Symptomatic samples were taken from five districts in Yogyakarta and Central Java provinces of Indonesia to survey the genetic diversity of Begomovirus, α and β satellites. A total of 14 samples were ...tested positive by PCR for tomato leaf curl New Delhi virus (ToLCNDV), pepper yellow leaf curl Indonesia virus (PepYLCIV), mungbean yellow mosaic India virus (MYMIV), and ageratum yellow vein China virus (AYVCNV) infections. Besides that, ageratum yellow vein alphasatellite (AYVA) was identified for the first time in Indonesia, and tomato leaf curl Java betasatellite (ToLCJaB) were detected for the first time in different hosts. Partial genome sequences of begomoviruses and complete sequences of the α and β satellites were recovered and registered in NCBI GenBank (OP846592-OP846615). Phylogenetic study showed that AYVA and ToLCJaB each had two separate lineages. Polymorphism and diversity analyses confirmed other reports that βC1 coding region of ToLCJaB genome is highly conserved. Comparison of phylogroups 1 and 2 of ToLCJaB produced a high FST value, indicated genetic isolation between them. This report could be a basis for future works on the less studied genetic variation of α and β satellites in Indonesia and other countries.
True shallot seed (TSS) is one of the alternative potential technologies to solve the availability of seed quality on shallot in Indonesia. Another problem in shallot production is infection by ...purple blotch and twisted disease. This research evaluated the potency of Rhizophagus intraradices and Trichoderma asperellum as bioprotectants and biofertilizer. T. asperellum was mixed in the soil before seedling transplanting, and R. intraradices was applied around the seedling roots at transplanting. The observed parameters were the shallot growth (the plant height, number of leaves, and length of root), plant health (disease incidence and intensity), and bulb resistance to Fusarium solani. The result showed that R. intraradices and T. asperellum increased the resistance of onion bulbs to the pathogen F. solani in the postharvest period, indicated by R. intraradices treatment that had an infection area of 21.99 mm2, followed by T. asperellum treatment 26.63 mm2, and control of 37.66 mm2. Keywords: Rhizophagus intraradices, Trichoderma asperellum, true shallot seed
Abstact. Probowati W, Somowiyarjo S, Hartono S. 2019. Molecular characterization of Mosaic Virus From the cocoa trees showing mosaic symptoms in Yogyakarta, Indonesia. Biodiversitas 20: 3698-3704. ...Indonesia is the world's second-biggest producer of cacao after Ivory Coast with its cacao plantations spreads over 1,652 million hectares and mostly managed by smallholders. Cacao as a beneficial commodity can provide job opportunities for over 1.64 million people, with its contribution of more than US-$ 1.6 billion/year to national income. However, pest and disease infections are inevitably common constraints for the cacao cultivators. One current disease is caused by Cacao Swollen Shoot Virus (CSSV). Despite its noticeable symptoms on the cacao trees suffering from the disease, the knowledge on both the virus existence and the prevention steps in dealing with it is lacking. The information on the diversity of mosaic virus will help us to comprehend its epidemiologic development and the needed countermeasures, as well as its evolution. This research is intended to study the mosaic disease virus molecularly, the virus was obtained from DR1 clones from Kalibawang cacao plantation in Kulon Progo, Yogyakarta. The virus morphology was observed using a transmission electron microscope applying quick dipping method. The PCR analysis with conserved region ORF1 primers was conducted to detect the viral existence in the infected trees. The identification of CSSV molecular characters was undertaken using PCR sequencing analysis which was then examined using BioEdit and Mega5 programs to initiate a relationship dendrogram. The result showed that the DR1 cacao tree clones from Kalibawang were infected by mosaic virus with mild visual severity of leaf typical symptom. From the electronic microscope observation, a ±100 nm rod-shaped viral particle with a diameter of 15.3 mm was found. On the molecular level, the cause of mosaic symptom has CSSV amplified at conserved regions with size 375 bp. The results are the first report confirming that the molecular cause of cacao mosaic disease in Indonesia is CSSV. The molecular characters of CSSV in Yogyakarta are very different from those found abroad.
The Indonesian government is obliged to ensure the public health of the people of Indonesia by the supervision of Fresh Food Originated from Plant (Pangan Segar Asal Tumbuhan PSAT) arriving from ...abroad. Therefore, the regulation of Minister of Agriculture Number 88 in 2011 was issued to regulate inspection requirement of PSAT. There are some challenges in the implementation of these regulations until 2015, such as the unavailability of accredited laboratories, the lack of communication between stakeholders, and limited human resource or utensil within testing laboratories. Most of the testing laboratories appointed by the government are not yet accredited. Only 60% are able to perform tests mandated listed in The Regulation of Minister of Agriculture No. 88 the Year 2011. On the other hand, private laboratories accredited by ISO/IEC 17025 showed higher capacity by being able to perform 77.8 to 100% of mandated tests. The implementation challenges were later addressed by the revision of the regulation and release of issue Regulation 04/2015 in ref. The Regulation of Minister of Agriculture 13/2016. These regulations acknowledge Food Safety System of the state of origin or their administration of the Testing Laboratory Registration. In other words, they put forward the implementation of supervision in the country of origin reducing Indonesia’s reliability on providing high level of testing laboratories itself. The implementation of The Regulation of Minister of Agriculture 04/2015 in ref. the Regulation of Minister of Agriculture 13/2016 expected Quarantine Measures on the importation of PSAT to be more effective and efficient. Therefore, impact of the implementation of this new regulation would shorten delay periods for cargo containers in ports (dwelling time), reduce handling cost of containers, minimize laboratory testing fees, and reduce risk of rejection of imported products because of incompliance.
Twisted disease caused by Fusarium spp. is one of the primary diseases on shallots with potency to cause enormous losses by causing stunting and bulb rot. One alternative disease control is the ...induction of plant resistance since the seed stage. The aim of this study was to determine the content of salicylic acid, jasmonic acid, and phenolic compounds of shallot bulb seeds coated with biological control agents as a resistance response to twisted disease. The shallot cultivar used was Crok kuning. The treatments used in this study were the type of biological control agents, including Rhizophagus intraradices and Trichoderma asperellum, combined with and seed coating application time (one month before planting and simultaneously at planting). Biological control agents in the form of powder formulation applied as seed coating material and seeds were stored for one month before planting. The results showed that application of biological agents delayed the occurrence of the twisted disease symptoms. The salicylic acid content from plant treated with R. intraradices at the time of planting was slightly higher than the control. The jasmonic acid content in T. asperellum plants treated at planting was higher than then control. Total phenolic content from plants treated with T. asperellum at planting time was higher than the control. In general, application of biological control agent as seed coat did not result in significant increase in salicylic acid, jasmonic acid nor the phenolic compounds, compared to the pathogen infected control.
Yellow curl disease caused by begomovirus is a major threat for horticulture in Indonesia. Control mea‐ sures for the disease face several constraints, one of which is the association between ...begomovirus and DNA satellites which can affect the severity of symptoms. In this study, we detected the presence of a DNA satellite associated with begomovirus in a highland area. The sample was obtained from Ketep, Magelang, located approximately 1400 meters above sea level. Begomovirus was detected using primers PAL1V1978/PAR1C715 that resulted in an amplicon of ap‐ proximately 1600bp. The presence of this satellite was detected using primers CLB36F/CLB37R, resulting in full‐length satellite genome of approximately 1300bp. Sequence analysis showed the sample was infected by Pepper yellow leaf curl Indonesia virus (PepYLCIV) and a non‐coding satellite which resembled some characteristics of common betasatellites with imperfect putative ORF βC1. SimPlot analysis revealed the recombination event between betasatellites and DNA‐B of PepYLCIV. The satellite found in this study is thought to be the result of recombination due to multiple infections in plants.
Various viruses can cause mosaic disease in tobacco plants. Proper detection of the cause of the mosaic disease helps determine effective control. The purpose of this study was to detect the presence ...of double infection of Rehmannia mosaic virus (ReMV) with Potato virus Y (PVY) using multiplex RT-PCR in tobacco plants from Central Java and Special Region of Yogyakarta. The viral suspension was inoculated on Chenopodium amaranticolor to obtain one viral colony from one local lesion. The multiplex RT-PCR method using Tobamovirus primers (TobRT-up1 and TobRT-do2) and Potyvirus primers (MJ1 and MJ2) can detect double infection caused by ReMV with PVY in tobacco plants distributed in Central Java and Special Region of Yogyakarta. The multiplex RT-PCR product showed that tobacco samples with mosaic symptoms from Temanggung, Klaten, Bantul, and Kalasan were positive ReMV. Multiplex RT-PCR has successfully detected double infection of ReMV and PVY on tobacco samples from Klaten and Kalasan. ReMV Bantul, Kalasan, and Klaten were homolog to ReMV USA isolate and ReMV Temanggung was homolog to ReMV Japanese isolate. PVY Klaten was homolog to PVY Turkey isolate, and PVY Kalasan was homolog to PVY Iran.
Viruses have been a problem on garlic cultivations in various countries. There are several viruses reported infecting garlic. Genera Potyvirus and Carlavirus are the most common viruses found ...infecting garlic. Mixed infection on garlic is often designated as a “garlic viral complex”. These viruses can be transmitted through imported garlic seeds. Therefore, it is necessary to conduct early detection of garlic seeds to prevent the epidemic of these viruses. This study aimed to detect Onion yellow dwarf virus (OYDV) and Shallot latent virus (SLV) on garlic. Garlic samples were obtained from Enrekang, Magelang, Temanggung, Tawangmangu, and Yogyakarta. Total RNA was extracted from the samples and subsequently used for RT-PCR using two pairs of specific primers SLV-F/SLV-R and OYDV-F/OYDV-R. Primary pair SLV-F/SLV-R in amplicons sized 276 bp, while OYDV-F/OYDV-R in amplicons sized 112 bp. RT-PCR results showed that OYDV was found in all samples tested in this study. Meanwhile, double infections (OYDV and SLV) were found in eight out of ten samples tested. These results indicated that double infections on garlic were common in Indonesia.
Gejala mosaik kuning dan keriting daun ditemukan pada pertanaman kacang panjang di Sleman, Yogyakarta. Begomovirus diketahui sebagai salah satu penyebab penyakit tersebut. Penelitian dilakukan untuk ...mengidentifikasi spesies Begomovirus dan DNA satelit yang berasosiasi dengan penyakit mosaik kuning kacang panjang. Ekstraksi DNA total dari tanaman bergejala dilanjutkan dengan amplifikasi fragmen DNA spesifik Begomovirus dan Betasatelit. Amplikon DNA berukuran ±1500 pb dan ±1300 pb berhasil diperoleh menggunakan berturut-turut primer universal Begomovirus dan primer spesifik Betasatelit. Analisis sekuen nukleotida mengonfirmasi identitas Begomovirus yang menginfeksi tanaman kacang panjang ialah Mungbean yellow mosaic India virus (MYMIV) dengan homologi 99% terhadap isolat MYMIV asal Indonesia. DNA satelit yang berasosiasi dengan MYMIV menunjukkan karakteristik Betasatelit, yaitu memiliki satellite common region (SCR) dengan struktur stem-loop dan sekuen TAATATTAC pada bagian loop, adenine rich region sebesar 54.96%, dan ORF (open reading frame) non-coding. Lebih lanjut, analisis rekombinasi menggunakan SimPlot mengindikasikan bahwa satelit non-coding MYMIV merupakan satelit rekombinan antara Betasatelit dan DNA-B Pepper yellow leaf curl Indonesia virus (PepYLCIV). Artikel ini merupakan laporan pertama asosiasi betasatelit DNA non-coding dengan MYMIV di Indonesia.
Begomovirus was reported as one of the most aggressive and destructive viruses on several commercial crops, including cucurbits in Indonesia. Plants that infected with Begomovirus show the mosaic ...symptom on the leaves, change in leaf shape, stunts, change in color and shape of fruit. It was recently observed in cultivated angled luffa Luffa acutangula (L.) Roxb around Yogyakarta and Central Java. The aim of this research was to identify the virus by using Polymerase chain reaction (PCR). The result of Begomovirus amplification from the total DNA samples amplification using primer Krusty-Homer showed that DNA of Begomovirus from angled luffa was amplified at ~580bp. The DNA sequencing of angled luffa’s leaf isolate GD1 had 97.8% homology with SCLV-China isolate MC1. However, amplification of DNA seed samples using the same primer showed negative result. It was concluded that Begomovirus was not a seed borne virus. This is the first molecular report on the occurence of Begomovirus in angled luffa in Yogyakarta.
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