored for 3 years. Methods: A total of 15 samples were examined, and these samples were previously examined by using a microscopic method, then continued with optimization steps. Result: The optimal PCR mixture used primers targeting COI gene for A. lumbricoides, 18S rDNA for T. trichiura and ITS1 for N. americanus, 15 µl of Go Taq Green Master Mix, 5 µl of the 3 pairs of primers, 5 µl of DNA template and 4 µl of DdH2O, and the condition was 30 minutes of 950C denaturation, 30 second of 530C annealing and 1 minute of 720C extension, repeated for 35 cycles. Conclusion: Multiplex PCR can be optimized for STH detection from Indonesian isolates. The successful detection using the multiplex PCR method was influenced by sample preparation prior to DNA isolation, which includes several steps i.e. homogenization of samples using bead beaters and passing samples on liquid nitrogen rapidly.

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Widayanti, Rini, Richo Apriladi Bagas Pradana, Rony Marsyal Kunda und Suhendra Pakpahan. „Genetic characterization and phylogenetic study of Indonesian cuscuses from Maluku and Papua Island based on 16S rRNA gene“. November-2020 13, Nr. 11 (2020): 2319–25. http://dx.doi.org/10.14202/vetworld.2020.2319-2325.

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Background and Aim: Indonesian cuscuses are now becoming scarce because of the reduction of habitat and poaching. Further, molecular characterization of Indonesian cuscuses is still very lacking. This study aimed to determine genetic markers and phylogenetic relationships of Indonesian cuscuses based on 16S rRNA gene sequences. Materials and Methods: This study used 21 cuscuses caught from two provinces and 16 islands: 13 from Maluku and eight from Papua. Cuscus samples were taken by biopsy following ethics guidelines for animals. The genome isolation was done using gSYNC DNA Mini Kit (Geneaid Biotech Ltd., Taiwan). The 16S rRNA gene was amplified by primers (16SKUSAF and 16SKUSAR), and the polymerase chain reaction product obtained was 1875 base pair (bp). The analysis of genetic characterization and the phylogenetic relationship was performed using MEGA version X software (https://www. megasoftware.net/). Results: 16S rRNA gene sequencing attained 1598 bp for all samples. Based on the 16S rRNA nucleotide sequences, cuscuses from Papua and Maluku belong to the genus Phalanger and Spilocuscus. Phalanger spp. and Spilocuscus spp. from Papua can be distinguished from Phalanger and Spilocuscus from Maluku, except Spilocuscus from Ternate has a very close relationship with cuscus from Sentani, Papua. Conclusion: Indonesian cuscuses were derived into two clades based on 16S rRNA gene sequence, one group to genus Phalanger and another group to Spilocuscus.

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Dhiaurridho, Mohammad Ilham, Firmansyah Tristadika Prakosa, Firna Fauziatul Karimah, Salsabilla Ramadhana, Ine Febriantama, Thoriq Aldri Bramastya, Ahmad Pramono und Muhammad Cahyadi. „Analysis of CSN2 variants in Friesian Holstein cows and their association with milk protein allergy and production traits“. Livestock and Animal Research 20, Nr. 1 (24.03.2022): 20. http://dx.doi.org/10.20961/lar.v20i1.57596.

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Objective: The objective of this study was to analyze CSN2 variants in Indonesian Friesian Holstein (FH) cow and their association with milk protein allergy and production traits.Methods: Genomic DNA was extracted from bloods of twelve Indonesian FH cow. Exon 7 of the CSN2 was amplified using novel primer pair to produce 683 bp amplicon. The primers were 5’-ACCCCAATTTCTTAACCAAACCA-3’ as a forward primer and 5’-CATCAGAAGTTAAACAGCACAGT-3’ as a reverse primer. The PCR products were analyzed to determine the nucleotide sequence of CSN2 using Bioedit version 7.2.5. Moreover, Hardy-Weinberg equilibrium (HWE) was calculated and one-way analysis of variance (ANOVA) was conducted to associate between CSN2 variants and milk production traits.Results: Two polymorphisms, c.350A>C and c.516G>C, were identified in the CSN2 exon 7. Base substitution from adenine (A) to cytosine (C) of c.350A>C changed amino acid codon from histidine (CAU) to proline (CCU), and base substitution guanine (G) to cytosine (C) of c.516G>C changed amino acid codon from arginine (AGG) to serine (AGC). The CC genotype frequency for c.350A>C SNP was 33% and they were able to produce A2 CSN2 variant which is favorable for preventing lactose intolerance. In addition, there were no association between c.350 A>C and c.516 G>C SNP of the CSN2 with milk production traits.Conclusions: In conclusion, A1 and A2 variants of CSN2 were identified in Indonesian FH population and they did not associate with milk production in Indonesian FH.

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Noflindawati, NFN, Aswaldi Anwar, Agus Sutanto und NFN Yusniwati. „Seleksi Marka SCAR untuk Identifikasi Dini Jenis Kelamin Tanaman Pepaya (The Selection of SCAR Markers for Early Sex Identification of Papaya)“. Jurnal Hortikultura 30, Nr. 1 (22.12.2020): 1. http://dx.doi.org/10.21082/jhort.v30n1.2020.p1-8.

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Identifikasi dini terhadap jenis kelamin tanaman pepaya merupakan hal penting yang dapat membantu petani dalam budidaya tanaman pepaya. Identifikasi kelamin pepaya berdasarkan marka morfologi dan fisiologi telah dilakukan, namun beberapa hasilnya masih bias karena faktor lingkungan. Identifikasi kelamin tanaman pepaya menggunakan marka molekuler bisa lebih cepat dan akurat. Penelitian tersebut telah banyak dilakukan, salah satu di antaranya adalah marka berbasis sequence characterized amplified region (SCAR) dan beberapa primer SCAR telah dihasilkan untuk identifikasi kelamin pepaya. Penelitian bertujuan untuk menyeleksi primer SCAR yang efektif dalam mengidentifikasi seks tanaman pepaya. Penelitian dilakukan pada bulan November 2018 sampai Juni 2019 di Laboratorium Molekuler dan Uji Mutu Kebun Percobaan Sumani Balai Penelitian Tanaman Buah Tropika di Solok. Primer SCAR yang diseleksi adalah W11,T12, PKBT5, Napf2, dan SDp. Tanaman referensi sebagai sampel umur 11–12 bulan adalah tanaman betina, jantan, dan hermaprodit masing-masing lima tanaman dari pepaya lokal dan Merah Delima. Hasil penelitian menunjukkan bahwa lima primer SCAR yang diuji hanya dapat membedakan tanaman betina dengan tanaman jantan dan hermaprodit tetapi belum dapat membedakan antara tanaman jantan dengan hermaprodit. Konsistensi pola amplifikasi dihasilkan dari primer SCAR W11, Napf2, dan T12 dengan posisi 800 bp. Primer SCAR W11, Napf2, dan T12 selanjutnya dapat digunakan sebagai marka untuk identifikasi kelamin tanaman betina dengan tanaman jantan dan hermaprodit.KeywordsSCAR; Identifikasi; Pepaya; Jantan, Hermaprodit AbstractThe determination of sex expression of papaya plants is important to farmers in its cultivation. The identification of papaya plant sex based on morphological and physiological characters have been previously carried out, however, the results were still biased due to environmental factors. Many studies have been carried out to identify this plant sex, such as the use of molecular and SCAR markers, based on sequence characterization on amplified regions. This research aims to select the SCAR primers that are effective in identifying papaya plant sex. The study was conducted from November 2018 to June 2019, at Laboratory of Molecular and Quality Testing of the Indonesian Tropical Fruit Research Institute in Solok. The selected SCAR primers were W11, T12, PKBT5, Napf2, and SDp, using a total of five female, male, and hermaphrodite plants are reference aged 11–12 month from local papaya and cv. Merah Delima. The five SCAR primers tested were only able to differentiate females from male and hermaphrodite plants. The consistency of the amplification pattern was obtained from the SCAR W11, T12, and Napf2 primers at 800 bp. In conclusion, SCAR W11, Napf2, and T12 primers are used as markers to distinguish female plants from male and hermaphrodite.

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Rha'ifa, Febrina Amaliya, Deiandra Jasmine Audrea, Lukman Hakim und Tuty Arisuryanti. „DNA Barcode of Barred Mudskipper (Periophthalmus argentilineatus Valenciennes, 1837) from Tekolok Estuary (West Nusa Tenggara, Indonesia) and Their Phylogenetic Relationship with Other Indonesian Barred Mudskippers“. Journal of Tropical Biodiversity and Biotechnology 6, Nr. 2 (20.05.2021): 59702. http://dx.doi.org/10.22146/jtbb.59702.

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Barred mudskipper (Periophthalmus argentilineatus) has a potency to be developed as protein for human consumption and ornamental fish. The fish also has an important role in mangrove ecosystems. Nevertheless, many barred mudskippers have been considered a cryptic species. Therefore, accurate identification is needed to clarify species identification of the barred mudskipper using DNA barcoding. This research aimed to identify barred mudskippers from Tekolok Estuary (East Lombok, West Nusa Tenggara, Indonesia) using COI mitochondrial gene as a DNA barcode and analyze genetic relationship with other barred mudskippers from several regions of Indonesia recorded in GenBank. This study used a PCR method with universal primers FishF2 and FishR2. The data was then analysed using DNASTAR, BLAST, Mesquite, MEGA, DnaSP, BEAST, GenAlEx, and NETWORK. The results revealed that barred mudskipper from Tekolok Estuary has been verified as Periophthalmus argentilineatus. The results also exhibited that P. argentilineatus from Tekolok Estuary has a close genetic relationship to P.argentilineatus from Tukad Bilukpoh (Jembrana, Bali). In addition, phylogenetic analysis showed that P.argentilineatus from Indonesia consisted of two clades with a genetic distance of approximately 6.64%. This analysis revealed evidence of the cryptic diversity of P.argentilineatus from Indonesia. Further detailed studies are needed to clarify whether Indonesian P.argentilineatus should be categorized into more than one species or single species with several subspecies.

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Joesidawati, Marita Ika, Nining Nursalim, Nenik Kholilah, Eka Maya Kurniasih, Ni Kadek Dita Cahyani und Ambariyanto Ambariyanto. „DNA Barcoding of Anchovy in Tuban Regency as Database of Indonesian Marine Genetic Diversity“. ILMU KELAUTAN: Indonesian Journal of Marine Sciences 28, Nr. 4 (28.08.2023): 383–91. http://dx.doi.org/10.14710/ik.ijms.28.4.383-391.

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Anchovy is the main catch and the primary consumption of coastal communities in Indonesia, and its production shows an increase of more than 10% in 2021. Tuban district, in East Java, Indonesia is part of the WPP 712 (Wilayah Pengelolaan Perikanan or Fisheries Management Area) and highly produces anchovies’ fisheries. Anchovy has a small size, making it difficult to identify morphologically. This study aimed to genetically identify anchovy samples obtained from North Java (Tuban) waters. Molecular identification was conducted by utilizing Cytochrome Oxidase Subunit I (COI) gene using jg-HCO and jg-LCO primers. This study observed 12 individual samples with 623 base pair sequence length. Five species were obtained, namely four species of anchovies (Encrasicholina heteroloba, Encrasicholina punctifer, Stolephorus waitei, and Stolephorus insularis) and one species of sardines (Dussumieria elopsoides) with 99.84-100% similarity to NCBI sequences data. Anchovies typically have a streamlined body with a slightly compressed shape. Anchovies have cycloid scales, which are smooth-edged and relatively small, ranging from a few centimeters to around 20 centimeters in length. Some of the genus from the Anchovy group are Encrasicholina and Stolephorus. The phylogenetic tree reconstruction leads into four clades with a genetic distance between clades of 17,9-24,5 %. This research provides methods and data on the genetic diversity of anchovies taxa caught in Tuban, East Java. The findings are expected to support promoting new standards for healthier and more sustainable anchovy stocks in the country. Overall, this study contributes to providing valuable insights for fisheries management and conservation efforts in Indonesia.

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Pancaningtyas, Sulistyani, Nur Afni Helia Dewi und Mukhamad Su’udi. „Identification of cocoa (Theobroma cacao L.) genetic uniformity through RAPD molecular markers.“ Pelita Perkebunan (a Coffee and Cocoa Research Journal) 39, Nr. 3 (19.12.2023): 173–83. http://dx.doi.org/10.22302/iccri.jur.pelitaperkebunan.v39i3.566.

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Theobroma cacao L. has been propagated through either generative or vegetative techniques. One of the vegetative methods of propagating cocoa is somatic embryogenesis. Somatic embryogenesis has been employed by the Indonesian Coffee and Cocoa Research Institute for producing cocoa seedlings. Plant breeding activities are hampered by the significant level of plant heterogeneity among their progeny. Mislabelling of genetic impurities can be an issue. Molecular markers can be used to detect genetic variation at an early stage. The most common marker is the RAPD molecular marker. The study aims to determine the polymorphic RAPD primers in the analysis of genetic uniformity between mother plants and the seedlings derived from somatic embryogenesis (SE). The analyzed samples consisted of twelve individuals: six mother plants and six seedlings derived from SE. The results revealed that the percentage of polymorphic bands was 100% with band sizes ranging from 295-2785 bp for primer GY169 while for primer GY107 percentage of polymorphic bands was 80% with band sizes ranging from 345-1678 bp. Primer GY169 and primer GY107 can be amplified and used for cocoa similarity and heterogeneity.

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Widayanti, Rini, Aris Haryanto, Wayan Tunas Artama und Suhendra Pakpahan. „Genetic variation and phylogenetic analysis of Indonesian indigenous catfish based on mitochondrial cytochrome oxidase subunit III gene“. Veterinary World 12, Nr. 6 (Juni 2019): 896–900. http://dx.doi.org/10.14202/vetworld.2019.896-900.

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Aim: This study aimed to analyze the genetic variation and phylogenetic reconstruction of Indonesian indigenous catfish using mitochondrial cytochrome oxidase subunit III sequences. Materials and Methods: A total of 19 samples of catfish were collected from seven rivers (Elo [EM], Progo [PM], Kampar [KR], Musi [MP], Mahakam [MS], Kapuas [KS], and Bengawan Solo [BSBJ]) in five different geographical locations in Indonesia. The genome was isolated from the tissue. Mitochondrial DNA cytochrome oxidase subunit III was amplified using polymerase chain reaction (PCR) with CO3F and CO3R primers. The PCR products were sequenced and continued to analyze genetic variation and phylogenetic relationship using MEGA version 7.0 software. Results: Cytochrome c oxidase (COX)-III gene sequencing obtained 784 nucleotides encoding 261 amino acids. Sequenced COX-III gene fragments were aligned along with other catfish from Genbank using ClustalW program and genetic diversity among species was analyzed using the MEGA Version 7.0 software. Among all samples, there were substitution mutations at 78 nucleotide sites, and there were 14 variations in amino acids. Catfish from PM, KR, MP, and KS had the same amino acids as Hemibagrus nemurus (KJ573466.1), while EM catfish had eight different amino acids and catfish BSBJhad 12 different amino acids. Conclusion: Indonesian catfish divided into four clades. BBSJ Catfish were grouped with Pangasianodon gigas, EM catfish were grouped with Mystus rhegma, and KS catfish were grouped with Hemibagrus spilopterus, while catfish MS, KR, PM, and MP were grouped with H. nemurus.

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Khairani, Hagia Sophia, Sintho Wahyuning Ardie und Fitra Parlindo. „FUSARIUM SPECIES FROM AN INDONESIAN GENOTYPE OF FOXTAIL MILLET SEEDS“. Indonesian Journal of Agricultural Science 23, Nr. 1 (15.08.2022): 7. http://dx.doi.org/10.21082/ijas.v23n1.2022.p7-14.

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As a generalist pathogen in cereals, Fusarium spp. become the most threatening fungi which can conduct its saprogenesis by infecting seeds. Determination of fungal identity and the yield loss risk is needed to modify the effective controlling strategies. However, there is no report on implementing methods for controlling Fusarium spp. on foxtail millet (Setaria italica L. Beauv.). This research was undertaken from July to September 2020 and November to December 2021 under ambient laboratory conditions to identify and evaluate the pathogenicity of seed-borne Fusarium species in foxtail millet. One hundred colonies of seed-borne fungi were isolated from foxtail millet genotype ICERI-6 which was dominated by Fusarium spp. Morphological characterization by observing the structure of colonies and microscopical features indicated that the six isolates (Fu1–Fu6) were identical to Fusarium solani, F. chlamydosporum, F. oxysporum, F. equiseti, F. proliferatum, and F. graminearum, respectively. Molecular identification for the 5.8s rDNA target gene with ITS1 and ITS4 primers has confirmed that the Fusarium spp. were determined as mentioned species. Pathogenicity test using potato dextrose agar medium showed that the germination percentage of seed inoculated by Fusarium spp. was only 1.2% on average at 7 days after incubation. These species led to germination failure as the seeds were covered by fungal mycelia. Seeds that could escape from germination failure performed necrotic spots on the seedlings. These abnormalities would contribute to low productivity in the field. The study has implication in controlling seed-borne disease and that resistant variety breeding becomes important issues to be addressed for future research.

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Wiyatno, Ageng, Ungke Antonjaya, Chairin Nisa Ma'roef, Silvita Fitri Riswari, Hofiya Djauhari, I. Made Artika, Corina Monagin et al. „Detection and identification of coxsackievirus B3 from sera of an Indonesian patient with undifferentiated febrile illness“. Journal of Infection in Developing Countries 10, Nr. 08 (31.08.2016): 880–83. http://dx.doi.org/10.3855/jidc.7573.

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Introduction: Coxsackievirus B3 (CVB3) virus has been implicated as the causative agent of various outbreaks of clinical disease, including hand, foot, and mouth diseases, aseptic meningitis, acute myocarditis, and inflammatory cardiomyopathy. Methodology: Two hundred and nine undiagnosed cryopreserved specimens obtained from factory workers in Bandung, Indonesia, who displayed symptoms of acute febrile illness were gathered. Total RNA was isolated from serum and tested by conventional polymerase chain reaction (PCR) using Enterovirus genus-level primers and confirmed by sequencing. Concurrently, the virus was isolated in LLC-MK2 cells. Results: CVB3 virus was identified in an archived specimen from a patient who presented with symptoms of fever, headache, myalgia, and nausea. Sequencing results of the VP1 region from both the clinical sample and tissue culture supernatant showed 97% homology to a CVB3 virus isolate from Taiwan. Virus propagation in LLC-MK2 cell culture exhibited severe cytopathic effects two days post-inoculation. Conclusions: We report the first case of CVB3 from an undifferentiated febrile illness specimen from Indonesia.

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Dewi, Mega H., Riska Anggraini, Laily M. K. Mastika, Murni Saptasari und Dwi Listyorini. „ISOLATION OF FLAVONOID 3’5’HYDROXILASE GENE FROM SNAKEWEED (Stachytarpheta indica auct. non. (L.) Vahl)“. KnE Life Sciences 2, Nr. 1 (20.09.2015): 41. http://dx.doi.org/10.18502/kls.v2i1.114.

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Stachytarpheta is one of Indonesian medicinal plants which have a wide species diversity. The bioactive component in snakeweed herb including naringenin, flavonol, and flavon are mainly derivate from phenyl propanoid (flavonoid). The gene encodes F3’5’Hydroxilation (F3’5H) involved in the biosynthesis of flavonoid product, by means of catalysis hydroxylation on the C atom #3 and #5 of benzene ring. Recently, has not yet meet publication about F3’5’H from snakeweed herb. The aim of this study was to isolate F3’5H gene from Stachytarpheta indica, using primers which were designed from conserve region of Petunia hybrida F3’5’H gene; HF1 and HF2 alleles. Forward primer is 5'-TGATGCTGCTAAAGCATTCT-3' and reverse primer is 5’GTGCACGCAGGTGACATATG-3’. The amplified fragments were un-specific non-consensus sequences, suggested that two homolog gene locus were isolated. Sequence analysis showed that both share two different domains; conserve-upstream and homolog-downstream domains. It is suggested that Stachytarpheta indica may possesses different alleles for F3’5’H, i.e. HF1 and HF2, as of Petunia hybrida. Keywords: F3’5’H gene, Stachytarpheta indica, snakeweed

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Nasrulloh, Mukh Fajar, Raden Wisnu Nurcahyo, Dwi Priyowidodo, Fitrine Ekawasti und Lintang Winantya Firdausy. „Molecular Detection of Eimeria bovis in Indonesian Beef Cattle Using Nested PCR Technique“. HAYATI Journal of Biosciences 31, Nr. 5 (19.06.2024): 980–87. http://dx.doi.org/10.4308/hjb.31.5.980-987.

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Eimeria bovis is a pathogenic protozoan that causes cattle digestive tract infections, which can cause economic losses to farmers. It is necessary to develop specific and accurate detection methods to conserve livestock and prevent coccidiosis in Indonesia. This study aims to detect E. bovis by nested PCR and determine the relationship with reference sequences. A total of 167 samples of beef cattle feces were taken randomly from community farms spread across 18 provinces in Indonesia. The feces were examined natively, and then the oocysts were purified by the sugar flotation method, extracted by KIT extraction, and amplified by the nPCR technique. Positive samples were followed by sequencing and phylogenetic analysis using MEGA 11 software. This study used two pairs of primers (outer and inner) taken from ITS-1 molecular markers. As many as 96 out of 167 samples (57.5%) were positive for Eimeria spp., and 48 of the 96 samples were positive for Eimeria spp. (50%) were detected to be positive for E. bovis based on the presence of a 238 bp DNA fragment. The results of the phylogenetic analysis showed that the study sample formed a separate cluster from the E. bovis cluster from abroad. In conclusion, E. bovis was detected in 16 out of 18 provinces in this study, and the nPCR technique proved to have better sensitivity and specificity.

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Fahmi, Melta R., Eni Kusrini, Erma P. Hayuningtiyas, Shofihar Sinansari und Rudhy Gustiano. „DNA BARCODING USING COI GENE SEQUENCES OF WILD BETTA FIGHTING FISH FROM INDONESIA: PHYLOGENY, STATUS AND DIVERSITY“. Indonesian Fisheries Research Journal 26, Nr. 2 (07.12.2020): 97. http://dx.doi.org/10.15578/ifrj.26.2.2020.97-105.

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The wild betta fish is a potential ornamental fish export commodity normally caught by traders or hobbyists in the wild. However, the population of wild betta in nature has declined and become a threat for their sustainability. This research was conducted to analyze the genetic diversity, phylogenetic relationships, and molecular identification through DNA COI gene sequence of Indonesian wild betta fish. A total of 92 wild betta fish specimens were collected in this study. Amplification of COI genes was carried out using Fish F1, Fish R1, Fish F2, and Fish R2 primers. The genetic diversity and phylogenetic relationships were analyzed using MEGA version 5 software program. Species identification of the specimen was conducted using BLAST program with 98-100% similarity value of the DNA sequences to indicate the same species. Phylogenetic tree construction showed seven monophyletic clades and showed that Betta smaragdina was the ancestral species of genus Betta in Indonesian waters. Genetic distance among species ranged from 0.02 to 0.30, whereas intra-species genetic distance ranged from 0 to 6.54.

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Sugama, Ketut, Abidin Nur, Isti Koesharyani, Haryanti und Hans P. Saluz. „A new species of pisang shrimp, Penaeus symplex revealed by molecular DNA analyses, as candidate species for aquaculture in Indonesia“. BIO Web of Conferences 112 (2024): 08004. http://dx.doi.org/10.1051/bioconf/202411208004.

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In Indonesia there are two species mainly farmed, these are Penaeus monodon and Litopenaeus vannamei. Due to disease outbreaks which were mainly caused by viruses, shrimp aquaculture is become a high risk, therefore is a need to find new species. Unknown species of shrimp named as udang pisang (Pisang shrimp) only found in Indonesian waters. In the present study, six species of shrimp available in Indonesia, those are Pisang shrimp (Penaeus sp.), P. monodon, P. merguensis, P. indicus, P. semisulcatus and L. vannamei were analysed by RAPD with two primers of 2AAM2 and AS15 to confirm their species. Preliminary trials on the culture of Pisang shrimp and P. monodon were carried out in earthen ponds to compare their growth. The results revealed that based on the gel banding pattern and molecules weight of DNA, Pisang shrimp genetically is different from other five species analyzed and morphology generally like P. monodon. The identity between Pisang shrimp and P. monodon was 92%, suggested the two species are different. Pisang shrimp is a new species named Penaeus symplex [14, 20] and has been validated. The growth of Pisang shrimp and P. monodon for 90 days of culture was comparable (19.89f1.71 g and 20.0111.08 g). Therefore, Pisang shrimp has high potential for aquaculture diversification.

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Hidayah, N., S. Pambudi, T. Widayanti, J. Suryanggono, M. Luqman, L. Mulyawati, I. Nurlaila, T. Novianti und N. Nie. „The cloning of ESAT-6, EspC and Rv2029c genes obtained from an Indonesian tuberculosis-infected patient“. IOP Conference Series: Earth and Environmental Science 1271, Nr. 1 (01.12.2023): 012091. http://dx.doi.org/10.1088/1755-1315/1271/1/012091.

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Abstract Early secreted antigenic target of 6-kDa protein (ESAT-6), a protein related to tuberculosis virulence (EspC) and latent antigen Rv2029c are important biomarkers for Mycobacterium tuberculosis prevention. Recent advances in subunit protein vaccines offer promising solutions to the inadequacies of existing BCG vaccines. In this study, these antigens were cloned into pET plasmid series to express the genes using the Escherichia coli expression system. Polymerase Chain Reaction was used to amplify the target genes from genome DNA isolated from Indonesia tuberculosis-infected patient’s sputum. A 309 bp of ESAT-6 fragment and a 337 bp of EspC fragment were inserted into pET-21b. Meanwhile, the 1038 bp of Rv2029c fragment was inserted into pET-32b. All constructs were transformed into Escherichia coli TOP10 and screened on Luria Bertani agar media containing ampicillin. The transformants were subjected to colony PCR using T7 universal primers followed by plasmid isolation to confirm the recombination. All genes were successfully cloned into the pET plasmid series. These results serve as a basis for further studies to express the recombinant protein as a booster vaccine.

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Pratama, Muhammad Zulfiqar Meizar, Zuliyati Rohmah und Tuty Arisuryanti. „Genetic Variation Within Four Captive Chital (Axis axis) Populations in Indonesia“. Journal of Tropical Biodiversity and Biotechnology 8, Nr. 1 (22.02.2023): 74728. http://dx.doi.org/10.22146/jtbb.74728.

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Chital is a native animal from South Asia. Chital had been introduced to many countries, including Indonesia. Chital was first introduced to Indonesia in 1811 at Bogor Palace and since had been kept captive around Indonesia. Currently, no research had been done concerning the genetic variation of Indonesian chital. Therefore, the purpose of this research was to analyze genetic variation and phylogenetic relationship of chital from Pusat Inovasi Agroteknologi Universitas Gadjah Mada (PIAT UGM), Prambanan Temple, Gembira Loka Zoo, and Bogor Palace, based on mitochondrial D-loop fragment. This study used a Polymerase Chain Reaction (PCR) method. DNA was extracted from faecal samples and amplified with L15995 and H16498 primers. The analysis used for this research were genetic variations, haplotype networking, and phylogenetic relationships between populations. This study detected 5 haplotypes out of 20 sequences with 10 polymorphic sites and 2 indels. The haplotype diversity and the nucleotide diversity were 0.443 and 0.002 respectively, and the genetic distance was between 0 and 2.03% (average 0.55%). This research also showed one main haplotype, labelled as haplotype 1, which consisted of all individuals from PIAT and Prambanan Temple, four individuals from Bogor Palace, and one individual from Gembira Loka. This grouping proves that the majority of chital population in Indonesia came from Bogor Palace. One individual from Gembira Loka has a considerable genetic divergence from the rest of the samples, which might indicate it originated from a different source population.

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Megarani, Dorothea Vera, Herjuno Ari Nugroho, Zahrah Prawita Andarini, Yura Dwi Risa B. R. Surbakti und Rini Widayanti. „Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene“. January-2020 13, Nr. 1 (2020): 96–103. http://dx.doi.org/10.14202/vetworld.2020.96-103.

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Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences. Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software. Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids). Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).

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Rahmasari, Ratika, Muhareva Raekiansyah, Syifa Naura Azallea, Marvella Nethania, Navany Bilqisthy, Anna Rozaliyani, Anom Bowolaksono und Rani Sauriasari. „Low-cost SYBR Green-based RT-qPCR assay for detecting SARS-CoV-2 in an Indonesian setting using WHO-recommended primers“. Heliyon 8, Nr. 11 (November 2022): e11130. http://dx.doi.org/10.1016/j.heliyon.2022.e11130.

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Ishak, Muhammad Alif, und Budi Setiadi Daryono. „Detection of Powdery Mildew Resistance Gene in Melon Cultivar Meloni Based on SCAR Markers“. Biosaintifika: Journal of Biology & Biology Education 12, Nr. 1 (23.04.2020): 76–82. http://dx.doi.org/10.15294/biosaintifika.v12i1.22198.

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Powdery mildew is one of the diseases caused by fungal infections that can reduce the production of melon fruit worldwide including in Indonesia. A powdery mildew-resistant cultivar of melon is needed to increase melon yield crops. This study aimed to detect resistance gene linked to powdery mildew using a sequence characterized amplified region (SCAR) markers. The melon cultivar Meloni was used in this study. SL-3, PI 371795, and Aramis cultivar were used to compare. Amplification of the marker was performed employing a pair of primers. The result showed that Meloni had a powdery mildew resistance gene by the presence of a DNA target band at 1058 base pair (bp). Based on this result, it could be concluded that Meloni was an excellent melon cultivar because of its ability to overcome the powdery mildew infections naturally. SCAR markers have been used for various purposes, especially to detect resistance genes to plant diseases. The present study had provided information for plant breeders about Meloni as the new melon cultivar that was genetically resistant against powdery mildew infections. Furthermore, Meloni could be proposed as an alternative to native Indonesian superior melon seeds.

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