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Detection and identification of Begomovirus infecting Cucurbitaceae and Solanaceae in Yogyakarta, Indonesia APRILIA SUFI SUBIASTUTI; SEDYO HARTONO; BUDI SETIADI DARYONO
Biodiversitas Journal of Biological Diversity Vol. 20 No. 3 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200318

Abstract. Subiastuti AS, Hartono S, Daryono BS. 2019. Detection and Identification of Begomovirus infecting Cucurbitaceae and Solanaceae in Yogyakarta, Indonesia. Biodiversitas 20: 738-744. Begomovirus genome has high plasticity that led to evolve rapidly. Begomovirus is one of a remarkably successful group of emerging viruses as the results from combination of many factors. Planting systems in Indonesia which often overlapping two or more plant species in one land has high possibility for occurring mixed infection. It is also suggested has high contribution to increase Begomovirus diversity. The aim of this research is to do preliminary identification of Begomovirus infected-Solanaceae and Cucurbitaceae in Yogyakarta based core coat protein (CP) gene sequence. A total of 50 melon, 50 chili, 30 eggplants, and 30 watermelon samples which showed Begomovirus symptoms were observed from several fields in Yogyakarta and Purworejo, Indonesia during 2016. Almost 90% of infected samples for each plant were tested by PCR and showed positive for Begomovirus. Based on coat protein (CP) gene nucleotide sequence identity, Begomovirus infected Solanaceae in Indonesia has close relationship with Pepper yellow leaf curl Indonesia virus (PepYLCIV) and Tomato yellow leaf curl Kanchanaburi virus (TYLCVKaV), while in Cucurbitaceae has close relationship with Squash leaf curl China virus (SLCCV) Tomato leaf curl New Delhi virus (ToLCNDV). All collected isolates showed highest sequence identity with isolates from South-East Asia and China. However, further analysis that including full genome characterization is still needed to explain Begomovirus evolution in Indonesia.

Phenotypic and genetic stability of new Indonesian melon cultivar (Cucumis melo L. ‘Melonia’) based on ISSR markers BUDI SETIADI DARYONO; APRILIA SUFI SUBIASTUTI; ARVITA FATMADANNI; DIAN SARTIKA
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200419

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%.

Local food diversification of foxtail millet (Setaria italica) cultivars in West Sulawesi, Indonesia: A case study of diversity and local culture Ramlah Ramlah; Marcia Bunga Pabendon; Budi Setiadi Daryono
Biodiversitas Journal of Biological Diversity Vol. 21 No. 1 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210110

Abstract. Daryono BS, Ramlah, Pabendon MB. 2020. Local food diversification of foxtail millet (Setaria italica) cultivars in West Sulawesi, Indonesia: A case study of diversity and local culture. Biodiversitas 21: 67-73. Foxtail millet (Setaria italica (L.) P.Beauv.) is one of the non-rice cereal crops that has long been domesticated in the world, including West Sulawesi-Indonesia as an alternative food crop instead of rice on local culture. Traditional millet cultivars may become an indispensable part of the local culture and traditions of millet-growing people across Asia over many generations. The existence of this germplasm in West Sulawesi Province, Indonesia has been observed morphologically and showed a close relationship with local culture. A total of six traditional millet cultivars (Tarreang) with different morphological characteristics have been found in this region and still preserved sustainably by the local farmers along with their local culture and traditions. The tradition of Sayyang pattu’duq may become a good example of this relationship. In this tradition, some traditional food is made by the local people like porridge tarreang, jelly tarreang, buras tarreang, jepa golla mamea, jepa anjoroi, dodol tarreang, also widely presented and used as a symbol in important ceremonies, such as celebrations in the month of Muharram, completed Al-Qur'an for children, weddings, births or show the baby's. This information may be useful as guidance for conservation and millet breeding programs in the future.

Phenotypic characters and genetic variations of lurik peanuts (Arachis hypogaea L. var. lurikensis) with Inter Simple Sequence Repeat Ikhsanudin Nur Rosyidi -; Budi Setiadi Daryono
Biodiversitas Journal of Biological Diversity Vol. 21 No. 2 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210227

Abstract. Rosyidi IN, Daryono BS. 2020. Phenotypic characters and genetic variations of lurik peanuts (Arachis hypogaea L. var. lurikensis) with Inter Simple Sequence Repeat. Biodiversitas 21: 629-635. Agriculture is a sector that supports national development, one of its commodities is peanut (Arachis hypogaea L.). The needs and demand for peanuts from the food industry sector increased throughout time. However, the current national production level is unable to fulfill the demand, so the number of peanut imports increased sharply.  Based on this condition, researches to improve peanuts production using Lurik peanuts should be held as a solution to fulfill the need for national consumption because lurik peanuts have a greater number of pods and seeds. This research was aimed to improve the quality and quantity of Lurik peanuts phenotype and analyze the successes through the variations and its molecular character. This research was done in May - July 2018 in Mutihan, Madurejo, Prambanan, Sleman, Yogyakarta and in the Laboratory of Genetics and Breeding of Faculty of Biology, Universitas Gadjah Mada (UGM), Yogyakarta, Indonesia. In this research, Lurik peanuts improvement was conducted by selection and induction with colchicine. The Data was collected qualitatively using Inter Simple Sequence Repeat (ISSR) with  ISSR 8, ISSR 9, UBC 825, UBC 841 primers and electrophoresis while the quantitative method was done using plant phenotype measurement and spectrophotometry, then followed by data analysis using one-way ANOVA and MVSP 3.1 program. The results of this research showed that the characters of Lurik peanuts were different from common peanuts such as in having higher plants, different numbers of seeds per pod, and pattern on the seed coat. These data were supported by the molecular results, with similarity index at 84% meaning that the Lurik peanuts and common peanuts are classified as one same species.

Genetic variation and phylogenetic relationships of Thelymitra javanica (Orchidaceae: Orchidoideae) in East and Central Java, Indonesia I Made Saka Wijaya; Budi Setiadi Daryono; Purnomo
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210343

Abstract. Wijaya IMS, Daryono BS, Purnomo. 2020. Genetic variation and phylogenetic relationships of Thelymitra javanica Blume (Orchidaceae: Orchidoideae) in East and Central Java, Indonesia. Biodiversitas 21: 1174-1181. Thelymitra J.R. Forst & G. Forst is a terrestrial orchid genera and mainly distributed in Australia as a center of its diversification. Moreover, Thelymitra javanica Blume is the only species of Thelymitra found in Asia, especially in Indonesia. In Australia and New Zealand, most of Thelymitra species easily found in lowland, whereas, T. javanica in Indonesia preferred to grows near the peaks of mountains around 2,000-3,000 m asl. The high altitude correlated with high light intensity and lower soil nutrients which require specific adaptation of plant to survive. The wide range of adaptation could be due to the presence of genetic variability among populations of Thelymitra. Therefore, this study was carried out to assess the genetic variability and phylogenetic relationships of T. javanica in East and Central Java. The genetic variability of Thelymitra was evaluated by molecular approaches, which is preferably utilized to determine the plant taxonomy to establish the taxonomic uncertainties. ITS-nrDNA is a popular DNA marker that widely used in phylogenetic study among various taxa. Sequences were analyses using Maximum Likelihood method with 11 in-group, 6 interspecies out-group of Thelymitra, and 2 intergeneric out-group of Thelymitrinae subtribe. The result showed that ITS-nrDNA sequences of T. javanica have no variation in nucleotide compositions and showing polytomy branch in cladogram. Thelymitra javanica also has a close relationship with Thelymitra longifolia J.R. Forst & G. Forst that are endemic to New Zealand.

The ligule ultrastructure of the tidal swamp rice (Oryza sativa) landraces of South Kalimantan, Indonesia, and their genetic diversity and relationship Dindin Hidayatul Mursyidin; Purnomo PURNOMO; Budi Setiadi Daryono
Biodiversitas Journal of Biological Diversity Vol. 22 No. 12 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d221207

Abstract. Mursyidin DH, Purnomo, Daryono BS. 2021. The ligule ultrastructure of the tidal swamp rice (Oryza sativa) landraces of South Kalimantan, Indonesia, and their genetic diversity and relationship. Biodiversitas 22: 5280-5285. In-depth characterization of rice landrace is needed in supporting the future conservation and crop breeding programs. Tidal swamp rice (Oryza sativa L.), belonging to this landrace, provided useful agronomic traits for both programs. In this study, the nine the tidal swamp rice ligule samples, mainly from South Kalimantan, Indonesia, were observed ultrastructurally using the SEM method. The diversity and relationships of this landrace based on the ligule ultrastructure were also determined using PCA and UPGMA methods. Generally the tidal swamp rice showed a unique ultrastructure of their ligule, composed of the large trichomes (prickle hair), small trichomes (micro hair), stomata-like structure, and silica cells, as well as the papillae that line along the veins. In this case, we found four patterns of the prickle hair on the ligule's abaxial surface, which has never been reported previously, namely scattered randomly, lined up on the vein, grid-step-like pattern, and unpatterned. The results of PCA and UPGMA showed that this landrace grouped into the same main three clusters, where Sardani (an outgroup) was included in the second cluster and joined with other cultivars from South Kalimantan. This information may be useful for the development of taxonomy and plant structures, and plant genetics and conservation.

Phenotypic and genetic diversity of watermelon (Citrullus lanatus) in East Java, Indonesia Achmad Amzeri; Kaswan Badami; Pawana Gita; Moh. Alfiyan Syah; Budi Setiadi Daryono
Biodiversitas Journal of Biological Diversity Vol. 22 No. 11 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d221161

Abstract. Amzeri A, Badami K, Pawana G, Alfiyan Syah M, Daryono BS. 2021. Phenotypic and genetic diversity of watermelon (Citrullus lanatus) in East Java, Indonesia. Biodiversitas 22: 5223-5230. The assembly of hybrid watermelon (Citrullus lanatus Thumb.) varieties with superior characters is an effort to meet the needs of watermelon seeds in Indonesia and reduce dependence on imports of watermelon seeds. The morphological characterization of exploratory watermelon plants is needed to support the assembly of superior varieties because morphological characterization will reveal the characteristics of each watermelon tested. In addition, the genetic and phenotypic diversity coefficients, heritability, and correlation between characters are needed to support the assembling of the desired variety. This research aimed to determine morphological diversity, genetic and phenotypic diversity coefficients, heritability, and correlation among characters of watermelon from East Java, Indonesia. The research used a randomized complete block design with ten genotypes as treatment and three replications,. The observed morphological characters were quantitative and qualitative characters. The number of characters was 60 characters. Eight quantitative characters, i.e., flowering date, harvesting date, fruit length, fruit diameter, skin thickness, fruit total soluble solids, number of seeds, and fruit weight were used to calculate the genetic and phenotypic diversity coefficient, heritability, and correlation between characters. Quantitative character data were subjected to analysis of variance, followed with a Duncan Multiple Range Test (p<0.05). The results showed that (i) Grouping based on morphological characters produces dendrograms with similarity coefficients ranging from 0.58 to 0.86 or there was a morphological diversity of 0.14 to 0.42, (ii) The phenotypic diversity coefficient (PDC) was greater than the genotypic diversity coefficient (PDC) in all observed quantitative characters, (iii) The broad sense Heritability values ?? of the tested watermelon genotypes ranged from 0.33 to 0.99, (iv) Fruit weight was significantly and positively correlated with fruit diameter, skin thickness, and number of seeds, (v) G1, G2, and G6 were the genotypes that can be used as parents to assemble superior watermelon varieties.

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