Like Chinese Silkie, Indonesian Ayam Cemani exhibits fibromelanosis or dermal hyperpigmentation and possesses complex segmental duplications on chromosome 20 that involve the endothelin 3 gene, EDN3. ...A genomic region, DR1 of 127 kb, together with another region, DR2 of 171 kb, was duplicated by unequal crossing over, accompanied by inversion of one DR2. Quantitative PCR and copy number variation analyses on the Cemani genome sequence confirmed the duplication of EDN3. These genetic arrangements are identical in Cemani and Silkie, indicating a single origin of the genetic cause of Fm. The two DR1s harbor two distinct EDN3 haplotypes in a form of permanent heterozygosity, although they remain allelic in the ancestral Red Jungle Fowl population and some domesticated chicken breeds, with their allelic divergence time being as recent as 0.3 million years ago. In Cemani and Silkie breeds, artificial selection favoring the Fm phenotype has left an unambiguous record for selective sweep that extends in both directions from tandemly duplicated EDN3 loci. This highly homozygous tract is different in length between Cemani and Silkie, reflecting their distinct breeding histories. It is estimated that the Fm phenotype came into existence at least 6600-9100 years ago, prior to domestication of Cemani and Silkie, and that throughout domestication there has been intense artificial selection with strength s > 50% in each breed.
Padi (Oryza sativa) termasuk ke dalam komoditas penting di Indonesia. Salah satu penyakit penting pada tanaman padi ialah penyakit hawar pelepah yang disebabkan oleh Rhizoctonia solani. Tujuan ...penelitian ini untuk mengetahui karakteristik dan kelompok anastomosis R. solani yang diisolasi dari tanaman padi varietas Ciherang, IR 64, Mekongga, dan Situ Bagendit; dan mengetahui keragaman genetiknya menggunakan primer universal, dan tingkat kekerabatannya. Penelitian dilaksanakan pada Oktober 2019 hingga Juli 2020 di Laboratorium Teknologi Pengendalian UGM. Pengambilan sampel dilaksanakan di Kecamatan Pandak, Bantul yang selanjutnya dilakukan isolasi dan pemurnian cendawan Rhizoctonia menggunakan medium agar-agar dekstrosa kentang. Isolat R. solani diklasifikasikan berdasarkan keragaman kultur, keragaman morfologi, jumlah inti sel, kemampuan anastomosis (AG), dan keragaman genetik. Analisis keragaman genetik dilakukan dengan PCR menggunakan primer universal ITS1 dan ITS4. Berdasarkan pengamatan keragaman kultur dan keragaman morfologi diperoleh hasil yang bervariasi. Hasil pengamatan jumlah inti sel pada keseluruhan isolat berkisar antara 5 hingga 7 inti pada sel yang termasuk dalam kategori multinukleat. Pengamatan kelompok anastomosis (AG) pada 13 isolat yang digunakan masuk ke dalam kategori C3 (anastomosis sempurna). Analisis PCR diperoleh pita DNA dengan hasil sesuai target yaitu 600–750 pb. Hasil secara sikuensing diketahui bahwa 12 isolat R. solani menunjukkan kekerabatan yang tinggi dengan isolat AG-1 IA, kecuali pada isolat CH 3.
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.
A research on Mitochondrial DNA analysis of genetic diversity in Sumatran elephant (Elephas maximus sumatranus) was conducted in this study. A 630 bp segment of mitochondrial DNA was amplified on ...105 samples of Sumatran elephant from 5 locations in Sumatera (Bentayan, Sugihan, Bukit Salero Lahat, Seblat, Way Kambas) using a set of primers: MDL3 (5’-CCCACAAT-TAATGGGCCC-GGAGCG-3’) and MDL5 (5’-TTACATGAATTGGCAGCCA-ACCAG-3’). The objectives of this study is to generate mitochondrial DNA D-loop sequences for all the Sumatran elephant samples under this study and to provide information haplotypes and nucleotide diversity of Sumatran elephant populations.            A total of 105 PCR product were successfully sequenced perfectly, with an average length of about 616 base pairs. However, mitochondrial DNA fragments for this analysis used the first 601 bases. Results showed six haplotypes (BP, BT, BS, BR, BX and BY) identified in Sumatera. The most of the sampled individuals are the haplotipe BT. BX and BY are most likely new haplotypes..  All haplotype, except for the haplotipe BP are belonging to the Sumatera clade. The haplotipe BX was derived from the haplotipe BT, and the haplotype BY was derived from the haplotipe BS by one transversion respectively. The other substitutions in this network were the transitions. The haplotype BP is widely distribute from Sri Lanka, Sumatera, Peninsular Malay and China). Although reported that the haplotype BU distributed Sumatera and Peninsular Malay, but BU haplotype not detected in this study.            Genetic distances within populations in Bentayan, Bukit Salero Lahat, Seblat, Sugihan and Way Kambas ranged from 0.0000 - 0003, and the genetic distance between the populations that is 0.0000 - 0. 0022. The distance between haplotypes of Sumatran elephant’s population is low.• The diversity of haplotypes and nucleotide in Sumatera island is low, the highest is in the region of Buki Salero Lahat and, lowest is in Bentayan and Sugihan. Overall, the results of analysis of Fu and Li's F * test statistic indicates that the population of Sumatran elephants in Sumatra is -0.78871, which means there is no inbreeding, but not significant at P> 0:10.  Keywords : Sumatran elephant, Elephas maximus sumatranus, mitochondrial DNA, haplotype
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.
The brown plant hopper (BPH) is a major pest of rice and as a vector of Rice ragged stunt virus (RRSV) and Rice grassy stunt virus (RGSV). Curently, numerous rice yellow stunt disease symptoms are ...found in the field that caused by the single and simultaneous infection of these two viruses. Brown plant hopper population correlate with the incidence and severity of the disease. Misuse of insecticides, would cause of BPH resistances to imidacloprid. This study aimed to investigate the ability of BPH imidacloprid-resistant and susceptible to transmit of rice yellow stunt disease on rice plants. The variables tested were the acquisition period, inoculation period, number of infesting BPH, and lifespans of the viruliferous BPH that used in this research. Experiments were set as separated Completely Randomized Design with 10 replications for each treatment within an experiment. The results showed that both resistant and susceptible BPH to imidacloprid was able to transmit the virus to healthy plants. The acquisition and inoculation period test showed the BPH could transmit the virus with the shortest acquisition time for 30 minutes followed 24 hours of inoculation, as well as the acquisition time of 10 days with the shortest inoculation time for 30 minutes. Based on the incubation time, symptoms variation, and disease severity, susceptible BPH were more effective in transmitting rice yellow stunt disease than imidacloprid-resistant BPH. Single imidacloprid-resistant or susceptible BPH was proven able to transmit rice yellow stunt disease to healthy plants during its lifespan. Lifespans BPH viruliferous of imidacloprid-resistant were shorter than susceptible, which was 16 days for resistant BPH and 21 days for susceptible BPH.
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.
Ageratum conyzoides is one of the common weeds in Indonesia. The presence of weed can decrease plant yield by resource competition and its role as alternative hosts for pests and diseases, especially ...begomoviruses transmitted by whitefly. The aim of this research is to detect and characterize the begomovirus-beta satellite in A. conyzoides. A. conyzoides showed severe yellowing symptoms were collected from Magelang, Central Java, Indonesia. Total DNA was extracted and analyzed using PCR method for begomovirus and beta satellite. Begomovirus detection was performed with universal primer Krusty-Homer, resulted a 500 bp DNA fragment. Betasatelit detection performed with specific primer β01/β02, resulted a 1300 bp DNA fragment, indicated presence of a beta satellite associated with the begomovirus. The sequence of begomovirus showed 95% similarity with Tomato Leaf Curl Java Virus (ToLCJaV). The sequence of beta satellites showed 85% similarity with Tomato Leaf Curl Betasatellite (ToLCB). Characterization of beta satellite showed three main characters of beta satellite, TAATATTAC stem-loop structure, Adenine-rich region, and 118 amino acids of putative ORF BC1.
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