Researcher Profile and Settings

Master

Affiliation (Master)

• Research Faculty of Agriculture　Research Innovation and Cooperation　Cooperative Promotion

Affiliation (Master)

• Research Faculty of Agriculture　Research Innovation and Cooperation　Cooperative Promotion

researchmap

Profile and Settings

Degree

• PhD (Agrobiology)（Hokkaido University）

Profile and Settings

• Name (Japanese)

  Dwiyanti

• Name (Kana)

  Maria Stefanie

• Name

  201701010580625114

Alternate Names

https://scholar.google.com/citations?user=kEAvYekAAAAJ&hl=ja

Achievement

Research Interests

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

Research Areas

• Environmental science/Agricultural science / Plant genetics and breeding

Research Experience

• 2016/10 - Today Research Faculty of Agriculture Assistant professor
• 2013/04 - 2016/10 International Rice Research Institute Postdoctoral Fellow
• 2011/04 - 2013/03 Field Science Center for Northern Biosphere, Hokkaido University

Education

• 2008/04 - 2011/03  Hokkaido University  Graduate School of Agriculture
• 2006/04 - 2008/03  Hokkaido University  Graduate School of Agriculture
• 2002/04 - 2006/03  Hokkaido University  Faculty of Agriculture

Published Papers

• 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 2024/03/29 

  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 2023/10/30 [Refereed]
  
• 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 2023/09/08 [Refereed][Not invited]
  
• 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 1757-1693 2023/02/20
• 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 [Refereed]
  
• 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 2022/12/18 

  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 2468-1458 2022/05 

  Importance of the work: Identifying potential low-copy nuclear genes as DNA barcodes is needed because there is little genetic information on Stenochlaena palustris. Objectives: To sequence the nuclear genes SQD1 and pgiC and to evaluate their suitability as DNA barcodes for S. palustris. Materials & Methods: SQD1 and pgiC were amplified using the DNA of 19 S. palustris samples collected from five locations in Central Kalimantan, Indonesia. The polymerase chain reaction (PCR) products were sequenced using direct Sanger sequencing methods and the chromatograms were examined. The resulting nucleotides were compared within S. palustris and with the known SQD1 and pgiC sequences of other ferns. Results: Direct sequencing showed that SQD1 was present as a single copy and the nucleotide sequence was highly conserved among S. palustris samples. It also showed nucleotide variations compared with SQD1 from other ferns. On the other hand, pgiC produced a single copy of sequence in seven samples but multiple PCR products in the remaining samples. Based on results of the seven samples, pgiC was conserved within S. palustris. Nucleotide variations were observed between pgiC from S. palustris and that from other Blechnaceae ferns. Main finding: This was the first report on the SQD1 and pgiC sequence of S. palustris. The availability of both sequences will support species identification of S. palustris, in addition to using chloroplast genes.
• 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 1344-7610 2022
• 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 1672-6308 2022/01 

  Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus, indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production.
• 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 日本作物学会 251 136 - 136 2021
• 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 2685-9297 2020/08/31 [Refereed]
   

  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 2020/05/26 [Refereed][Not invited]
   

  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 [Refereed][Not invited]
   

  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 2019/11/21 [Refereed][Not invited]
   

  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) 1940-3372 2019/11 [Refereed][Not invited]
   

  Recent analyses using single nucleotide polymorphism (SNP) are a feasible mean for local collections which potentially possess useful, but not large, genetic variations. Genomic sequences of more than 3000 accessions released by the International Rice Research Institute (IRRI) can be used to characterize various local rice (Oryza sativa) populations. The aim of this study was to develop a method to facilitate genomic characterization of local rice populations. We mainly used 99 indica rice accessions (81 landraces and 18 improved varieties) from the Mekong Delta Development Research Institute (MDI). We obtained 2301 SNPs after a genomic sequencing analysis of the 99 rice accessions and subsequent filtering. Within the IRRI's dataset, the landraces fell into a cluster consisting of accessions from Southeast Asian countries (Ind3 cluster), and the MDI improved varieties were grouped in a cluster containing IRRI improved varieties (Ind1B cluster). A principal component analysis suggested that geographical location strongly affects phylogenetic relationships, and the MDI landraces were placed into a Vietnam+Cambodia group. To detect the nucleotide diversity within a population, pi-value is commonly used. We think that whole genome distribution of pi-values representing the nucleotide diversity of each population can be used to characterize local populations. Our simple profiling using low pi-value genomic regions was able to reveal regional characteristics of rice genomes and should be useful for identifying local rice populations.
• 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  1939-8425 2019/07 [Refereed][Not invited]
  
• 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 1757-1693 2019/01/01 [Not refereed][Not invited]
   

  © 2019 The Authors. GCB Bioenergy Published by John Wiley & Sons Ltd To improve the efficiency of breeding of Miscanthus for biomass yield, there is a need to develop genomics-assisted selection for this long-lived perennial crop by relating genotype to phenotype and breeding value across a broad range of environments. We present the first genome-wide association (GWA) and genomic prediction study of Miscanthus that utilizes multilocation phenotypic data. A panel of 568 Miscanthus sinensis accessions was genotyped with 46,177 single nucleotide polymorphisms (SNPs) and evaluated at one subtropical and five temperate locations over 3 years for biomass yield and 14 yield-component traits. GWA and genomic prediction were performed separately for different years of data in order to assess reproducibility. The analyses were also performed for individual field trial locations, as well as combined phenotypic data across groups of locations. GWA analyses identified 27 significant SNPs for yield, and a total of 504 associations across 298 unique SNPs across all traits, sites, and years. For yield, the greatest number of significant SNPs was identified by combining phenotypic data across all six locations. For some of the other yield-component traits, greater numbers of significant SNPs were obtained from single site data, although the number of significant SNPs varied greatly from site to site. Candidate genes were identified. Accounting for population structure, genomic prediction accuracies for biomass yield ranged from 0.31 to 0.35 across five northern sites and from 0.13 to 0.18 for the subtropical location, depending on the estimation method. Genomic prediction accuracies of all traits were similar for single-location and multilocation data, suggesting that genomic selection will be useful for breeding broadly adapted M. sinensis as well as M. sinensis optimized for specific climates. All of our data, including DNA sequences flanking each SNP, are publicly available. By facilitating genomic selection in M. sinensis and Miscanthus × giganteus, our results will accelerate the breeding of these species for biomass in diverse environments.
• 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 1757-1693 2019/01/01 [Not refereed][Not invited]
   

  © 2019 The Authors. GCB Bioenergy Published by John Wiley & Sons Ltd. To breed improved biomass cultivars of Miscanthus ×giganteus, it will be necessary to select the highest-yielding and best-adapted genotypes of its parental species, Miscanthus sinensis and Miscanthus sacchariflorus. We phenotyped a diverse clonally propagated panel of 569 M. sinensis and nine natural diploid M. ×giganteus at one subtropical (Zhuji, China) and five temperate locations (Sapporo, Japan; Leamington, Ontario, Canada; Fort Collins, CO; Urbana, IL; and Chuncheon, Korea) for dry biomass yield and 14 yield-component traits, in trials grown for 3 years. Notably, dry biomass yield of four Miscanthus accessions exceeded 80 Mg/ha in Zhuji, China, approaching the highest observed for any land plant. Additionally, six M. sinensis in Sapporo, Japan and one in Leamington, Canada also yielded more than the triploid M. ×giganteus ‘1993-1780’ control, with values exceeding 20 Mg/ha. Diploid M. ×giganteus was the best-yielding group at the northern sites. Genotype-by-environment interactions were modest among the five northern trial sites but large between Zhuji, and the northern sites. M. sinensis accessions typically yielded best at trial sites with latitudes similar to collection sites, although broad adaptation was observed for accessions from southern Japan. Genotypic heritabilities for third year yields ranged from 0.71 to 0.88 within locations. Compressed circumference was the best predictor of yield. These results establish a baseline of data for initiating selection to improve biomass yield of M. sinensis and M. ×giganteus in a diverse set of relevant geographies.
• Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice.

  Descalsota-Empleo GI, Noraziyah AAS, Navea IP, Chung C, Dwiyanti MS, Labios RJD, Ikmal AM, Juanillas VM, Inabangan-Asilo MA, Amparado A, Reinke R, Cruz CMV, Chin JH, Swamy BPM

  Genes 10 (1) 2019/01 [Refereed][Not invited]
  
• 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 [Refereed][Not invited]
   

  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 EGN, Magalit GA, Dwiyanti MS, Habib MA, Diaz MG, Hernandez J, Huelgas Z, Malabayabas ML, Das SK, Yamano T

  Scientific reports 8 (1) 14920  2018/10 [Refereed][Not invited]
  
• 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  1939-8425 2017/08 [Refereed][Not invited]
   

  Background: Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit "sweet spot" for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice. Results: Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina's production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing similar to 7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material. Conclusions: The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.
• 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  1939-8425 2017/03 [Refereed][Not invited]
   

  Background: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding. Results: A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes. Conclusions: The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in improving and diversifying resistance to BB.
• 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  0014-2336 2017/02 [Refereed][Not invited]
  
• 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) 0014-2336 2017/02 [Refereed][Not invited]
   

  Climate change is projected to have a serious impact on the yield potential of rice in tropical as well as in temperate countries. It is therefore essential to develop rice varieties which are climate change ready and with stable yield when grown under low inputs of irrigation water and fertilizer. In this study, the effects of the shift from temperate to tropical environment as well as the different levels of water regime-phosphorus application were evaluated using a set of temperate recombinant inbred lines (RILs) derived from a cross between Dasanbyeo (Tongil-type indica) and TR22183 (temperate japonica). Here, we have identified genetic mechanisms for yield stability mainly by observing the panicle length in the RILs and the parental lines. TR22183 grown in the Philippines showed no reduction in panicle length whereas the Dasanbyeo exhibited a considerable reduction in panicle length when grown in the Philippines compared to those grown in Korea. In the RILs, a total of 18 QTLs for panicle length were identified across 12 chromosomes except in chromosomes 6 and 7. There were six interesting panicle length QTLs, qPL1.4, qPL2.1, qPL2.2, qPL4.1, qPL9.2, and qPL11.2 on chromosomes 1, 2, 4, 9, and 11 respectively. They were clustered together with other yield-related QTLs such as spikelet number and grain number in two different years. Except for qPL2.1, all the beneficial alleles originated from TR22183. The panicle length QTLs were identified across different water-P treatments. Interestingly, qPL1.4, qPL2.1, qPL4.1, and qPL11.2 were constantly detected in the low-input tropical condition. No QTL for panicle length was identified in the parallel experiment conducted under temperate conditions in Korea suggesting that the QTLs identified in tropical conditions could be useful in breeding programs to develop rice varieties that have stable yield potential under a warming temperate climate.
• 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 1344-7610 2016/09 [Refereed][Not invited]
   

  Alpha-tocopherol is one of four tocopherol isoforms and has the highest vitamin E activity in humans. Most cultivated soybean seeds contain gamma-tocopherol as the predominant form, and the ratio of alpha-tocopherol content to total tocopherol content (alpha-tocopherol ratio) is <10%. Three soybean accessions from Eastern Europe have a-tocopherol ratios of >20%. This higher content is likely due to mutations in the promoter region of the gamma-tocopherol methytransferase-3 (gamma-TMT3) gene. We surveyed a wild soybean germplasm collection and detected 16 accessions with stable seed a-tocopherol ratios of >20% under different growth conditions. The alpha-tocopherol ratios were greatly reduced when the plants were grown under cool temperatures during seed maturation, but increased to varying degrees at higher temperatures. Sequence analysis of the gamma-TMT3 promoter of 11 of the accessions identified four haplotypes, one of which corresponded to that of cultivars with higher contents. These wild accessions can thus serve as novel donors for breeding cultivars with high alpha-tocopherol ratios and for better understanding the genetic basis of alpha-tocopherol synthesis in soybean.
• 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 1744-6961 2014/09 [Not refereed][Not invited]
   

  Species within the genus Miscanthus show potential as sustainable bioenergy crops given their low nutrient requirements and high biomass yields. One such species, Miscanthus sinensis, has a wide natural distribution and wide phenotypic variation, including its seed germination characteristics. Such characteristics need to be considered, particularly in ensuring plant establishment in regions with harsh winters. Germination rates were measured for 33 M. sinensis accessions from different latitudinal regions in Japan. Generally, seeds of accessions from regions of higher latitude germinate earlier than those from more southerly regions under both warm (30 degrees C/20 degrees C day/night) and cool temperature (15 degrees C/10 degrees C day/night) treatments. However, accessions that had lighter seeds germinated late regardless of origin. This survey serves as a basis for identifying M. sinensis accessions that are able to germinate early under low-temperature conditions.
• 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 1939-1234 2013/06 [Refereed][Not invited]
   

  Miscanthus xgiganteus, a triploid hybrid between tetraploid M. sacchariflorus and diploid M. sinensis, has considerable potential as a bioenergy crop. Currently only one genotype is widely cultivated, increasing its vulnerability to diseases during production. Finding new hybrids is important to broaden genetic resources of M. xgiganteus. Three putative triploid hybrids were discovered in a sympatric population of tetraploid M. sacchariflorus and diploid M. sinensis in Kushima, Japan. The hybrid nature of the triploids was determined by morphological analysis and sequencing the ribosomal DNA internal transcribed spacer (ITS) region. The triploids had awns on their florets, which is a common characteristic of diploid M. sinensis, and sheath hairs, which is typical of tetraploid M. sacchariflorus. All triploids showed heterozygosity in their ribosomal DNA ITS sequences. Based on these results, it is confirmed that the triploids are hybrids and novel genotypes of M. xgiganteus. Natural crossing between tetraploid M. sacchariflorus x diploid M. sinensis may also lead to the production of tetraploid hybrids. ITS analysis of tetraploid plants showed that one maternal parent of the triploid hybrids, K-Ogi-1, had heterozygous ITS, which was different than the other analyzed tetraploid, M. sacchariflorus. Thus, K-Ogi-1 was likely of hybrid origin. These tetraploid hybrids can also be utilized as parents in M. xgiganteus breeding. Since all hybrids identified in this study had tetraploid M. sacchariflorus as maternal parents, collecting and analyzing seeds from tetraploid M. sacchariflorus in sympatric areas could be an effective strategy to identify natural Miscanthus hybrids that can be used as bioenergy crops.
• 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  1471-2229 2011/11 [Refereed][Not invited]
   

  Background: Improvement of alpha-tocopherol content is an important breeding aim to increase the nutritional value of crops. Several efforts have been conducted to improve the alpha-tocopherol content in soybean [Glycine max (L.) Merr.] through transgenic technology by overexpressing genes related to alpha-tocopherol biosynthesis or through changes to crop management practices. Varieties with high alpha-tocopherol content have been identified in soybean germplasms. The heritability of this trait has been characterized in a cross between high alpha-tocopherol variety Keszthelyi Aproszemu Sarga (KAS) and low alpha-tocopherol variety Ichihime. In this study, the genetic mechanism of the high alpha-tocopherol content trait of KAS was elucidated. Results: Through QTL analysis and fine mapping in populations from a cross between KAS and a Japanese variety Ichihime, we identified gamma-TMT3, which encodes gamma-tocopherol methyltransferase, as a candidate gene responsible for high alpha-tocopherol concentration in KAS. Several nucleotide polymorphisms including two nonsynonymous mutations were found in the coding region of gamma-TMT3 between Ichihime and KAS, but none of which was responsible for the difference in alpha-tocopherol concentration. Therefore, we focused on transcriptional regulation of gamma-TMT3 in developing seeds and leaves. An F(5) line that was heterozygous for the region containing gamma-TMT3 was self-pollinated. From among the progeny, plants that were homozygous at the gamma-TMT3 locus were chosen for further evaluation. The expression level of gamma-TMT3 was higher both in developing seeds and leaves of plants homozygous for the gamma-TMT3 allele from KAS. The higher expression level was closely correlated with high alpha-tocopherol content in developing seeds. We generated transgenic Arabidopsis plants harboring GUS gene under the control of gamma-TMT3 promoter from KAS or Ichihime. The GUS activity assay showed that the activity of gamma-TMT3 promoter from KAS was higher than that of Ichihime. Conclusions: The genetic variation in gamma-TMT3, which plays a major role in determining alpha-tocopherol concentration, provides significant information about the regulation of tocopherol biosynthesis in soybean seeds. This knowledge will help breeding programs to develop new soybean varieties with high alpha-tocopherol content.
• 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 1344-7610 2007/03 [Refereed][Not invited]
   

  Tocopherols, known as members of vitamin E, are the major lipophilic antioxidants in soybean. Since soybean seeds contain a low concentration of alpha-tocopherol (alpha-Toc), the tocopherol isoform with the highest vitamin E activity, some breeding efforts have been implemented to increase the alpha-tocopherol content in the seeds. In the present study, we used F-2 seed and F-2 plant (173 seeds) populations derived from a cross between a variety with a high alpha-tocopherol content, Keszthelyi A.S. (alpha-Toc 20-30%) and a Japanese cultivar, Ichihime (alpha-Toc < 10%) for genetic analysis of the high alpha-tocopherol concentration. There was no significant correlation between the alpha-tocopherol and total tocopherol contents in the F-2 plant (173 seeds) population, suggesting that the alpha-tocopherol and total tocopherol contents were regulated independently in the seeds. Therefore, it may be possible to increase the alpha-tocopherol concentration without affecting the total tocopherol content. Broad-sense heritability value for the alpha-tocopherol concentration trait was estimated to be 0.645 in the F-2 seeds, suggesting that the gamma-tocopherol concentration trait was highly heritable. Chi-square goodness-of-fit test for evaluating the relationship between genotype of certain SSR markers and the alpha-tocopherol concentration showed that the Sat_243 and Sat_167 markers (linkage group K) were significantly associated with the alpha-tocopherol concentration (P < 0.05). These markers could be used for marker-assisted selection to breed soybean cultivars with high alpha-tocopherol concentrations. Analysis of the F-2 seeds and the F-2 plants (173 seeds) for tocopherol composition showed that there was a significantly negative correlation between the alpha-tocopherol and gamma-tocopherol concentrations, suggesting that the activity of gamma-tocopherol methyltransferase, the enzyme that converts gamma-tocopherol to alpha-tocopherol, is high in individuals with a high alpha-tocopherol concentration.

MISC

• S. palustris leaves sampling and RNA extraction v1

  Maria Stefanie Dwiyanti  2024/10/02  

  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.

• 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  2020/06
• 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  [Not refereed][Not invited]
  
• 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  [Not refereed][Not invited]
   

  Rhizomatous and perennial warm-season C-4 grasses such as Miscanthus spp. and switchgrass (Panicum virgatum) are potential bioenergy crops for temperate regions. However, lignin in Miscanthus and switchgrass inhibits the cellulose digestion process during bioethanol production. One of the targets for improvement of forages from feedstocks to bioenergy crops is to develop a cost-efficient biorefinery process through lignin content manipulation. Numerous reports have shown that RNAi suppression of lignin-biosynthesis pathway genes can increase biomass fermentable sugar yields for biofuel production. These studies have also reported that RNAi suppression of cell-wall lignin biosynthesis can decrease biomass yield and resistance to biotic stress in the transgenic plants. Transcriptome and metabolome approaches can be used to clarify the networks and pathways of lignin biosynthesis to facilitate the identification of appropriate target genes for transformation. However, whole-genome sequencing of the forage species, which provides much-needed genomic information, is limited. Germplasm of natural, low-lignin mutants also plays a role in identification of genetic regulation of lignin content and this would be useful breeding material. Molecular markers have been developed and utilised to accelerate identification of quantitative trait loci/genes for traits relating to the biorefinery process. All of these studies will serve as basic information for supporting genetic improvement through classical breeding or genetic transformation, and offer the opportunity to develop cultivars which have enhanced biomass and are cost-efficient for biorefinery process.
• 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  2013/08/01  [Not refereed][Not invited]
   

  Through selection by humans, crop plants are adapted to produce optimal yield in the areas where they are cultivated. Climate changes may cause stress to plants, disturb plant growth, and decrease plant yield. Food shortages due to crop failure may cause hunger particularly in poor countries. Therefore, it is important to develop new crop cultivars that can adapt to climate changes. This chapter summarizes quantitative trait loci (QTL) analysis and findings for candidate genes of traits related to tolerance to drought, heat, salinity, macronutrient and micronutrient deficiency, flooding, frost, particularly in major cereal crops. In addition, QTL studies on flowering time of cereal crops are also deliberated. Flowering time is a critical plant phase that determines the transition from the vegetative to the reproductive phase. The optimal time of flowering largely affects the overall yield. Information obtained from QTL analysis has been utilized in the development of stress-tolerant cultivars. Indeed, several stress-tolerant cultivars have been released in stress-prone areas. However, QTLs for most of the traits have not been elucidated. Fortunately, development in sequencing technologies has accelerated elucidation of the genomic regions conferring stress tolerance. This chapter also provides information regarding several recent technologies and approaches in QTL/gene mapping and also in plant breeding.
• 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  2013/08/01  [Not refereed][Not invited]
   

  Through selection by humans, crop plants are adapted to produce optimal yield in the areas where they are cultivated. Climate changes may cause stress to plants, disturb plant growth, and decrease plant yield. Food shortages due to crop failure may cause hunger particularly in poor countries. Therefore, it is important to develop new crop cultivars that can adapt to climate changes. This chapter summarizes quantitative trait loci (QTL) analysis and findings for candidate genes of traits related to tolerance to drought, heat, salinity, macronutrient and micronutrient deficiency, flooding, frost, particularly in major cereal crops. In addition, QTL studies on flowering time of cereal crops are also deliberated. Flowering time is a critical plant phase that determines the transition from the vegetative to the reproductive phase. The optimal time of flowering largely affects the overall yield. Information obtained from QTL analysis has been utilized in the development of stress-tolerant cultivars. Indeed, several stress-tolerant cultivars have been released in stress-prone areas. However, QTLs for most of the traits have not been elucidated. Fortunately, development in sequencing technologies has accelerated elucidation of the genomic regions conferring stress tolerance. This chapter also provides information regarding several recent technologies and approaches in QTL/gene mapping and also in plant breeding.
• Germplasm Resources of Miscanthus and Their Application in Breeding

  Maria Stefanie Dwiyanti, J. Ryan Stewart, Toshihiko Yamada  Bioenergy Feedstocks: Breeding and Genetics  49  -66  2013/04/25  [Not refereed][Not invited]
  
• 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  2011/03/29  [Not refereed][Not invited]
  
• 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  2009/09/25  [Not refereed][Not invited]
  
• 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-  2008/08  [Not refereed][Not invited]
  
• 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-  2008/08  [Not refereed][Not invited]
  

Books etc

• Nutraceuticals in Soybean: Biosynthesis, Advanced Genetic Research, and Usage in Food

  Dwiyanti, M.S, Gunawan-Puteri, M.D.P.T (Joint workPage 1-37)
  Springer 2023/06 (ISBN: 9789811936272)

Presentations

• Recent Progress in Soybean Tocopherol Biosynthesis Studies  [Not invited]

  Maria Stefanie Dwiyanti

  International Plant & Animal Genome Conference : PAG 30  2023/01
• DNA Barcoding of Weed Species in Hokkaido and Application to ex-situ Evaluate of Their Abundance  [Not invited]

  Maria Stefanie Dwiyanti, Toshiyuki Hirata, Hironori Nagano, Junya Yamagishi, Masahiro Akimoto

  10th Asian Crop Science Association Conference  2021/09
• Discovering genetic variations associated with high α-tocopherol content in soybean and wild soybean  [Invited]

  Maria Stefanie Dwiyanti

  The 6th International Conference on Food, Agriculture, and Natural Resources (IC-FANRES)  2021/08
• Haplotype analysis of γ-tocopherol methyltransferase and its relation to α- tocopherol content in soybean and wild soybean  [Not invited]

  Maria Stefanie Dwiyanti, Cheolwoo Park, Atsushi J Nagano, Baohui Liu, Tetsuya Yamada, Jun Abe

  PB20-Plant Biology Worldwide Summit  2020/07
• How to promote wet-lab genetics research in Southeast Asia?  [Not invited]

  Maria Stefanie Dwiyanti

  Symposium: Challenges for the Education Development on Agriculture and Food Resources in Tropical Asia  2019/09
• Sequence analysis and marker development for high α-tocopherol soybean: targeting γ-tocopherol methyltransferase gene γ-TMT3  [Not invited]

  Maria Stefanie Dwiyanti, Cheolwoo Park, PP Ariana, Jun Abe

  The 9th International Conference on Legume Genetics and Genomic  2019/05
• Quantitative trait loci analysis regulating seed α-tocopherol ratio in wild soybean  [Not invited]

  Cheolwoo Park, Maria Stefanie Dwiyanti, Atsushi J Nagano, Tetsuya Yamada, Jun Abe

  The 9th International Conference on Legume Genetics and Genomic  2019/05
• Genomic characterization of the local rice resources in the Mekong Delta of Vietnam  [Not invited]

  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  2018/09
• QTL analysis for a high seed α-tocopherol ratio in wild soybean  [Not invited]

  Cheolwoo Park, Maria Stefanie Dwiyanti, Atsushi J Nagano, Tetsuya Yamada, Jun Abe

  The 133rd Japanese Society of Breeding Meeting  2018/03
• Comparison of genomic selection methods for predicting Miscanthus sinensis yield  [Not invited]

  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  2018/01
• Genetic Analysis Underlying High Alpha-tocopherol Content in Wild Soybean  [Not invited]

  Maria Stefanie Dwiyanti, Cheol Woo Park, Jun Abe

  INDONESIAN BREEDING SCIENCE SOCIETY (PERIPI)  2017/10
• Bridging The Genetic Resources and Crop Improvement Through Genomics  [Invited]

  Maria Stefanie Dwiyanti

  the 14th Hokkaido Indonesia Student Scientific Meeting (HISAS 14)  2017/03

Association Memberships

• American Society of Plant Biologists   JAPANESE SOCIETY OF BREEDING   

Research Projects

• 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

  Hirose Foundation：

  Date (from‐to) : 2019/12 -2024/10 

  Author : Maria Stefanie Dwiyanti, 小出 陽平
• 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

  北海道大学：ロバスト農林水産工学研究プログラム

  Date (from‐to) : 2019/04 -2021/03 

  Author : 平田聡之, Maria Stefanie Dwiyanti, 長野宏則, 山岸潤也, 秋本正博
• Genetic Analysis of High Vitamin E Content from Wild Soybean

  Fuji Foundation for Protein Research：

  Date (from‐to) : 2018/04 -2019/03 

  Author : Maria Stefanie, DWIYANTI, Cheolwoo PARK, Atsushi NAGANO, Tetsuya YAMADA, Jun ABE
• Genetic and nutraceutical analyses of Indonesian fern Kelakai (Stenochlaena palustris) for new food crop development

  Hokkaido University：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

  Date (from‐to) : 2018/04 -2019/03 

  Author : Maria Stefanie Dwiyanti