Researcher basic information

• PhD (Agrobiology), Hokkaido University

• https://researchmap.jp/mdwiyanti?lang=en

• https://orcid.org/0000-0001-9042-0612
• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=201701010580625114
• https://scholar.google.com/citations?user=kEAvYekAAAAJ&hl=ja

• 70796606

• https://orcid.org/0000-0001-9042-0612

• 201701010580625114

• Light response
• Shading
• Vitamin E
• Indonesia
• Complex genome
• Orphan crops
• Structural variation
• Stenochlaena palustris
• Tocopherol
• Fern
• Miscanthus
• Soybean
• Underutilized crop
• Nutritional compounds
• Secondary metabolites
• Bioinformatics
• Genetic diversity
• Plant Genetics

• Environmental Science/Agriculture Science, Science in plant genetics and breeding

• Bachelor's degree program, School of Agriculture
• Master's degree program, Graduate School of Global Food Resources
• Doctoral (PhD) degree program, Graduate School of Global Food Resources

Research activity information

• Independent Origin of Phenol Non-responsive Phenotype Caused By Phr1 Variation During Domestication of Asian and African Rice.
  Thet Htar San; Kokoro Iguchi; Daichi Ujiie; Shuhei Okada; Intan Widia Santika; Kiwamu Hikichi; Yoshiyuki Yamagata; Daisuke Fujita; Maria Stefanie Dwiyanti; Yuji Kishima; Yohei Koide
  Rice (New York, N.Y.), 22 Jan. 2026, [International Magazine]
  English, Scientific journal, Phenol color reaction has been used to distinguish between two subspecies of Asian rice (Oryza sativa), indica and japonica. The trait is controlled by one single Phr1 gene, which encodes a PPO enzyme that catalyzes the oxidation of phenolic compounds into brown or black pigments upon contact to phenol solution. In O. sativa, ssp. indica responds to phenol chemical assay by altering the rice hull color to black, whereas ssp. japonica remains unaffected due to mutations that render the gene non-functional. Although the different characteristics between subspecies in Asian rice is well known, there is no information about the variation of this trait in African rice, Oryza glaberrima, which was originated and domesticated independently of Asian rice. In this study, we found both phenol negative and positive lines in O. glaberrima and its wild ancestor O. barthii and detected the responsible non-functional mutation (1-bp deletion) in the exon 1 of the Phr1 gene. Geographical distribution of its haplotype suggested that this mutation originated in O. barthii in Mali and was later inherited by O. glaberrima. The predominance of the non-functional Phr1 alleles in O. glaberrima lines and the occurrence of the identical haplotypes in negative group of both O. barthii and O. glaberrima suggest that the negative phenol reaction was favored during domestication and breeding selection. The presence of a selection event is also supported by low nucleotide diversity of Phr1 locus. However, genetic diversity of Phr1 persists in African rice germplasm, as the functional alleles are still present in O. glaberrima. We also compared the nucleotide diversity of Phr1 in African rice with that in Asian rice and found that their origins of the phenol responsive phenotype are independent. These findings expand the current understanding of African rice domestication and offer the valuable molecular marker for improved rice breeding.
• Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.
  Elias George Balimponya; Maria Stefanie Dwiyanti; Koichi Yamamori; Shuntaro Sakaguchi; Yoshitaka Kanaoka; Yohei Koide; Yuji Kishima
  Plant methods, 21, 1, 125, 125, 03 Oct. 2025, [International Magazine]
  English, Scientific journal, BACKGROUND: The use of Illumina sequencing technologies has enabled the identification and removal of mutations in various plant species. However, the Illumina sequencing method requires a considerable amount of data to ensure its integrity and quality due to the enormous number of false positives. This study aimed to explore an effective genomic data analysis for the detection of heterozygous variant (HV) in rice varieties. RESULTS: We compared the accuracy of four combinations of mapping tools and variant calling pipelines and selected BWA-MEM2 with GATK4.3 HaplotypeCaller. To detect heterozygous de novo polymorphisms such as HVs in the three different rice varieties (Nipponbare, Kitaake, and Hinohikari), we adopted the following cost-saving procedures; secondary references were created in Nipponbare and Kitaake, and generation-based comparison was performed in Hinohikari. The similar HVs were estimated by the three varieties to range from 2.55814 × 10-8 to 4.41860 × 10-8, with an average of 3.10278 × 10-8 per nucleotide in a single rice plant, a rate consistent with observations in other organisms. Of 107 HVs identified in all eight plant samples, nine were found to be non-synonymous, resulting in an average of one non-synonymous HV per plant in a single generation. CONCLUSIONS: We have developed a methodology for the detection of true positive HVs within Illumina sequencing techniques. This system removed false positive HVs, allowing for the estimation of true positive HVs and, consequently, the estimation of the mutation rate. The study outlines a clear, step-by-step procedure that can be employed to detect true HVs in different organisms.
• Organ-Specific Long-Read Transcriptome Assembly of Stenochlaena palustris and Annotation of Anthocyanin Biosynthesis Genes
  Maria Stefanie Dwiyanti; Della Rahmawati; Maria Dewi Puspitasari Tirtaningtya Gunawan Puteri; Deshika Panapitiya; Yanetri Asi Nion; Elza Wijaya; Filiana Santoso
  bioRxiv, Cold Spring Harbor Laboratory, 31 Jul. 2025, [Lead author]
  English, Background: Stenochlaena palustris is valued as a vegetable and medicinal fern native to Southeast Asia; however, it remains largely underrepresented in genomic studies. People in Kalimantan (Indonesia) collect young leaves and fronds from wild populations for use as vegetables or medicines to treat conditions, such as ulcers, stomachaches, fever, diarrhoea, and skin infections. The young leaves and fronds of S. palustris contain flavonoids, polyphenols, and anthocyanins. Here, we present a high-quality organ-specific transcriptome assembly of S. palustris based on long-read RNA sequencing of young leaves. Results: The de novo assembly yielded 47,759 transcripts, with an N50 of 1,524 bp and a BUSCO completeness of 66.6%, consistent with organ-specific transcriptomes. Functional annotation identified key structural and regulatory genes involved in anthocyanin biosynthesis, including genes for chalcone synthase (CHS) and dihydroflavonol 4-reductase (DFR). We further analysed the expression of the selected CHS and DFR genes via qRT-PCR of three phenotypically contrasting young leaf samples. Although no strong correlation was observed between gene expression levels and anthocyanin pigmentation, the results suggest that complex regulation involves post-transcriptional control or developmental timing.Conclusions: This study provides the first long-read transcriptomic resource for S. palustris and valuable data for future investigations of secondary metabolism and gene regulation in ferns. Our findings complement broader fern transcriptome studies by offering tissue-specific resolution and a focused view of pigment biosynthesis.
• Elucidating the relationship between chlorophyll degradation and tocopherol biosynthesis in soybeans through shading
  PDDM Panapitiya; T Nakashima; MS Dwiyanti
  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, 65, 46, 47, Dec. 2024, [Last author]
  English, Research society
• Pigmentation of soybean seed coats via a mutation that abolishes production of multiple-phased siRNAs of chalcone synthase genes.
  Mashiro Yuhazu; Shun Mikuriya; Ayumi Mori; Maria Stefanie Dwiyanti; Mineo Senda; Akira Kanazawa
  Genes & genetic systems, 99, 29 Mar. 2024, [Domestic magazines]
  English, Scientific journal, Lack of pigmentation in seed coats of soybean is caused by natural RNA silencing of chalcone synthase (CHS) genes. This phenomenon is an evolutionary consequence of structural changes in DNA that resulted in the production of double-stranded RNAs (dsRNAs) that trigger RNA degradation. Here we determined that a mutant with pigmented seed coats derived from a cultivar that lacked the pigmentation had a deletion between DNA regions ICHS1 and a cytochrome P450 gene; the deletion included GmIRCHS, a candidate gene that triggers CHS RNA silencing via production of CHS dsRNAs. We also characterized CHS short interfering RNAs (siRNAs) produced in the wild-type seed coats that had CHS RNA silencing. Phased 21-nt CHS siRNAs were detected in all 21 phases and were widely distributed in exon 2 of CHS7, which indicates commonality in the pattern of RNA degradation in natural CHS RNA silencing between distantly related species. These results with the similarities in the rearrangements found in spontaneous mutants suggest that the structural organization that generates dsRNAs that trigger phased siRNA production is vulnerable to further structural changes, which eventually abolish the induction of RNA silencing.
• Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids
  Joyce Njuguna; Lindsay Clark; Alexander Lipka; Kossonou Anzoua; Larisa Bagme; Pavel Chebukin; Maria Dwiyanti; Elena Dzyubenko; Nicolay Dzyubenko; Bimal Ghimire; Xiaoli Jin; Douglas Johnson; Jens Kjeldsen; Hironori Nagano; Ivone Oliverira; Junhua Peng; Karen Petersen; Andrey Sabitov; Eun Seong; Toshihiko Yamada; Ji Yoo; Chang Yu; Hua Zhao; Patricio Munoz; Stephen Long; Erik Sacks
  The Plant Genome, 30 Oct. 2023, [Peer-reviewed]
  English
• Genome-wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus
  Joyce Njuguna; Lindsay Clark; Alexander Lipka; Kossonou Anzoua; Larisa Bagme; Pavel Chebukin; Maria Dwiyanti; Elena Dzyubenko; Nicolay Dzyubenko; Ghimire Bimal; Xiaoli Jin; Douglas Johnson; Hironori Nagano; Junhua Peng; Karen Petersen; Andrey Sabitov; Eun Seong; Toshihiko Yamada; Ji Hye Yoo; Chang Yeon Yu; Hua Zhao; Stephen Long; Erik Sacks
  Global Change Biology Bioenergy, 08 Sep. 2023, [Peer-reviewed]
  English
• Biomass yield in a genetically diverse Miscanthus sacchariflorus germplasm panel phenotyped at five locations in Asia, North America and Europe
  Joyce N. Njuguna; Lindsay V. Clark; Kossonou G. Anzoua; Larisa Bagmet; Pavel Chebukin; Maria S. Dwiyanti; Elena Dzyubenko; Nicolay Dzyubenko; Bimal Kumar Ghimire; Xiaoli Jin; Douglas A. Johnson; Uffe Jørgensen; Jens Bonderup Kjeldsen; Hironori Nagano; Junhua Peng; Karen Koefoed Petersen; Andrey Sabitov; Eun Soo Seong; Toshihiko Yamada; Ji Hye Yoo; Chang Yeon Yu; Hua Zhao; Stephen P. Long; Erik J. Sacks
  GCB Bioenergy, Wiley, 20 Feb. 2023
  Scientific journal
• Genotype by environment model predictive ability in Miscanthus
  Sarah Widener; Joyce N. Njuguna; Lindsay V. Clark; Kossonou G. Anzoua; Larisa Bagme; Pavel Chebukin; Maria S. Dwiyanti; Elena Dzyubenko; Nicolay Dzyubenko; Bimal Kumar Ghimire; Xiaoli Jin; Uffe Jørgensen; Jens Bonderup Kjeldsen; Hironori Nagano; Junhua Peng; Karen Koefoed Peterse; Andrey Sabitov; Eun Soo; Toshihiko; Ji Hye Yoo; Chang Yeon Yu; Hua Zhao; Diego; Erik Sacks; Alexander E. Lipka
  Global Change Biology Bioenergy, 2023, [Peer-reviewed]
  English
• Identification of a Saltol-Independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung.
  Tam Thanh Nguyen; Maria Stefanie Dwiyanti; Shuntaro Sakaguchi; Yohei Koide; Dung Viet Le; Toshihiro Watanabe; Yuji Kishima
  Rice (New York, N.Y.), 15, 1, 65, 65, 18 Dec. 2022, [International Magazine]
  English, Scientific journal, The Mekong Delta River in Vietnam is facing salinity intrusion caused by climate change and sea-level rise that is severely affecting rice cultivation. Here, we evaluated salinity responses of 97 rice accessions (79 landraces and 18 improved accessions) from the Mekong Delta population by adding 100 mM NaCl to the nutrient solution for up to 20 days. We observed a wide distribution in salinity tolerance/sensitivity, with two major peaks across the 97 accessions when using the standard evaluation system (SES) developed by the International Rice Research Institute. SES scores revealed strong negative correlations (ranging from - 0.68 to - 0.83) with other phenotypic indices, such as shoot elongation length, root elongation length, shoot dry weight, and root dry weight. Mineral concentrations of Na+ in roots, stems, and leaves and Ca2+ in roots and stems were positively correlated with SES scores, suggesting that tolerant accessions lower their cation exchange capacity in the root cell wall. The salinity tolerance of Mekong Delta accessions was independent from the previously described salinity tolerance-related locus Saltol, which encodes an HKT1-type transporter in the salinity-tolerant cultivars Nona Bokra and Pokkali. Indeed, genome-wide association studies using SES scores and shoot dry weight ratios of the 79 accessions as traits identified a single common peak located on chromosome 1. This SNP did not form a linkage group with other nearby SNPs and mapped to the 3' untranslated region of gene LOC_Os01g32830, over 6.5 Mb away from the Saltol locus. LOC_Os01g32830 encodes chloroplast glycolate/glycerate translocator 1 (OsPLGG1), which is responsible for photorespiration and growth. SES and shoot dry weight ratios differed significantly between the two possible haplotypes at the causal SNP. Through these analyses, we characterize Doc Phung, one of the most salinity-tolerant varieties in the Mekong Delta population and a promising new genetic resource.
• Evaluation of low-copy nuclear genes SQD1 and pgiC as DNA barcodes for Stenochlaena palustris
  Maria Stefanie Dwiyanti; Naoki Matsuda; Febbyandi Isnanda Pandiangan; Della Rahmawati; Yanetri Asi Nion; Maria D.P.T. Gunawan-Puteri
  Agriculture and Natural Resources, 56, 3, 597, 604, May 2022
  Scientific journal
• Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds
  Elias G. Balimponya; Maria S. Dwiyanti; Toshiaki Ito; Shuntaro Sakaguchi; Koichi Yamamori; Yoshitaka Kanaoka; Yohei Koide; Yoshifumi Nagayoshi; Yuji Kishima
  Breeding Science, Japanese Society of Breeding, 2022
  Scientific journal
• Ionomic Profiling of Rice Genotypes and Identification of Varieties with Elemental Covariation Effects
  Zhang Chengming; Nobuhiro Tanaka; Maria Stefanie Dwiyanti; Matthew Shenton; Hayato Maruyama; Takuro Shinano; Chu Qingnan; Xie Jun; Toshihiro Watanabe
  RICE SCIENCE, 29, 1, 76, 88, Jan. 2022
  English, Scientific journal
• DNA barcoding for identification of major Hokkaido weed species using a variable region in cpDNA
  Hirata Toshiyuki; Nagano Hiroyuki; Dwiyanti Maria Stefanie; Akimoto Masahiro
  Abstracts of Meeting of the CSSJ, 251, 136, 136, CROP SCIENCE SOCIETY OF JAPAN, 2021
  Japanese
• Soybean and wild soybean genetic diversity for new functional food resources, focusing on tocopherol, lutein, and saponin
  Maria Stefanie Dwiyanti
  Journal of Functional Food and Nutraceutical, 2, 1, 29, 42, Academic Research and Community Service Swiss German University, 31 Aug. 2020, [Peer-reviewed], [Lead author]
  Scientific journal, Soybean has been a major protein source for people in East and Southeast Asia. It contains numerous secondary metabolites that are useful for human and animal health, such as isoflavones, polyphenols, tocopherols, lutein, carotenoids, and saponins. Isoflavones are the most popular nutraceutical compounds of soybean. Several soybean varieties having high isoflavones have been developed and utilized as functional food resources. Tocopherols, lutein, and saponins are also antioxidants present in soybean seeds. Tocopherols are known as vitamin E, whereas lutein has potential to prevent age-related macular degeneration. DDMP saponins in soybean is reported to inhibit HIV infection in vitro and prevent colon cancer. Screening of soybean germplasm showed that soybean holds a large genetic diversity of content and composition of tocopherols, lutein and saponins that can be utilized to breed new soybean cultivars. In addition, the wild counterpart of soybean (wild soybean) can also be source of genetic variations useful for soybean breeding. This review will summarize studies on genetic diversity of tocopherols, lutein, and saponins found in soybean and wild soybean.
• Training Population Optimization for Genomic Selection in Miscanthus
  Marcus O. Olatoye; Lindsay V. Clark; Nicholas R. Labonte; Hongxu Dong; Maria S. Dwiyanti; Kossonou G. Anzoua; Joe E. Brummer; Bimal K. Ghimire; Katarzyna Głowacka; Kweon Heo; Xiaoli Jin; Hironori Nagano; Junhua Peng; Chang Y. Yu; Ji H. Yoo; Hua Zhao; Stephen P. Long; Toshihiko Yamada; Erik J. Sacks; Alexander E. Lipka
  G3: Genes|Genomes|Genetics, g3.401402.2020, g3.401402.2020, Genetics Society of America, 26 May 2020, [Peer-reviewed]
  English, Scientific journal, Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus × giganteus (M×g) beyond the single clone used in many programs. Germplasm from the corresponding parental species M. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of M×g clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the genomic selection (GS) prediction accuracies within a 538-member diversity panel of predominately Msi individuals and a 598-member diversity panels of Msa individuals. We then assessed the ability of these two diversity panels to train GS models that predict breeding values in an interspecific diploid 216-member M×g F₂ panel. Low and negative prediction accuracies were observed when various subsets of the two diversity panels were used to train these GS models. To overcome the drawback of having only one interspecific M×g F₂ panel available, we also evaluated prediction accuracies for traits simulated in 50 simulated interspecific M×g F₂ panels derived from different sets of Msi and diploid Msa parents. The results revealed that genetic architectures with common causal mutations across Msi and Msa yielded the highest prediction accuracies. Ultimately, these results suggest that the ideal training set should contain the same causal mutations segregating within interspecific M×g populations, and thus efforts should be to ensure that individuals in the training and validation sets are as closely related as possible.
• A Soybean Deletion Mutant That Moderates the Repression of Flowering by Cool Temperatures.
  Jingyu Zhang; Meilan Xu; Maria Stefanie Dwiyanti; Satoshi Watanabe; Tetsuya Yamada; Yoshihiro Hase; Akira Kanazawa; Takashi Sayama; Masao Ishimoto; Baohui Liu; Jun Abe
  Frontiers in plant science, 11, 429, 429, 2020, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Ambient growing temperature and photoperiod are major environmental stimuli that summer annual crops use to adjust their reproductive phenology so as to maximize yield. Variation in flowering time among soybean (Glycine max) cultivars results mainly from allelic diversity at loci that control photoperiod sensitivity and FLOWERING LOCUS T (FT) orthologs. However, variation in the thermal regulation of flowering and its underlying mechanisms are poorly understood. In this study, we identified a novel mutant (ef1) that confers altered thermal regulation of flowering in response to cool ambient temperatures. Mapping analysis with simple sequence repeat (SSR) markers located the mutation in the upper part of chromosome 19, where no QTL for flowering has been previously reported. Fine-mapping and re-sequencing revealed that the mutation was caused by deletion of a 214 kbp genomic region that contains 11 annotated genes, including CONSTANS-LIKE 2b (COL2b), a soybean ortholog of Arabidopsis CONSTANS. Comparison of flowering times under different photo-thermal conditions revealed that early flowering in the mutant lines was most distinct under cool ambient temperatures. The expression of two FT orthologs, FT2a and FT5a, was dramatically downregulated by cool temperature, but the magnitude of the downregulation was lower in the mutant lines. Cool temperatures upregulated COL2b expression or delayed peak expression, particularly at the fourth trifoliate-leaf stage. Intriguingly, they also upregulated E1, a soybean-specific repressor of FT orthologs. Our results suggest that the ef1 mutation is involved in thermal regulation of flowering in response to cool ambient temperature, and the lack of COL2b in the mutant likely alleviates the repression of flowering by cool temperature. The ef1 mutant can be used as a novel gene resource in breeding soybean cultivars adapted to cool climate and in research to improve our understanding of thermal regulation of flowering in soybean.
• Identification of quantitative trait loci for increased α-tocopherol biosynthesis in wild soybean using a high-density genetic map.
  Cheolwoo Park; Maria Stefanie Dwiyanti; Atsushi J Nagano; Baohui Liu; Tetsuya Yamada; Jun Abe
  BMC plant biology, 19, 1, 510, 510, 21 Nov. 2019, [Peer-reviewed], [Corresponding author], [International Magazine]
  English, Scientific journal, BACKGROUND: Soybean is one of the most important crop sources of tocopherols (Toc). However, the content of α-Toc, an isoform with the highest vitamin E activity in humans, is low in most cultivars. With the aim of broadening genetic variability, we performed quantitative trait locus (QTL) analysis for a high seed α-Toc trait detected in a wild soybean and characterized the sequence polymorphisms and expression profiles of γ-tocopherol methyltransferase (γ-TMT) genes as potential candidates. RESULTS: A recombinant inbred line population was developed from a cross between the low α-Toc breeding line TK780 and the high α-Toc wild accession B04009. The α-Toc content in seeds correlated strongly with the ratio of α-Toc to γ-Toc contents. QTL analysis using a high-density map constructed with 7710 single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA sequencing detected six QTLs involved in α-Toc biosynthesis. Of these, three in chromosomes (Chr) 9, 11, and 12 produced consistent effects during a 2-year trial. B04009 allele at QTLs in Chr9 and Chr12 and TK780 allele at the QTL in Chr11 each promoted the conversion of γ-Toc to α-Toc, which elevated the seed α-Toc content. SNPs and indels were detected between the parents in three γ-TMT genes (γ-TMT1, γ-TMT2, and γ-TMT3) co-located in the QTLs in Chr9 and Chr12, of which some existed in the cis-regulatory elements associated with seed development and functions. In immature cotyledons, γ-TMT3 was expressed at higher levels in B04009 than TK780, irrespective of two thermal conditions tested, whereas the expression of γ-TMT2 was markedly upregulated under higher temperatures, particularly in B04009. CONCLUSIONS: We identified QTLs consistently controlling α-Toc biosynthesis in wild soybean seeds in 2-year trials. The QTL on Chr9 had been previously identified in soybean, whereas the QTLs on Chr11 and Chr12 were novel. Further molecular dissections and characterization of the QTLs may facilitate the use of high α-Toc alleles from wild soybean in soybean breeding and an understanding of the molecular mechanisms underlying α-Toc biosynthesis in soybean seeds.
• Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations
  Nguyen Thanh Tam; Dwiyanti, Maria Stefanie; Koide, Yohei; Nagano, Atsushi J.; Ky, Huynh; Huynh Quang Tin; Nguyen Loc Hien; Le Viet Dung; Kishima, Yuji
  PLANT GENOME, 12, 3, Nov. 2019, [Peer-reviewed]
  English, Scientific journal
• 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice.
  Arbelaez JD; Dwiyanti MS; Tandayu E; Llantada K; Jarana A; Ignacio JC; Platten JD; Cobb J; Rutkoski JE; Thomson MJ; Kretzschmar T
  Rice (New York, N.Y.), 12, 1, 55, Jul. 2019, [Peer-reviewed]
• Genome-wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America
  Lindsay V. Clark; Maria S. Dwiyanti; Kossonou G. Anzoua; Joe E. Brummer; Bimal Kumar Ghimire; Katarzyna Głowacka; Megan Hall; Kweon Heo; Xiaoli Jin; Alexander E. Lipka; Junhua Peng; Toshihiko Yamada; Ji Hye Yoo; Chang Yeon Yu; Hua Zhao; Stephen P. Long; Erik J. Sacks
  GCB Bioenergy, 01 Jan. 2019
• Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential
  Lindsay V. Clark; Maria S. Dwiyanti; Kossonou G. Anzoua; Joe E. Brummer; Bimal Kumar Ghimire; Katarzyna Głowacka; Megan Hall; Kweon Heo; Xiaoli Jin; Alexander E. Lipka; Junhua Peng; Toshihiko Yamada; Ji Hye Yoo; Chang Yeon Yu; Hua Zhao; Stephen P. Long; Erik J. Sacks
  GCB Bioenergy, 01 Jan. 2019
• Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice
  Gwen Iris Descalsota-Empleo; Abd Aziz Shamsudin Noraziyah; Ian Paul Navea; Chongtae Chung; Maria Stefanie Dwiyanti; Reuben Jacob Dicen Labios; Asmuni Mohd Ikmal; Venice Margarette Juanillas; Mary Ann Inabangan-Asilo; Amery Amparado; Russell Reinke; Casiana M. Vera Cruz; Joong Hyoun Chin; B.P. Mallikarjuna Swamy
  Genes, 10, 1, Jan. 2019, [Peer-reviewed]
  Scientific journal
• Characterization and quantitative trait locus mapping of late-flowering from a Thai soybean cultivar introduced into a photoperiod-insensitive genetic background.
  Fei Sun; Meilan Xu; Cheolwoo Park; Maria Stefanie Dwiyanti; Atsushi J Nagano; Jianghui Zhu; Satoshi Watanabe; Fanjiang Kong; Baohui Liu; Tetsuya Yamada; Jun Abe
  PloS one, 14, 12, e0226116, 2019, [Peer-reviewed], [International Magazine]
  English, Scientific journal, The timing of both flowering and maturation determine crop adaptability and productivity. Soybean (Glycine max) is cultivated across a wide range of latitudes. The molecular-genetic mechanisms for flowering in soybean have been determined for photoperiodic responses to long days (LDs), but remain only partially determined for the delay of flowering under short-day conditions, an adaptive trait of cultivars grown in lower latitudes. Here, we characterized the late-flowering (LF) habit introduced from the Thai cultivar K3 into a photoperiod-insensitive genetic background under different photo-thermal conditions, and we analyzed the genetic basis using quantitative trait locus (QTL) mapping. The LF habit resulted from a basic difference in the floral induction activity and from the suppression of flowering, which was caused by red light-enriched LD lengths and higher temperatures, during which FLOWERING LOCUS T (FT) orthologs, FT2a and FT5a, were strongly down-regulated. QTL mapping using gene-specific markers for flowering genes E2, FT2a and FT5a and 829 single nucleotide polymorphisms obtained from restriction-site associated DNA sequencing detected three QTLs controlling the LF habit. Of these, a QTL harboring FT2a exhibited large and stable effects under all the conditions tested. A resequencing analysis detected a nonsynonymous substitution in exon 4 of FT2a from K3, which converted the glycine conserved in FT-like proteins to the aspartic acid conserved in TERMINAL FLOWER 1-like proteins (floral repressors), suggesting a functional depression in the FT2a protein from K3. The effects of the remaining two QTLs, likely corresponding to E2 and FT5a, were environment dependent. Thus, the LF habit from K3 may be caused by the functional depression of FT2a and the down-regulation of two FT genes by red light-enriched LD conditions and high temperatures.
• DNA fingerprinting at farm level maps rice biodiversity across Bangladesh and reveals regional varietal preferences
  Kretzschmar, T.; Mbanjo, E.G.N.; Magalit, G.A.; Dwiyanti, M.S.; Habib, M.A.; Diaz, M.G.; Hernandez, J.; Huelgas, Z.; Malabayabas, M.L.; Das, S.K.; Yamano, T.
  Scientific Reports, 8, 1, 14920, Oct. 2018, [Peer-reviewed]
  Scientific journal
• Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications
  Michael J. Thomson; Namrata Singh; Maria S. Dwiyanti; Diane R. Wang; Mark H. Wright; Francisco Agosto Perez; Genevieve DeClerck; Joong Hyoun Chin; Geraldine A. Malitic-Layaoen; Venice Margarette Juanillas; Christine J. Dilla-Ermita; Ramil Mauleon; Tobias Kretzschmar; Susan R. McCouch
  RICE, 10, 1, 40, Aug. 2017, [Peer-reviewed]
  English, Scientific journal
• Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm
  Christine Jade Dilla-Ermita; Erwin Tandayu; Venice Margarette Juanillas; Jeffrey Detras; Dennis Nicuh Lozada; Maria Stefanie Dwiyanti; Casiana Vera Cruz; Edwige Gaby Nkouaya Mbanjo; Edna Ardales; Maria Genaleen Diaz; Merlyn Mendioro; Michael J. Thomson; Tobias Kretzschmar
  RICE, 10, 1, 8, Mar. 2017, [Peer-reviewed]
  English, Scientific journal
• Identification of quantitative trait loci for panicle length and yield related traits under different water and P application conditions in tropical region in rice (Oryza sativa L.) (vol 213, 37, 2017)
  Ian Paul Navea; Maria Stefanie Dwiyanti; Jonghwa Park; Backki Kim; Sangbum Lee; Xing Huang; Hee-Jong Koh; Joong Hyoun Chin
  EUPHYTICA, 213, 2, 48, Feb. 2017, [Peer-reviewed]
  English, Scientific journal
• Identification of quantitative trait loci for panicle length and yield related traits under different water and P application conditions in tropical region in rice (Oryza sativa L.)
  Ian Paul Navea; Maria Stefanie Dwiyanti; Jonghwa Park; Backki Kim; Sangbum Lee; Xing Huang; Hee-Jong Koh; Joong Hyoun Chin
  EUPHYTICA, 213, 2, Feb. 2017, [Peer-reviewed]
  English, Scientific journal
• Natural diversity of seed alpha-tocopherol ratio in wild soybean (Glycine sofa) germplasm collection
  Maria Stefanie Dwiyanti; Shouhei Maruyama; Mari Hirono; Masako Sato; Euiho Park; Sei Hyung Yoon; Tetsuya Yamada; Jun Abe
  BREEDING SCIENCE, 66, 4, 653, 657, Sep. 2016, [Peer-reviewed]
  English, Scientific journal
• Natural variation in Miscanthus sinensis seed germination under low temperatures
  Maria S. Dwiyanti; J. Ryan Stewart; Aya Nishiwaki; Toshihiko Yamada
  GRASSLAND SCIENCE, 60, 3, 194, 198, Sep. 2014
  English, Scientific journal
• Genetic Analysis of Putative Triploid Miscanthus Hybrids and Tetraploid M. sacchariflorus Collected from Sympatric Populations of Kushima, Japan
  Maria S. Dwiyanti; Arthur Rudolph; Kankshita Swaminathan; Aya Nishiwaki; Yoshiko Shimono; Shotaro Kuwabara; Hiroya Matuura; Marhamah Nadir; Stephen Moose; J. Ryan Stewart; Toshihiko Yamada
  BIOENERGY RESEARCH, 6, 2, 486, 493, Jun. 2013, [Peer-reviewed]
  English, Scientific journal
• Genetic variation of gamma-tocopherol methyltransferase gene contributes to elevated alpha-tocopherol content in soybean seeds
  Maria S. Dwiyanti; Tetsuya Yamada; Masako Sato; Jun Abe; Keisuke Kitamura
  BMC PLANT BIOLOGY, 11, 152, Nov. 2011, [Peer-reviewed]
  English, Scientific journal
• Genetic analysis of high alpha-tocopherol content in soybean seeds
  Maria Stefanie Dwiyanti; Aya Ujiie; Le Thi Bich Thuy; Tetsuya Yamada; Keisuke Kitamura
  BREEDING SCIENCE, 57, 1, 23, 28, Mar. 2007, [Peer-reviewed], [Lead author]
  English, Scientific journal

• S. palustris leaves sampling and RNA extraction v1
  Maria Stefanie Dwiyanti, 02 Oct. 2024, [Lead author]
  

  This is a protocol for leaf sampling of S. palustris in natural habitats as well as RNA extraction method using CTAB+PVP buffer. The extraction will require 3 days.

  , ZappyLab, Inc.
• Morphogenesis modeling of seed pods of soybean
  曳地究; 徳山芳樹; DWIYANTI M.; 小出陽平, 育種学研究, 23, 2021
• 野生ダイズ由来の高ビタミンE含有量の遺伝解析—Genetic Analysis of High Vitamin E Content from Wild Soybean—第22回研究報告会記録
  マリア ステファニ ドゥイヤンティ; Cheolwoo Park; 永野 惇; 山田 哲也; 阿部 純, 大豆たん白質研究 / 不二たん白質研究振興財団 [編], 22, 40, 24, 28, Jun. 2020
  不二たん白質研究振興財団, Japanese
• Genetic Analysis of High Vitamin E Content from Wild Soybean
  DWIYANTI Maria Stefanie; PARK Cheolwoo; 永野惇; 山田哲也; 阿部純, 大豆たん白質研究, 22, 2020
• Relationship between antioxidant ability and total polyphenol content in soybean seeds
  Hayashi Y; Dwiyanti M S; Suzuki T; Nagano A; Abe J; Yamada T, Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, 58, 0, 46, 47, 2017
  日本育種学会・日本作物学会北海道談話会, Japanese
• Forages for feedstocks of biorefineries in temperate environments: review of lignin research in bioenergy crops and some insight into Miscanthus studies
  Maria S. Dwiyanti; J. Ryan Stewart; Toshihiko Yamada, CROP & PASTURE SCIENCE, 65, 11, 1199, 1206, 2014
  English, Book review
• Molecular mapping and breeding for genes/QTLS related to climate change
  Maria Stefanie Dwiyanti; Toshihiko Yamada, Genomics and Breeding for Climate-Resilient Crops, 1, 179, 212, 01 Aug. 2013
  Springer-Verlag Berlin Heidelberg, English
• Molecular mapping and breeding for genes/QTLS related to climate change
  Maria Stefanie Dwiyanti; Toshihiko Yamada, Genomics and Breeding for Climate-Resilient Crops, 1, 179, 212, 01 Aug. 2013
  Springer-Verlag Berlin Heidelberg, English
• Germplasm Resources of Miscanthus and Their Application in Breeding
  Maria Stefanie Dwiyanti; J. Ryan Stewart; Toshihiko Yamada, Bioenergy Feedstocks: Breeding and Genetics, 49, 66, 25 Apr. 2013
  John Wiley and Sons, English
• ダイズの高α‐トコフェロール含有性に関わる候補遺伝子のプロモーター領域における変異性とその特徴づけ
  DWIYANTI Maria S; 山田哲也; 阿部純; 喜多村啓介, 育種学研究, 13, 35, 29 Mar. 2011
  Japanese
• ダイズにおける3つのγ‐トコフェロールメチルトランスフェラーゼ遺伝子の特徴づけ
  MARIA S. Dwiyanti; 山田哲也; 阿部純; 喜多村啓介, 育種学研究, 11, 148, 25 Sep. 2009
  Japanese
• AGFD 26-Breeding trials for enhancing a-tocopherol and lutein contents in seeds of soybean [Glycine max (L.) Merr.]
  Keisuke Kitamura; Shaodong Wang; Kyohei Kanamaru; Maria S. Dwiyanti; Tetsuya Yamada, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 236, Aug. 2008
  English, Summary international conference
• AGFD 28-Development of simple sequence repeat (SSR) markers for breeding soybeans with high alpha-tocopherol concentration
  Maria S. Dwiyanti; Tetsuya Yamada; Jun Abe; Keisuke Kitamura, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 236, Aug. 2008
  English, Summary international conference

• Nutraceuticals in Soybean: Biosynthesis, Advanced Genetic Research, and Usage in Food
  Dwiyanti, M.S; Gunawan-Puteri; M.D.P.T, Page 1-37
  Springer, Jun. 2023, 9789811936272, [Joint work]

• Transcriptome Profiles of Developing Seeds of Two Soybean Varieties Contrasting in Seed Shape
  Maria Stefanie Dwiyanti
  Plant Biology 2024, English, Poster presentation
  22 Jun. 2024 - 26 Jun. 2024, 33961962
• Recent Progress in Soybean Tocopherol Biosynthesis Studies
  Maria Stefanie Dwiyanti
  International Plant & Animal Genome Conference : PAG 30, 17 Jan. 2023, English, Oral presentation
  13 Jan. 2023 - 18 Jan. 2023
• DNA Barcoding of Weed Species in Hokkaido and Application to ex-situ Evaluate of Their Abundance
  Maria Stefanie Dwiyanti; Toshiyuki Hirata; Hironori Nagano; Junya Yamagishi; Masahiro Akimoto
  10th Asian Crop Science Association Conference, 09 Sep. 2021, English, Poster presentation
  08 Sep. 2021 - 10 Sep. 2021
• Discovering genetic variations associated with high α-tocopherol content in soybean and wild soybean
  Maria Stefanie Dwiyanti
  The 6th International Conference on Food, Agriculture, and Natural Resources (IC-FANRES), 05 Aug. 2021, English, Invited oral presentation
  04 Aug. 2021 - 05 Aug. 2021, [Invited]
• Haplotype analysis of γ-tocopherol methyltransferase and its relation to α- tocopherol content in soybean and wild soybean
  Maria Stefanie Dwiyanti; Cheolwoo Park; Atsushi J Nagano; Baohui Liu; Tetsuya Yamada; Jun Abe
  PB20-Plant Biology Worldwide Summit, Jul. 2020, English, Poster presentation
  27 Jul. 2020 - 31 Jul. 2020
• How to promote wet-lab genetics research in Southeast Asia?
  Maria Stefanie Dwiyanti
  Symposium: Challenges for the Education Development on Agriculture and Food Resources in Tropical Asia, Sep. 2019, English, Oral presentation
  Sep. 2019 - Sep. 2019
• Sequence analysis and marker development for high α-tocopherol soybean: targeting γ-tocopherol methyltransferase gene γ-TMT3
  Maria Stefanie Dwiyanti; Cheolwoo Park; PP Ariana; Jun Abe
  The 9th International Conference on Legume Genetics and Genomic, May 2019, English, Oral presentation
  15 May 2019 - 17 May 2019
• Quantitative trait loci analysis regulating seed α-tocopherol ratio in wild soybean
  Cheolwoo Park; Maria Stefanie Dwiyanti; Atsushi J Nagano; Tetsuya Yamada; Jun Abe
  The 9th International Conference on Legume Genetics and Genomic, May 2019, English, Poster presentation
  15 May 2019 - 17 May 2019
• Genomic characterization of the local rice resources in the Mekong Delta of Vietnam
  Nguyen TT; Maria Stefanie Dwiyanti; Yohei Koide; Atsushi J Nagano; Ky Huynh; QT Huynh; VD Le VD; Yuji Kishima
  The 16th International Symposium on Rice Functional Genomics, Sep. 2018, English, Poster presentation
  05 Sep. 2018 - 07 Sep. 2018
• QTL analysis for a high seed α-tocopherol ratio in wild soybean
  Cheolwoo Park; Maria Stefanie Dwiyanti; Atsushi J Nagano; Tetsuya Yamada; Jun Abe
  The 133rd Japanese Society of Breeding Meeting, Mar. 2018, Japanese, Oral presentation
  25 Mar. 2018 - 26 Mar. 2018
• Comparison of genomic selection methods for predicting Miscanthus sinensis yield
  Maria Stefanie Dwiyanti; Lindsay V. Clark; Kossonou Anzoua; Joe E. Brummer; Katarzyna Glowacka; Megan Hall; Kweon Heo; Xiaoli Jin; Alexander E. Lipka; Junhua Peng; Ji Hye Yoo; Chang Yeon Yu; Hua Zhao; Stephen Long; Toshihiko Yamada; Erik J. Sacks
  Plant & Animal Genome Conference, Jan. 2018, English, Poster presentation
  13 Jan. 2018 - 18 Jan. 2018
• Genetic Analysis Underlying High Alpha-tocopherol Content in Wild Soybean
  Maria Stefanie Dwiyanti; Cheol Woo Park; Jun Abe
  INDONESIAN BREEDING SCIENCE SOCIETY (PERIPI), Oct. 2017, English, Oral presentation
  02 Oct. 2017 - 03 Oct. 2017
• Bridging The Genetic Resources and Crop Improvement Through Genomics
  Maria Stefanie Dwiyanti
  the 14th Hokkaido Indonesia Student Scientific Meeting (HISAS 14), 17 Mar. 2017, English, Invited oral presentation
  [Invited]

• 国際農学概論Ⅱ, 2024年, 学士課程, 農学部
• 人口・食料・環境学総論, 2024年, 修士課程, 農学院
• 国際農学特論Ⅱ, 2024年, 修士課程, 農学院
• 大学院共通授業科目（教育プログラム）：One program for Global Goals, 2024年, 修士課程, 大学院共通科目
• 大学院共通授業科目（教育プログラム）：One program for Global Goals, 2024年, 修士課程, 大学院共通科目
• 大学院共通授業科目（教育プログラム）：One program for Global Goals, 2024年, 修士課程, 大学院共通科目
• 一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), 2024年, 学士課程, 全学教育
• 生物資源科学特講, 2024年, 学士課程, 農学部
• 専門横断科目（一般科目）：複合領域, 2024年, 学士課程, 専門横断科目

• Jun. 2020 - Present
  American Society of Plant Biologists
• JAPANESE SOCIETY OF BREEDING

• 新規食品・薬用植物の開発に向けたシダ「カラカイ」の成分分析、遺伝的多様性、網羅的遺伝子発現解析
  アジア地域重点学術研究助成
  Apr. 2024 - Mar. 2025
  公益財団法人平和中島財団, Principal investigator
• ダイズ種子形状と成分を決める発達数理モデルの構築および制御遺伝子の同定
  Dec. 2019 - Oct. 2024
  Maria Stefanie Dwiyanti; 小出 陽平
  Hirose Foundation, Principal investigator
• 北海道雑草種の DNA バーコーディングと群集評価技術への応用
  ロバスト農林水産工学研究プログラム
  Apr. 2019 - Mar. 2021
  平田聡之; Maria Stefanie Dwiyanti; 長野宏則; 山岸潤也; 秋本正博
  北海道大学
• Genetic Analysis of High Vitamin E Content from Wild Soybean
  Apr. 2018 - Mar. 2019
  Maria Stefanie; DWIYANTI; Cheolwoo PARK; Atsushi NAGANO; Tetsuya YAMADA; Jun ABE
  Fuji Foundation for Protein Research
• Genetic and nutraceutical analyses of Indonesian fern Kelakai (Stenochlaena palustris) for new food crop development
  総長室等事業推進経費：総長奨励による若手教員海外派遣支援事業
  Apr. 2018 - Mar. 2019
  Maria Stefanie Dwiyanti
  Hokkaido University