Dr. Rizky Dwi Satrio, S.Si., M.Si.

Complete chloroplast genome of the underutilized legume jack bean (Canavalia ensiformis, Fabaceae) reveals genetic makeup, mutational hotspots, and phylogenetic relationships

Updated information on qualitative leaf anatomical characters of Eusideroxylon zwageri from East Kalimantan, Indonesia

Abstract. Dewi AP, Wulansari TYI, Senjaya SK, Arifiani D, Wanda IF, Lisnawati Y, Sunardi, Prawestri AD, Martiansyah I, Evana, Satrio RD, Hartono AMNK, Suyoko, Yuswandi AY, Syukur M, Sari DK, Rasyl CA. 2025. Updated information on qualitative leaf anatomical characters of Eusideroxylon zwageri from East Kalimantan, Indonesia. Nusantara Bioscience 17: 322-336. Eusideroxylon zwageri, the sole species of its genus (Eusideroxylon) and one of the most economically and culturally significant timbers of Borneo known as Bornean ironwood or “kayu ulin”, has been extensively studied for its ecology, genetics, and conservation, yet its foliar anatomy remains poorly documented. This study provides an updated qualitative assessment of leaf anatomical characters of E. zwageri based on 66 accessions representing five subpopulations in East Kalimantan, Indonesia. Transverse and paradermal sections of the lamina, midrib, and petiole were prepared following standard microtechnique procedures, and 37 anatomical traits were recorded. The results showed that most foliar anatomical features of E. zwageri are consistent with the Lauraceae family. A single character appears diagnostic for E. zwageri—osteosclereids present in the mesophyll of the lamina. Several anatomical features of E. zwageri indicate functional adaptation, including superficial stomata (related to efficient CO2 intake), sclereids (contributing to the hardness and durability of the wood), oil cell distribution (which helps prevent pest attacks), suggesting functional adaptations related to gas exchange efficiency, mechanical reinforcement, and defense against herbivory. Nevertheless, understanding pronounced lignification of sclerenchyma and sclereids may constrain regeneration, posing challenges for conservation. These updated anatomical data provide a foundation for future taxonomic, ecological, and conservation research, particularly in developing propagation strategies to support large-scale restoration of this Vulnerable species.

Genome-Wide SNP Discovery and Population Structure Analysis of 244 Indonesian Local Rice Accessions

Single Nucleotide Polymorphism (SNP) markers are essential tools for the genetic management and breeding of rice, enabling precise characterization of genetic diversity. However, SNP datasets specifically developed for analyzing the population structure of Indonesian local rice remain limited. This study aimed to identify polymorphic SNP markers and analyze the lineage and population structure of 244 Indonesian local rice accessions. BAM files of these accessions were obtained from the 3K Rice Genome Project via the International Rice Informatics Consortium. High-quality SNPs were generated through variant calling and stringent filtering, followed by annotation and population analyses using IR64, DJ123, and Nipponbare as references. A total of 3,839,961 high-quality SNP loci were identified across the 12 rice chromosomes. Hierarchical clustering and principal coordinate analysis consistently grouped the accessions into three major clusters, corresponding to Indica, Japonica, and admixed groups. Population structure analysis confirmed two main subpopulations: Indica and Japonica, with Japonica further divided into Temperate and Tropical subgroups. Eleven accessions showed admixed ancestry. This study provides essential insights into the genetic diversity and population structure of Indonesian local rice, supporting genetic resource conservation, trait discovery, and breeding efforts.

Comparative analysis of the complete chloroplast genome of jack bean (Canavalia ensiformis, Fabaceae) revealed mutational hotspots and phylogenetic relationships

Abstract In recent years, the study of chloroplast genomes has gained increasing attention due to its significance in understanding plant evolution, phylogenetics, and genetic engineering. Canavalia ensiformis, commonly known as jack bean, is a leguminous plant of agricultural and ecological importance, with its chloroplast genome offering potential insights into adaptive mechanisms, species divergence, and biotechnological applications. This study focuses on the structure, organization, and gene content of the C. ensiformis chloroplast genome and its comparative analysis with other members of Phaseoleae (Fabaceae). We assembled and annotated the complete chloroplast genome of C. ensiformis using a combination of Illumina short-reads and Oxford Nanopore long-reads available on GenBank. The C. ensiformis chloroplast genome was organized as a single circular structure of 157,809 bp in length and divided into four main regions: a large single-copy (77,529 bp), a small single-copy (18,934 bp), and a pair of inverted repeat regions (30,673 bp). The genome encoded 95 protein-coding genes, 8 rRNA, and 37 tRNA genes. To explore evolutionary relationships, we conducted a comparative analysis of plastid genomes across Phaseoleae species. Structural variations, gene rearrangements, and divergence in non-coding regions were assessed, revealing conserved synteny and lineage-specific differences within the tribe. The phylogenomic analysis based on plastid genome sequences further clarified the evolutionary placement of C. ensiformis within Phaseoleae. The results contribute to a broader understanding of plastid genome evolution in legumes, one of the most species-rich plant families, and provide valuable genomic resources for future research in molecular phylogenetics and crop improvement.

Identification Hierarchical Selection of Expressed Sequence Tags and their Expression under Drought Stress in Rice

The key components of drought-stress signaling that are responsible for drought tolerance in rice have not been identified yet. Although many expressed sequence tags (ESTs) of rice grown under drought stress have been identified and deposited in the GenBank, they have not been optimally used for functional analyzes. This research was thus established to analyze an EST dataset in order to understand the global gene expression profile induced by drought stress in rice, to discover novel droughttolerance genes using in silico study, and to confirm them through qRT-PCR analysis. A dataset of drought-response-related ESTs in rice was downloaded from the NCBI, preprocessed and grouped into clusters for functional analysis to obtain stressresponsive contigs. These contigs were then hierarchically selected to identify those related to transcription factors. The selected contigs were then incorporated into the drought-tolerant QTL on rice physical maps. The gene expression of each selected locus was evaluated in rice cv. Hawara Bunar and IR64 under drought stress. Gene Ontology analysis showed that the contigs consisted of genes encoding proteins involved in metabolic and cellular processes, related to catalytic and binding function, and located in the nucleus, cell membrane, and endomembrane organelles. Ten candidate genes potentially involved in regulating tolerance of drought stress were identified. They were located on rice chromosomes 1, 2, 3, 4, 6 and 9, and colocalized with the QTL for the drought-tolerance trait. Based on in silico and qRT-PCR analyzes, Os03g0160100, Os03g0815100, Os06g0601000 and Os09g0553100 were considered to be candidates for uncharacterized drought-responsive regulatory genes that potentially being used for manipulating drought tolerance in rice.

SNP-Based molecular characterization of TAD1 , GS3 , and ABA8ox2 genes in Indonesian Rice for early marker discovery

Abstract Improving rice ( Oryza sativa L.) breeding efficiency is essential to address challenges from climate change and population growth. Single-nucleotide polymorphisms (SNPs) serve as valuable markers for detecting genetic variation linked to agronomic traits. This study characterized SNP-based variation in three candidate genes ( TAD1 , GS3 , and ABA8ox2 genes) from Indonesian local and hybrid rice cultivars to identify early diagnostic markers. Primers were designed in silico using UGENE and Primer3Plus, targeting conserved regions and functional domains. Genomic DNA from three cultivars (Hawara Bunar, IPB 3S, and IPB 13S) was amplified using PCR, yielding 522 bp ( TAD1 ), 502 bp ( GS3 ), and 583 bp ( ABA8ox2 ) fragments. TAD1 gene showed the highest SNP count in Hawara Bunar (105 SNPs; 20.11%) and is associated with tall phenotypes, indicating potential as a negative selection marker in semi-dwarf breeding. ABA8ox2 gene displayed moderate variation (4.8%–9.6%) and may support as a positive selection marker. Due to sequencing failure in two cultivars, GS3 gene analysis was limited to IPB 3S, which showed low variation (0.59%), suggesting conservation in this grain size regulator. Despite the lack of phenotypic validation, SNP variations in TAD1, ABA8ox2 , and GS3 highlight their potential as early molecular markers for traits such as tiller number, drought tolerance, and grain size. Integrating phenotypic data in future studies will enable more precise selection in rice breeding programs.

Rice QTL hotspots related with seed grain size, shape, weight, and color based on genome wide association study and linkage mapping

Rice is a staple crop worldwide, with seed traits such as size, shape, weight, and color playing crucial roles in agricultural productivity and consumer preferences. Despite significant progress, the genetic basis underlying the variation in hulled and unhulled seed grain traits remains partially unexplored. This study presents a comprehensive analysis combining GWAS and QTL mapping to dissect the genetic architecture of hulled and unhulled seed characteristics in rice. The aim is to identify quantitative trait loci (QTLs) associated with these traits using an integration of multi-model approach genome-wide association studies (GWAS) and linkage mapping analysis. The study analyzed 244 local rice varieties for GWAS and 90 Recombinant Inbred Lines for linkage mapping analysis. The traits observed included hulled and unhulled seed grain area, perimeter, length, width, length-to-width ratio, circularity, weight, and color (RGB, HSV, Lab, yCbCr). A total of 23 QTL regions were identified, with two major QTL hotspots located on chromosomes 7 and 2. Specifically, QTL hotspots on chromosome 7 were associated with grain size, shape, and weight, while those on chromosome 2 were linked to seed color. A total of 530 SNPs significantly associated with the traits were distributed across 12 rice chromosomes, corroborating the QTL hotspot regions. Six genes on chromosome 7 and seven genes on chromosome 2 were proposed as candidate genes regulating seed grain traits. These findings provide valuable insights into the genetic control of rice seed traits and offer potential targets for breeding programs aimed at improving rice quality and yield.

Temperature, Relative Humidity and Photosynthetic Photon Flux Density Affects the Growth of Phyllanthus niruri L. Seedling

In order to obtain high-quality seedlings, the effects of temperature, relative humidity, and photosynthetic photon flux density (PPFD), the seed of Phyllanthus niruri L. (meniran) were investigated in different microclimate (temperature, relative humidity, PPFD) environments. The present study was conducted from February to May 2024 at the experimental greenhouse and screen house of the National Research and Innovation Agency, Banten, Indonesia. Microclimate parameters were observed thrice daily at 8 am, 12 pm, and 3 pm during the research. The two environments significantly differ in microclimate. The average temperatures, relative humidity, and PPFD of environment 1 are 35.30±5.04 oC, 60.95±17.40%, and 483.33±406.00 µmol m-2 S-1, while environment 2 are 33.07±4.84 oC, 70.47±16.63% and 356.4±339.55 µmol m-2 S-1. All treatments were repeated 18 times. After the 21-day treatment during the seedling stage, P. niruri seedlings were observed, including the germination rate, number of leaves, shoot length, and chlorophyll content index. Results showed that the germination rate, leaves, shoot length, and chlorophyll content index significantly differ between P. niruri seedlings in both environments. Phyllanthus niruri that grow in environment 1 have a higher germination rate than in environment 2, likewise, the number of leaves, shoot length, and chlorophyll content index. This initial research showed that P. niruri seedling grows better in an environment with temperature, relative humidity, and PPFD, respectively 35.30±5.04 oC, 60.95±17.40%, and 483.33±406.00 µmol m-2 S-1.

Allelopathic Activity of Leaf and Root Extracts of Clidemia hirta to Morpho-Physiological Characters of Rice (Oryza sativa) and Some Weeds of Rice Field

The decline in worldwide rice production could be attributed to weed infestations. Weeds hinder the growth of rice plants, leading to reduced rice production. Conversely, the study and potency of extract of Clidemia hirta D.Don as bioherbicide in rice is limited. Based on these characteristics, Cl. hirta is suspected to have allelopathic potential as an herbicide to enhance rice production by inhibiting weed growth. Therefore, this research aimed to analyze the extract of the invasive alien species (IAS) plant Cl. hirta as an allelopathic agent in inhibiting weed growth in rice cultivation. The research methods include the identification and inventory of plant seeds, the preparation of leaf and root extracts of Cl. hirta in a water-based solvent, allelopathy extract tests on rice and weeds in the seedling and vegetative growth stages, morphological character analysis as a physiological response to the extract, and phytochemical tests. The tested weed species include Ageratum conyzoides, Echinochloa crus-galli, Cyperus iria and Ludwigia octovalvis, while the rice variety used is IR64 as a control. In summary, both leaf and root extracts of Cl. hirta inhibit the growth of A. conyzoides, E. crusgalli, Cy. iria and L. octovalvis. In contrast, rice growth was actually stimulated by the extract. Therefore, this study is expected to serve as a reference for the development of bioherbicides for rice cv. IR64.

Tools and Techniques Used at Global Scale Through Genomics, Transcriptomics, Proteomics, and Metabolomics to Investigate Plant Stress Responses at the Molecular Level

A complete chloroplast and mitochondrial genome for velvet bean (Mucuna pruriens, Fabaceae), with genome structure and intergenomic sequence transfers analyses

Abstract Mucuna pruriens , commonly known as the velvet bean, holds considerable economic and cultural importance as a member of the Fabaceae family. The economic value of this plant is derived from its high protein content, medicinal properties, and potential applications in agriculture and industry. Although the entire nuclear genome consisting of 11 chromosomes of M. pruriens has been published, the comprehensive assembly of the organelle genome, specifically the mitochondria, has not been previously accomplished. The evaluation of sequence transfer from both the chloroplast and mitochondrial genomes to the nuclear genome has not been conducted. The complete chloroplast and mitochondrial genome of M. pruriens var. utilis was assembled and annotated through the utilization of a hybrid approach involving Illumina short-reads and Oxford Nanopore long-reads. The genome of chloroplasts was found to be arranged in a singular circular structure measuring 155,617 bp in length. This structure encompassed a total of 75 genes responsible for encoding proteins, along with 4 genes for ribosomal RNA and 28 genes for transfer RNA. The organization of the mitochondrial genome consisted of a singular circular structure measuring 410,745 bp in length, encompassing a total of 39 protein-coding genes, 4 ribosomal RNA genes, and 16 transfer RNA genes. Through the analysis of sequence transfer, it has been determined that a total of 154,498 bp and 158,285 bp of DNA, derived from the chloroplast and mitochondrial genome respectively, have been incorporated into the nuclear genome. These transfer events predominantly occurred in a relatively recent timeframe. The frequency of transfers of chloroplast to nuclear genome sequences was found to be similar to that of transfers of mitochondrial to nuclear genome sequences. This study presents the initial assembly of the entire organelle, specifically the mitochondrial genome of M. pruriens , which serves as a valuable tool for comprehending the genomic evolution within the diverse Fabaceae family.

Preliminary study on variations in local varieties of bornean ironwood (Eusideroxylon zwageri Teijsm. & Binn.) based on vegetative characters

Abstract Bornean Ironwood ( Eusideroxylon zwageri ), a monotypic species of Eusideroxylon , is threatened due to its rarity in its natural habitat. It is a Class I timber commodity in Indonesia and known with several local varieties determined by local people. This study aimed to described the local varieties of ironwood from Kalimantan by taxonomic study. Field exploration had been carried out during 2022 to 2023 in North Kalimantan, East Kalimantan, and West Kalimantan provinces to collect herbarium specimens of ironwood local varieties. The specimens were then observed and characterized in Laboratory of Plant Biosystematics-BRIN. Observation was also done for ironwood collection available at Herbarium Bogoriense. Fourty one characters extracted from vegetative parts, such as stems, twigs and leaves were used to find clades within ironwood species. Phenetic analysis generated six clades in which hair characters on twigs and leaves and color variations of twigs and petiole were the main informative characters that differentiate between clades at an infraspecific level. Anatomical characters cannot be used as supporting characters in this study. Support from deeper morphological analysis involving more specimens and species groups affiliated with the genus Eusideroxylon , as well as molecular analysis is needed to strengthen the grouping at an infra-specific level.

Integrating Differential Expression and Weighted Correlation Network Analysis for Identifying Genes Controlling Shoot Development in Sorghum Bicolor

Mapping and identification of QTL for agro-physiological traits in rice (Oryza sativa L.) under drought stress

Integrating differential expression and weighted correlation network analysis for identifying genes controlling shoot development in Sorghum bicolor

Supplementery materials of journal article "Integrating differential expression and weighted correlation network analysis for identifying genes controlling shoot development in Sorghum bicolor"

Construction of an ultra-high-density consensus genetic map and analysis of recombination rate variation in Sorghum bicolor

Abstract. Satrio RD, Nikmah IA, Fendiyanto MH, Pratami MP, Awwanah M, Sari NIP, Farah N, Nurhadiyanta. 2022. Construction of an ultra-high-density consensus genetic map and analysis of recombination rate variation in Sorghum bicolor. Asian J Agric 6: 47-54. Sorghum is one of the most widely grown cereal crops on a global scale. A consensus map is a method for combining genetic information from multiple populations, and it is an effective way to increase genome coverage and marker density. This study constructed a consensus map by combining publicly available marker data from four mapping populations. A total of 3449 non-redundant polymorphic markers at the nucleotide level were used to construct a single consensus map on 10 sorghum chromosomes. This study generated an ultra-high-density sorghum consensus map consisting of a large number of markers spanning 1571.68 cM and averaging one marker per 0.46 cM. Due to the high density of the markers, it is only 0.06% of the markers had an interval greater than 5 cM. The rates of local recombination were estimated using a set of all markers genetic and physical positions along each of the 10 chromosomes. The analysis of the recombination rate on 10 sorghum chromosomes revealed that it decreased as the centromere position was getting closer. The consensus map generated in this study can be used to integrate information related to sorghum genetic resources and QTLs to the genome sequence, thereby accelerating the discovery of novel potential genes in sorghum.

Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress

Construction of an Ultra-High-Density Consensus Linkage Map in Sorghum bicolor

A consensus genetic map were created by merging linkage maps from four published studies (Ji et al. 2017; Lopez et al. 2017; Kong et al. 2018; Phuong et al. 2019) using package LPmerge of R software.

Short Communication: Identification of spoilage fungi in Myristica fragrans using DG18 and CYA Media

Abstract. Fendiyanto MH, Satrio RD, Pratami MP, Nikmah IA. 2021. Short Communication: Identification of spoilage fungi in Myristica fragrans using DG18 and CYA Media. Asian J Trop Biotechnol 18: 51-54. To date, very few studies have been conducted on the identification of spoilage fungi in Myristica fragrans. Therefore, this study aimed to identify the spoilage fungi in Myristica fragrans growing on DG18 media and CYA Identification Media. Isolation of the fungus was carried out by the dilution plating method using a dilution range of 10-1 to 10-5. The isolation results at 10-2 and 10-3 dilutions on nutmeg (Myristica fragrans) seed samples indicated the presence of Aspergillus niger and A. flavus. The fungal species that could be found and identified using the direct plating method were A. niger, A. flavus, Penicillium citrinum, and Fusarium sp. The results of fungal isolation showed that the species of spoilage fungi on postharvest of M. fragrans seeds, including Aspergillus flavus, A. niger, A. tamarii, Endomyces fibuliger, Eurotium chevalieri, E. repens, and Penicillium citrinum, Trichoderma sp. The highest population of spoilage fungi isolated from Myristica fragrans seeds was Aspergillus niger. This finding indicates that A.niger can be identified as spoilage fungi isolated from Myristica fragrans.

Potential of invasive alien species Clidemia hirta as antibacterial against Salmonella typhi and Staphylococcus aureus

Abstract. Pratami MP, Fendiyanto MH, Satrio RD, Widana IDKK, Nikmah IA, Sari NIP, Awwanah M, Farah N, Darmadi D. 2021. Potential of invasive alien species Clidemia hirta as antibacterial against Salmonella typhi and Staphylococcus aureus. Biodiversitas 22: 3363-3369. Clidemia hirta D. Don is an invasive alien species (IAS) that is a threat to biodiversity in tropical country particularly Indonesia, and remains underutilized to date. Conversely, prevalence of typhus in Indonesia is generally higher every year. Thus, the aim of this study was to detect phytochemicals in ethanolic and aqueous extracts of C. hirta and their antibacterial activity against Salmonella typhi and Staphylococcus aureus. The research methods included sample identification, generating the simplicia, determination of water content, extraction, phytochemical screening tests, and antibacterial activity tests. Identification was made based on morphological characteristics. The water content in the dried powder of simplicia was 12.26 ± 0.39%. Phytochemical results showed that 70% ethanol extract of C. hirta contained flavonoids, saponins, tannins, and triterpenoids compounds. In addition, aqueous extract of C. hirta showed positive results on flavonoids, saponins, tannins, and steroids tests. Antibacterial activity results showed that ethanolic extracts of C. hirta inhibited S. typhi and S. aureus at all concentrations, while aqueous extract inhibited bacterial growth in only 12.5% ??and 25% concentrations. These findings indicate that C. hirta has antibacterial activity that inhibits S. typhi and S. aureus. This information can be used for adding preliminary data to metabolite interest researchers, i.e., biologists and biotechnologists in the future.

OsGERLP: A novel aluminum tolerance rice gene isolated from a local cultivar in Indonesia

There is a decrease in the land available for rice cultivation due to the rapid conversion to urban uses. Subsequently, acid soil could be an alternative land cultivating rice, but will require the use of aluminum (Al)-tolerant rice varieties. This Al tolerance trait is genetically controlled, and there is a need to discover more genes needed to develop Al-tolerant rice. Therefore, the objective of this study was to clone and characterize a novel Al tolerance gene isolated from a local cultivar of Indonesian rice. The gene cloning was conducted based on the rye/rice microsynteny relationship. In addition, the root growth and gene expression analyses were performed to verify the role of the gene on Al tolerance in gene-silenced rice and in overexpressed transgenic tobacco. The results showed an Al tolerance candidate gene, OsGERLP, was successfully cloned from rice cv. Hawara Bunar, with its gene encoding a protein similar to a bacterial ribosomal L32 protein. Additionally, the analysis showed that low gene expression caused the gene-silenced rice to be sensitive to Al, while high expression induced the Al tolerance in transgenic tobacco. Furthermore, it was discovered that the gene expression level in both plants was in line with the lower expression of the OsFRDL4 gene in the silenced rice and the high expression of the MATE gene in transgenic tobacco also with the higher citrate secretion from transgenic tobacco roots. In conclusion, the OsGERLP gene could act as a regulator for other Al tolerance genes, with the potential to develop Al-tolerant rice varieties.

Differential hierarchical metabolites expression of red/white Salacca sumatrana arillus and its molecular docking studies

Abstract. Fendiyanto MH, Satrio RD, Widana IDKK, Pratami MP, Nikmah IA, Darmadi D. 2021. Differential hierarchical metabolites expression of red/white Salacca sumatrana Arillus and its molecular docking studies. Biodiversitas 22: 1014-1024. Salak Sidempuan (Salacca sumatrana) is one of the medicinal plants originating from tropical countries. However, there is very little research on the study of finding bioactive compounds in S. sumatrana using the metabolomic approach. Here, we use two population types of S. sumatrana, e.g., fruit with red and white arillus. We extracted the compounds from the two tissues using the GC-MS technique and further analyzed their antiviral potential using an in-silico molecular docking technique. Fold change analysis showed that in white arillus there were 21 upregulated compounds and 25 downregulated compounds. Metabolites that have high expression in white arillus tissue are ranxinic acid, nicotinic alcohol, stearic acid, 2-furan carboxaldehyde, and others. Six accessions from S. sumatrana based on PCA analysis and separate dendrogram according to the type of arillus, i.e., red and white arillus. Two compounds that act as antivirals found in this study are stearic acid and palmitic acid based on preliminary molecular docking studies. These two compounds could be used for further studies as a preventive measure against SARS-Cov-2 in the future, however, it needs further comprehensive and clinical analysis the future. In conclusion, metabolites in white arillus were distinctly different from red arillus of Snake fruits. In addition, studies on differential metabolite expression on two types of arillus (red/white) can be used as markers in identifying arillus color early by plant breeders.

Analysis of Superoxide Dismutase (OsSOD) Gene Expression using qRT- PCR, its Morphophysiological Characters and Path Analysis in Rice Variety IR64 Under Aluminum Stress

Rice treated with aluminum (Al) can produce active oxygen species (AOS). The existence of AOS can cause the rice plants to become morpho-physiologically damaged and eventually cause a decrease in productivity. The AOS reductive compounds are physiologically responded by plants using antioxidant compounds, one of which is the superoxide dismutase enzyme (SOD). Therefore, this research aimed to analyze FeSOD, MnSOD and CuZnSOD gene expressions in IR64 rice variety as information for selection and genetic improvement of rice to overcome national food security. We tested the root architecture, analyzed SOD gene expression and performed path analysis tests. The results showed that rice treated with aluminum (Al) showed dramatically increased CuZnSOD and FeSOD gene expression, while MnSOD gene expression was relatively the same under Al stress or normal conditions. The level of expression of the two genes positively correlated with physiological characteristics such as chlorophyll and root length. Thus, these two genes can be used as markers in studying Al tolerance in Indica cv. rice. IR64.

Genomic Improvement of Rice for Drought, Aluminum, and Iron Toxicity Stress Tolerance

Identification, aflatoxin content, and antagonistic test of spoilage fungi in bread to Aspergillus niger

Abstract. Fendiyanto MH, Satrio RD. 2020. Identification, aflatoxin content, and antagonistic test of spoilage fungi in bread to Aspergillus niger. Bioteknologi 17: 60-66. The major problem in shelf storage life in bread is contamination by molds, fungi and mycotoxins. The growth of spoilage fungi indicates that the bread has structural damage. Infection from this fungus will affect the shelf life of the bread to be shorter. Contaminated bread may influenced human health in the future. One of the many solutions to overcome the fungi-contamination of bread is the use of biological agents. Aspergillus niger has the ability, as a biological agent, to suppress food-destroying pathogens in many foods, including bread. However, there are few reports about the antagonistic test in bread, particularly between A.niger as biological control agent to spoilage fungi. Therefore, this study aimed to analyze the growth antagonistic test of A. niger against food spoilage fungi, expecting the storage life of bread could be extended and mycotoxin contamination avoided. The antagonistic test was in the form of a test that utilizes the properties of microorganisms that grow faster than pathogens or produce antibiotic compounds. The methods used in this study included isolation and identification of fungi, water content analysis, aflatoxin test, and antagonistic test. Interestingly, the antagonist test results showed A. niger can inhibit the growth of spoilage fungi on bread. In conclusion, the species of fungus with the highest inhibition value was Hyphopichia burtonii, while the lowest was Saccharomyces cerevisiae. These findings indicate that A.niger can be used as a biological control in extending bread shelf storage in the future.

Metabolic profiling and pathway analysis in red arillus of Salacca sumatrana demonstrate significant pyruvate, sulfur, and fatty acid metabolisms

Abstract. Fendiyanto MH, Satrio RD, Darmadi D. 2020. Metabolic profiling and pathway analysis in red arillus of Salacca sumatrana demonstrate significant pyruvate, sulfur, and fatty acid metabolisms. Biodiversitas 21: 4361-4368. Salak or snake fruit (Salacca Reinw.; Arecaceae) is a tropical fruit that has high biodiversity in a tropical country such as Indonesia. Several types of salak can be found in Indonesia, one of which is Salacca sumatrana (Becc.) Mogea. Research on profiling metabolites in S. sumatrana has not been conducted. Therefore, the aim of this study was to determine the metabolite profile and pathway analysis in S. sumatrana, especially in red arillus tissue. This research was conducted by the method of gas chromatography-mass spectrometry (GC-MS) and the study of bioinformatics through metabolomics approaches. The results showed that red arillus had metabolites consisting of groups of fatty acids, esters, alcohols, xylene, phenols, etc.. Significant metabolites found were isobutyl acetate, palmitic acid, formic acid, 2-pentanoic acid, ethylic acid, n-hexadecoic acid, hydroxypentanoic acid, etc. There was a tendency that metabolite ethylic acid, identified as C00033 accession, was a key metabolite in either the pyruvate metabolism pathway or sulfur metabolisms with relatively high impact values. Pathway analysis using bioinformatics studies using MetaboAnalyst shows that four of ten pathways detected had a high log-ratio (p)/pathway impact, i.e., pyruvate metabolism, sulfur metabolism, fatty acid biosynthesis, and biosynthesis of unsaturated fatty acids. Thus, pyruvate, sulfur, and fatty acid metabolisms are important pathways in the red arillus of S. sumatrana. This study can be used as a reference in early metabolomic studies on S. sumatrana using GC-MS and the metabolites identified as metabolite markers can be used for plant breeding and biologists to understand the metabolic mechanism of the red arillus tissues from S. sumatrana.

QTL for aluminum tolerance on rice chromosome 3 based on root length characters.

Correlation among Snpb11 markers, root growth, and physiological characters of upland rice under aluminum stress

Abstract. Fendiyanto MH, Satrio RD, Suharsono, Tjahjoleksono A, Miftahudin. 2019. Correlation among Snpb11 markers, root growth, and physiological characters of upland rice under aluminum stress. Biodiversitas 20: 1243-1254. The cultivation of upland rice in acid soils faces aluminum (Al) toxicity. Development of Al-tolerant rice could be one of the solutions to overcome the problem. Marker-assisted breeding to develop Al-tolerant rice requires at least a molecular marker for foreground selection. Snpb11 is a molecular marker developed from the nucleotide differences in a specific allele between Al-tolerant and sensitive rice. Snpb11 has never been used as a molecular marker in rice. Therefore this study aimed to examine the correlation among Snpb11 marker, root growth, and physiological characters under Al stress in upland rice. We used physiological characters and the Snpb11 marker to justify the Al tolerance level in several upland rice varieties. We found that physiological characters, i.e.: primary root length, total root length, chlorophyll, and carotenoid content showed positive correlation to Snpb11. Conversely, root malondialdehyde content, which represents the level of lipid peroxidation showed a negative correlation to Snpb11. There is evidence that the Snpb11 highly correlated with primary and total root length characters, which are the Al tolerance parameters used in rice. Therefore, Snpb11 markers can be used to distinguish the Al tolerance level in upland rice.

Identification of drought-responsive regulatory genes by hierarchical selection of expressed sequence tags and their expression under drought stress in rice.

Identifikasi Gen Responsif Kekeringan Melalui Analisis Profil Ekspresi Gen-Gen pada Tanaman Padi.

IAS (Invasive Alien Species) clidemia hirta d.don sebagai antibakteri dalam upaya mengatasi penyakit tifus