Faculty Profiles - MONDEN Yuki

Papers - MONDEN Yuki

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Molecular polymorphisms of the nuclear and chloroplast genomes among African melon germplasms reveal abundant and unique genetic diversity, especially in Sudan. International journal

Odirichi Nnennaya Imoh, Gentaro Shigita, Mitsuhiro Sugiyama, Tran Phuong Dung, Katsunori Tanaka, Mami Takahashi, Kazusa Nishimura, Yuki Monden, Hidetaka Nishida, Mashaer Goda, Michel Pitrat, Kenji Kato

Annals of botany 2025.4

Language：English Publishing type：Research paper (scientific journal)

BACKGROUND AND AIMS: Africa is rich in wild species of Cucumis and is considered one of the origins of melon. However, our knowledge of African melon is limited, and genetic studies using melon germplasms with wide geographical coverage are required. Here, we analyzed the genetic structure of African melons, with emphasis on Sudan. METHODS: Ninety-seven accessions of African melon were examined along with 77 reference accessions representing Asian melon and major horticultural groups. Molecular polymorphisms in the nuclear and chloroplast genomes were investigated using 12 RAPD, 7 SSR, and 3 SNP markers. Horticultural traits, including seed size, were measured for 46 accessions, mainly from Sudan. KEY RESULTS: African melons were divided into large and small seed-types based on seed length: large seed-type from Northern Africa and small seed-type from Western and Southern Africa. Both seed types are common in Sudan. Molecular genetic diversity in these geographical populations was as high as in India, the Asian center of melon domestication. Large seed-type from Northern Africa were assigned to Pop4 by structure analysis and had Ib cytoplasm in common with Cantalupensis, Inodorus, and Flexuosus. Small seed-types were highly diversified and geographically differentiated; specifically, Pop1 with Ia cytoplasm in Southern Africa and South Asia, Pop2 with Ia in East Asia, including Conomon and Makuwa, and Pop3 with Ia or Ic in Africa. Sudanese small seed-types were grouped in Pop3, while their cytoplasm type was the mixture of Ia and Ic. Sudanese Tibish had Ic cytoplasm that was unique in Africa, common in Western Africa and Sudan, and also found in wild or feral types. CONCLUSIONS: Melon of Ic lineage, including Tibish, originated from wild melon in the "western Sudan region," and independently of melon with Ia or Ib cytoplasm that originated in Asia. This clearly indicates the polyphyletic origin of melon.

DOI： 10.1093/aob/mcaf028

Workflow for development of CAPS markers with one type of restriction enzyme to identify citrus cultivars Reviewed

Kazusa Nishimura, Maho Okuma, Junko Kaneyoshi, Atsu Yamasaki, Kyoka Nagasaka, Kazuki Murata, Yuki Monden, Kenji Kato, Hidetaka Nishida, Tetsuya Nakazaki, Ryohei Nakano

Tree Genetics & Genomes 20 ( 5 ) 2024.8

Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC

Abstract

Given the ease of propagating fruit tree species through cloning, the economic viability of their breeding programs hinges on protecting breeders' rights. This necessitates the development of highly accurate DNA markers for cultivar identification. Here, we present a methodology for the rapid design of cleaved amplified polymorphic sequence (CAPS) markers to discriminate newly bred Japanese citrus cultivars from genetically related cultivars. We first compared the performance of ddRAD-seq and MIG-seq in citrus germplasm. The ddRAD-seq libraries generated using EcoRI and HindIII restriction enzymes yielded the highest number of polymorphisms. Subsequently, ddRAD-seq with EcoRI and HindIII was employed to analyze 29 citrus cultivars and thus identify 331,801 genome-wide polymorphisms. A semi-automated bioinformatics pipeline was then utilized to identify candidate CAPS markers, resulting in the discovery of 14,072 potential markers. Of these candidates, 52 were chosen for validation based on their recognition by the PstI restriction enzyme. This evaluation resulted in the development of 11 highly discriminative CAPS markers. Remarkably, a combination of only six such markers was sufficient to differentiate newly bred cultivars from their genetically related parents. The single restriction enzyme employed for these markers facilitates straightforward multiplexing. Finally, a combination of one multiplex marker testing two loci and four singleplex markers was successfully selected that completely discriminated the cultivars other than the bud sports used in this study. The pipeline established here extends beyond citrus and has the potential to simplify marker development and cultivar protection in various plant species.

DOI： 10.1007/s11295-024-01661-x

Other Link： https://link.springer.com/article/10.1007/s11295-024-01661-x/fulltext.html

Propagation path of a flowering cherry (Cerasus × yedoensis) cultivar ‘Somei-Yoshino’ traced by somatic mutations Reviewed

Kenta Shirasawa, Tomoya Esumi, Akihiro Itai, Katsunori Hatakeyama, Tadashi Takashina, Takuji Yakuwa, Katsuhiko Sumitomo, Takeshi Kurokura, Eigo Fukai, Keiichi Sato, Takehiko Shimada, Katsuhiro Shiratake, Munetaka Hosokawa, Yuki Monden, Makoto Kusaba, Hidetoshi Ikegami, Sachiko Isobe

DNA Research 31 ( 5 ) 2024.8

Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP)

Abstract

In the long history of human relations with flowering cherry trees in Japan, ‘Somei-Yoshino’ occupies an exceptional position among a variety of flowering trees: it is a self-incompatible interspecific hybrid but has been enthusiastically planted by grafting throughout Japan, due most likely to its flamboyant appearance upon full bloom. Thus, ‘Somei-Yoshino’ gives us a rare opportunity to trace and investigate the occurrence and distribution of somatic mutations within a single plant species through analysis of the genomes of the clonally propagated trees grown under a variety of geographical and artificial environments. In the studies presented here, a total of 46 samples of ‘Somei-Yoshino’ trees were collected and their genomes were analysed. We identified 684 single nucleotide mutations, of which 71 were present in more than two samples. Clustering analysis of the mutations indicated that the 46 samples were classified into eight groups, four of which included 36 of the 46 samples analysed. Interestingly, all the four tree samples collected in Ueno Park of Tokyo were members of the four groups mentioned above. Based on comparative analysis of their mutations, one of the four trees growing in Ueno Park was concluded to be the closest to the original ancestor. We propose that somatic mutations may be used as tracers to establish the ancestral relationship amongst clonally propagated individuals.

DOI： 10.1093/dnares/dsae025

Other Link： https://academic.oup.com/dnaresearch/article-pdf/31/5/dsae025/59001111/dsae025.pdf

Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East Reviewed

Gentaro Shigita, Koichiro Shimomura, Tran Phuong Dung, Naznin Pervin Haque, Thuy Thanh Duong, Odirich Nnennaya Imoh, Yuki Monden, Hidetaka Nishida, Katsunori Tanaka, Mitsuhiro Sugiyama, Yoichi Kawazu, Norihiko Tomooka, Kenji Kato

Theoretical and Applied Genetics 137 ( 7 ) 2024.7

Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC

Abstract

Key message

Genotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia.

Abstract

The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber.

DOI： 10.1007/s00122-024-04683-0

Other Link： https://link.springer.com/article/10.1007/s00122-024-04683-0/fulltext.html

Polyphyletic domestication and inter-lineage hybridization magnified genetic diversity of cultivated melon,Cucumis meloL

Katsunori Tanaka, Gentaro Shigita, Tran Phuong Dung, Phan Thi Phuong Nhi, Mami Takahashi, Yuki Monden, Hidetaka Nishida, Ryuji Ishikawa, Kenji Kato

2024.7

Publisher：Cold Spring Harbor Laboratory

Abstract

A total of 212 melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9 mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp.meloand the East Asian subsp.agrestiswere characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence in both nuclear and cytoplasm genomes. In contrast, in South and Southeast Asia, in addition to the Europe/US and East Asian types, recombinant types were also frequently found, indicating unclear genetic differentiation in South and Southeast Asia. Such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types of melon. Seed length was intermediate, between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib in Momordica, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp.agrestisof the Ic type proved to be endemic to Africa, indicating its African origin.

DOI： 10.1101/2024.06.27.601017

国外への苗木流出抑止のためのCAPSとC-PAS検定法のカンキツ穂木への適用について

遠藤朋子, 鈴木信裕, 奥貞丈博, 門田有希, 竹内朋幸, 高崎一人, 岡本充智, 藤井浩, 野中圭介

DNA多型 32 77 - 81 2024.7

Analysis of genetic diversity and population structure in Cambodian melon landraces using molecular markers Reviewed

Pervin Mst Naznin, Odirichi Nnennaya Imoh, Katsunori Tanaka, Ouch Sreynech, Gentaro Shigita, Yon Sophea, Sakhan Sophany, Ouk Makara, Norihiko Tomooka, Yuki Monden, Hidetaka Nishida, Kenji Kato

Genetic Resources and Crop Evolution 2023.7

Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC

Abstract

Genetic diversity of Cambodian melons was evaluated by the analysis of 12 random amplified polymorphic DNA (RAPD) and 7 simple sequence repeat (SSR) markers using 62 accessions of melon landraces and compared with 231 accessions from other areas for genetic characterization of Cambodian melons. Among 62 accessions, 56 accessions were morphologically classified as small-seed type with seed lengths shorter than 9 mm, as in the horticultural groups Conomon and Makuwa. Gene diversity of Cambodian melons was 0.228, which was equivalent to those of the groups Conomon and Makuwa and smaller than those of Vietnamese and Central Asian landraces. A phylogenetic tree constructed from a genetic distance matrix classified 293 accessions into three major clusters. Small-seed type accessions from East and Southeast Asia formed clusters I and II, which were distantly related with cluster III consisting of large-seed type melon from other areas. All Cambodian melons belonged to cluster I (except three accessions) along with those from Thailand, Myanmar, Yunnan (China), and Vietnam (“Dua thom” in the northwest), thus indicating genetic similarity in these areas. In addition, the Cambodian melons were not differentiated among geographical populations. Conomon and Makuwa were classified into cluster II, together with melon groups from the plains of Vietnam. The presence of two groups of melons in Southeast Asia was also indicated by population structure and principal coordinate analysis. These results indicated a close genetic relationship between Cambodia and the neighboring countries, thus suggesting that Cambodian melons are not directly related to the establishment of Conomon and Makuwa.

DOI： 10.1007/s10722-023-01677-7

Other Link： https://link.springer.com/article/10.1007/s10722-023-01677-7/fulltext.html

Chromatographic printed array strip (C-PAS) method for cultivar-specific identification of sweetpotato cultivars ‘Beniharuka’ and ‘Fukumurasaki’ Reviewed

Yuki Monden, Maho Kakigi, Emdadul Haque, Tomoyuki Takeuchi, Kazuto Takasaki, Masaru Tanaka

Breeding Science 73 ( 3 ) 313 - 321 2023

A target cultivar-specific identification system based on the chromatographic printed array strip method for eight prominent Japanese citrus cultivars Reviewed

Mitsutoshi Okamoto, Yuki Monden, Akiko Shindo, Tomoyuki Takeuchi, Tomoko Endo, Yukinori Shigematsu, Kazuto Takasaki, Hiroshi Fujii, Takehiko Shimada

Breeding Science 73 ( 2 ) 146 - 157 2023

Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection Reviewed

Gentaro Shigita, Tran Phuong Dung, Mst. Naznin Pervin, Thanh-Thuy Duong, Odirich Nnennaya Imoh, Yuki Monden, Hidetaka Nishida, Katsunori Tanaka, Mitsuhiro Sugiyama, Yoichi Kawazu, Norihiko Tomooka, Kenji Kato

Breeding Science 73 ( 3 ) 269 - 277 2023

Comprehensive survey of transposon mPing insertion sites and transcriptome analysis for identifying candidate genes controlling high protein content of rice Reviewed International journal

Yuki Monden, Hirona Tanaka, Ryota Funakoshi, Seiya Sunayama, Kiyotaka Yabe, Eri Kimoto, Kentaro Matsumiya, Takanori Yoshikawa

Frontiers in Plant Science 13 969582 - 969582 2022.9

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Frontiers Media SA

Rice is the most important crop species in the world, being staple food of more than 80% of people in Asia. About 80% of rice grain is composed of carbohydrates (starch), with its protein content as low as 7–8%. Therefore, increasing the protein content of rice offers way to create a stable protein source that contributes to improving malnutrition and health problems worldwide. We detected two rice lines harboring a significantly higher protein content (namely, HP5-7 and HP7-5) in the EG4 population. The EG4 strain of rice is a unique material in that the transposon mPing has high transpositional activity and high copy numbers under natural conditions. Other research indicated that mPing is abundant in the gene-rich euchromatic regions, suggesting that mPing amplification should create new allelic variants, novel regulatory networks, and phenotypic changes in the EG4 population. Here, we aimed to identify the candidate genes and/or mPing insertion sites causing high protein content by comprehensively identifying the mPing insertion sites and carrying out an RNA-seq-based transcriptome analysis. By utilizing the next-generation sequencing (NGS)-based methods, ca. 570 mPing insertion sites were identified per line in the EG4 population. Our results also indicated that mPing apparently has a preference for inserting itself in the region near a gene, with 38 genes in total found to contain the mPing insertion in the HP lines, of which 21 and 17 genes were specific to HP5-7 and HP7-5, respectively. Transcriptome analysis revealed that most of the genes related to protein synthesis (encoding glutelin, prolamin, and globulin) were up-regulated in HP lines relative to the control line. Interestingly, the differentially expressed gene (DEG) analysis revealed that the expression levels of many genes related to photosynthesis decreased in both HP lines; this suggests the amount of starch may have decreased, indirectly contributing to the increased protein content. The high-protein lines studied here are expected to contribute to the development of high protein-content rice by introducing valuable phenotypic traits such as high and stable yield, disease resistance, and abundant nutrients.

DOI： 10.3389/fpls.2022.969582

Exploiting the miniature inverted-repeat transposable elements insertion polymorphisms as an efficient DNA marker system for genome analysis and evolutionary studies in wheat and related species Reviewed International journal

Benjamin Ewa Ubi, Yasir Serag Alnor Gorafi, Beery Yaakov, Yuki Monden, Khalil Kashkush, Hisashi Tsujimoto

Frontiers in Plant Science 13 995586 - 995586 2022.9

Language：English Publishing type：Research paper (scientific journal) Publisher：Frontiers Media SA

Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of “full site” insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 “full sites,” respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.

DOI： 10.3389/fpls.2022.995586

Mapping of Nematode Resistance in Hexaploid Sweetpotato Using a Next-Generation Sequencing-Based Association Study Reviewed

Nozomi Obata, Hiroaki Tabuchi, Miyu Kurihara, Eiji Yamamoto, Kenta Shirasawa, Yuki Monden

Frontiers in Plant Science 13 2022.3

Authorship：Last author,　Corresponding author Publishing type：Research paper (scientific journal) Publisher：Frontiers Media SA

The southern root-knot nematode (SRKN; Meloidogyne incognita) is a typical parasitic nematode that affects sweetpotato [Ipomoea batatas (L.) Lam.], causing a significant decrease in crop yield and commercial value. In Japan, the SRKN is classified into 10 races: SP1–SP5, SP6-1, SP6-2, and SP7–SP9, with the dominant race differing according to the cultivation area. Soil insecticides have previously been used to reduce the soil density of SRKNs; however, this practice is both costly and labor intensive. Therefore, the development of SRKN-resistant sweetpotato lines and cultivars is necessary. However, due to the complexity of polyploid inheritance and the highly heterogeneous genomic composition of sweetpotato, genetic information and research for this species are significantly lacking compared to those for other major diploid crop species. In this study, we utilized the recently developed genome-wide association approach, which uses multiple-dose markers to assess autopolyploid species. We performed an association analysis to investigate resistance toward SRKN-SP2, which is the major race in areas with high sweetpotato production in Japan. The segregation ratio of resistant and susceptible lines in the F₁ mapping population derived from the resistant “J-Red” and susceptible “Choshu” cultivars was fitted to 1: 3, suggesting that resistance to SP2 may be regulated by two loci present in the simplex. By aligning the double digest restriction-site associated DNA sequencing reads to the published Ipomoea trifida reference sequence, 46,982 single nucleotide polymorphisms (SNPs) were identified (sequencing depth &gt; 200). The association study yielded its highest peak on chromosome 7 (Chr07) and second highest peak on chromosome 3 (Chr03), presenting as a single-dose in both loci. Selective DNA markers were developed to screen for resistant plants using the SNPs identified on Chr03 and Chr07. Our results showed that SRKN-SP2-resistant plants were selected with a probability of approximately 70% when combining the two selective DNA markers. This study serves as a model for the identification of genomic regions that control agricultural traits and the elucidation of their effects, and is expected to greatly advance marker-assisted breeding and association studies in polyploid crop species.

DOI： 10.3389/fpls.2022.858747

Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato Reviewed

Kanoko Nokihara, Yoshihiro Okada, Shinichiro Ohata, Yuki Monden

Plants 10 ( 8 ) 1535 - 1535 2021.7

Authorship：Last author,　Corresponding author Publishing type：Research paper (scientific journal) Publisher：MDPI AG

Because weevils are the most damaging pests of sweetpotato, the development of cultivars resistant to weevil species is considered the most important aspect in sweetpotato breeding. However, the genes and the underlying molecular mechanisms related to weevil resistance are yet to be elucidated. In this study, we performed an RNA sequencing-based transcriptome analysis using the resistant Kyushu No. 166 (K166) and susceptible Tamayutaka cultivars. The weevil resistance test showed a significant difference between the two cultivars at 30 days after the inoculation, specifically in the weevil growth stage and the suppressed weevil pupation that was only observed in K166. Differential expression and gene ontology analyses revealed that the genes upregulated after inoculation in K166 were related to phosphorylation, metabolic, and cellular processes. Because the weevil resistance was considered to be related to the suppression of larval pupation, we investigated the juvenile hormone (JH)-related genes involved in the inhibition of insect metamorphosis. We found that the expression of some terpenoid-related genes, which are classified as plant-derived JHs, was significantly increased in K166. This is the first study involving a comprehensive gene expression analysis that provides new insights about the genes and mechanisms associated with weevil resistance in sweetpotato.

DOI： 10.3390/plants10081535

Correction to: Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. International journal

Michiko Nemoto, Sayako Iwaki, Hisao Moriya, Yuki Monden, Takashi Tamura, Kenji Inagaki, Shigeki Mayama, Kiori Obuse

Marine biotechnology (New York, N.Y.) 23 ( 1 ) 157 - 157 2021.2

Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data Reviewed International journal

Eiji Yamamoto, Kenta Shirasawa, Takumi Kimura, Yuki Monden, Masaru Tanaka, Sachiko Isobe

G3 Genes|Genomes|Genetics 10 ( 8 ) 2661 - 2670 2020.8

Language：English Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP)

<title>Abstract</title>
Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, for high precision genetic analysis, the complicated genetic segregation mode in polyploid organisms requires high-coverage NGS data and elaborate analytical algorithms. In the present study, we propose a simple strategy for the genetic mapping of polyploids using low-coverage NGS data. The validity of the strategy was investigated using simulated data. Previous studies indicated that accurate allele dosage estimation from low-coverage NGS data (read depth &lt; 40) is difficult. Therefore, we used allele dosage probabilities calculated from read counts in association analyses to detect loci associated with phenotypic variations. The allele dosage probabilities showed significant detection power, although higher allele dosage estimation accuracy resulted in higher detection power. On the contrary, differences in the segregation patterns between the marker and causal genes resulted in a drastic decrease in detection power even if the marker and casual genes were in complete linkage and the allele dosage estimation was accurate. These results indicated that the use of a larger number of markers is advantageous, even if the accuracy of allele dosage estimation is low. Finally, we applied the strategy for the genetic mapping of autohexaploid sweet potato (Ipomoea batatas) populations to detect loci associated with agronomic traits. Our strategy could constitute a cost-effective approach for preliminary experiments done performed to large-scale studies.

DOI： 10.1534/g3.120.401433

Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. Reviewed International journal

Michiko Nemoto, Sayako Iwaki, Hisao Moriya, Yuki Monden, Takashi Tamura, Kenji Inagaki, Shigeki Mayama, Kiori Obuse

Marine biotechnology (New York, N.Y.) 2020.6

Language：English Publishing type：Research paper (scientific journal)

Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms.

DOI： 10.1007/s10126-020-09976-1

Molecular discrimination of Japanese tetraploid grape cultivars based on retrotranspon sequences

高田翔太, 藤田景子, 福永健二, 門田有希

DNA多型 28 ( 1 ) 46 - 50 2020.6

Developing transposable element marker system for molecular breeding Reviewed

R. S. Bhat, K. Shirasawa, Y. Monden, H. Yamashita, M. Tahara

Methods in Molecular Biology 2107 233 - 251 2020.1

© Springer Science+Business Media, LLC, part of Springer Nature 2020. Transposable element (TE) marker system was developed considering the useful properties of the transposable elements such as their large number in the animal and plant genomes, high rate of insertion polymorphism, and ease of detection. Various methods have been employed for developing a large number of TE markers in several crop plants for genomics studies. Here we describe some of these methods including the recent whole genome search. We also review the application of TE markers in molecular breeding.

DOI： 10.1007/978-1-0716-0235-5_11

QTL analysis and GWAS of agronomic traits in sweetpotato (Ipomoea batatas L.) using genome wide SNPs Reviewed

Emdadul Haque, Hiroaki Tabuchi, Yuki Monden, Keisuke Suematsu, Kenta Shirasawa, Sachiko Isobe, Masaru Tanaka

Breeding Science 70 ( 3 ) 283 - 291 2020

Language：English Publishing type：Research paper (scientific journal) Publisher：Japanese Society of Breeding

<p>While sweetpotato (Ipomoea batatas L.) improvement has generally been done by field-based selection, molecular genetic studies on traits of interest, i.e., molecular markers are needed for enhancing the breeding program of this world's 7^th most important crop, as such markers facilitate marker-assisted selection. Here, we performed a combined approach of QTLs analyses and GWAS of storage root β-carotene content (BC), dry-matter (DM) and starch content (SC) using the genetic linkage maps constructed with 5,952 and 5,640 SNPs obtained from F₁ progenies between cultivars 'J-Red' and 'Choshu'. BC was negatively correlated with DM (r = –0.45) and SC (r = –0.51), while DM was positively correlated with SC (r = 0.94). In both parental maps, a total of five, two and five QTL regions on linkage groups 7 and 8 were associated with BC, DM and SC, respectively. In GWAS of BC, one strong signal (P = 1.04 × 10^–9) was observed on linkage group 8, which co-located with one of the above QTL regions. The SNPs markers found here, particularly for β-carotene, would be useful base resources for future marker-assisted selection program with this trait.</p>

DOI： 10.1270/jsbbs.19099

DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification Reviewed

Chiharu Hirata, Takamitsu Waki, Katsumi Shimomura, Takuya Wada, Seiya Tanaka, Hidetoshi Ikegami, Yousuke Uchimura, Keita Hirashima, Yoshiko Nakazawa, Kaori Okada, Kiyoshi Namai, Makoto Tahara, Yuki Monden

Breeding Science 70 ( 2 ) 231 - 240 2020

Genome-Wide Association Studies (GWAS) for Yield and Weevil Resistance in Sweet potato (Ipomoea batatas (L.) Lam). Reviewed International journal

Yoshihiro Okada, Yuki Monden, Kanoko Nokihara, Kenta Shirasawa, Sachiko Isobe, Makoto Tahara

Plant cell reports 38 ( 11 ) 1383 - 1392 2019.11

Language：English

KEY MESSAGE: We apply the GWAS to sweet potato genome, and identified the SNPs associated with yield and weevil resistance. The sweet potato (Ipomoea batatas (L.) Lam) is a highly heterozygous, outcrossing, polyploid species, which presents challenges for genetic analysis. Therefore, we considered that genome-wide association studies (GWAS) may be applied to the study of the sweet potato genome. The yield of two sweet potato varieties [Purple Sweet Lord (PSL) and 90IDN-47] was assessed at two locations (Kumamoto and Okinawa prefectures) in Japan in 2013 and the yield scores were used for GWAS. The results showed that there were several single nucleotide polymorphisms (SNP) above the significance thresholds in PSL; two peaks were detected in Kumamoto and Okinawa on the Ib03-3 and Ib01-4 linkage groups of PSL, respectively. As for 90IDN-47, one relatively high peak was detected in Kumamoto on the Ib13-8 linkage group. Interestingly, although high peaks above significance thresholds were detected in Kumamoto and Okinawa in PSL, the peaks were located in different linkage groups. This result suggests that the genetic regions controlling yield may change in response to environmental conditions. Additionally, we investigated the degree of weevil damage to the plants, which is the greatest problem in sweet potato cultivation in Okinawa. In this experiment, no SNPs were identified above the significance thresholds. However, one relatively high peak was found in the 90IDN-47 genotype, which showed resistance to weevils. On the other hand, one relatively high peak was also detected in the PSL genotype, which showed susceptibility to weevils. These results suggest that two regions could affect weevil resistance and may contain the gene(s) controlling weevil resistance.

DOI： 10.1007/s00299-019-02445-7

Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. Reviewed International journal

Rumi Sasai, Hiroaki Tabuchi, Kenta Shirasawa, Kazuki Kishimoto, Shusei Sato, Yoshihiro Okada, Akihide Kuramoto, Akira Kobayashi, Sachiko Isobe, Makoto Tahara, Yuki Monden

DNA research : an international journal for rapid publication of reports on genes and genomes 26 ( 5 ) 399 - 409 2019.10

Authorship：Last author,　Corresponding author Language：English Publisher：Oxford University Press ({OUP})

The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.

DOI： 10.1093/dnares/dsz018

Impairment of Lhca4, a subunit of LHCI, causes high accumulation of chlorophyll and the stay-green phenotype in rice Reviewed

Hiroshi Yamatani, Kaori Kohzuma, Michiharu Nakano, Tsuneaki Takami, Yusuke Kato, Yoriko Hayashi, Yuki Monden, Yutaka Okumoto, Tomoko Abe, Toshihiro Kumamaru, Ayumi Tanaka, Wataru Sakamoto, Makoto Kusaba

Journal of Experimental Botany 69 ( 5 ) 1027 - 1035 2018.2

Southern root-knot nematode race SP6 is divided into two races Reviewed

Hiroaki Tabuchi, Toshikazu Kuranouchi, Akira Kobayashi, Yuki Monden, Kazuki Kishimoto, Makoto Tahara, Yoshihiro Okada, Hideaki Iwahori

Nematological Research (Japanese Journal of Nematology) 47 ( 2 ) 29 - 33 2017.12

Development of cultivar discrimination technique for foreign wheat cultivars

25 ( 1 ) 68 - 71 2017

Assessment of Simplified Cultivar Identification Method in Azuki Processed Products Using Single Tag Hybridization (STH) Chromatographic Printed Array Strip (PAS)

25 ( 1 ) 88 - 91 2017

Genetic linkage analysis using DNA markers in sweetpotato Reviewed

Yuki Monden, Makoto Tahara

Breeding Science 67 ( 1 ) 41 - 51 2017

色素原料用サツマイモ品種の識別に利用可能なレトロトランスポゾンRtsp-1挿入箇所の選定

田中勝, 岡田吉弘, 高畑康浩, 門田有希, 田原誠

DNA多型 24 115 - 118 2016

レトロトランスポゾン挿入多型を利用したリンゴの品種識別マーカー開発

西谷千佳子, 山本俊哉, 藤井浩, 岡田和馬, 門田有希, 田原誠

DNA多型 24 101 - 107 2016

DNAクロマトを利用したアズキ品種識別法の開発

高崎一人, リズティアン, 門田有希, 田原誠, 布藤聡

DNA多型 24 134 - 137 2016

稲糯品種におけるイネトランスポゾンmPingの品種間挿入多型調査 Reviewed

岸本和樹, 門田有希, 相川祥胤, 湯浅まり恵, 田原誠, 齋木萌, 高橋剛

DNA多型 24 8 - 14 2016

Plant Transposable Elements and Their Application to Genetic Analysis via High-throughput Sequencing Platform Reviewed

Yuki Monden, Makoto Tahara

HORTICULTURE JOURNAL 84 ( 4 ) 283 - 294 2015.10

Authorship：Lead author Language：English Publisher：JAPAN SOC HORTICULTURAL SCI

Transposable elements (TEs) are mobile genetic elements in the eukaryotic genome. They are divided into two classes (class I: retrotransposons and class II: DNA transposons) based on their structure and manner of transposition. TEs are major components of the eukaryotic genome and retrotransposons are especially abundant in higher-plant genomes. As retrotransposon insertions with high copy numbers are dispersed throughout the genome and are inherited genetically, insertion polymorphisms among crop cultivars have been used as molecular markers. Recently, we developed an efficient method for screening the long terminal repeats (LTRs) of retrotransposon families that exhibit high levels of insertion polymorphisms among crop cultivars using a next-generation sequencing (NGS) platform. This method focuses on the primer binding site (PBS) that is adjacent to the 5' LTR and has a conserved DNA sequence among different LTR retrotransposon families. Construction of a sequencing library through PCR amplification using the PBS conserved sequence allowed us to acquire a large number of LTR sequences and their insertion sites throughout the genome. From our data analysis, we screened the LTR sequences that showed high levels of insertion polymorphism among closely related cultivars. In addition, we identified the insertion sites of these identified LTR retrotransposon families at the genome-wide scale in a number of cultivars with an NGS platform, which enabled us to reveal the genetic relationships among the cultivars and acquire a number of molecular markers for cultivar screening. Our results indicated that the target sequencing of these retrotransposon insertion sites was highly effective for DNA genotyping and marker development without requiring any whole-genome sequence information. This review describes the genomic structure and evolutionary aspects of TEs and discusses the development of molecular markers based on retrotransposon insertion polymorphisms.

DOI： 10.2503/hortj.MI-IR02

Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing Reviewed

Yuki Monden, Takuya Hara, Yoshihiro Okada, Osamu Jahane, Akira Kobayashi, Hiroaki Tabuchi, Shoko Onaga, Makoto Tahara

BREEDING SCIENCE 65 ( 2 ) 145 - 153 2015.3

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：JAPANESE SOC BREEDING

Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90). Although sweetpotato is one of the world's most important crops, genetic analysis of the species has been hindered by its genetic complexity combined with the lack of a whole genome sequence. In the present study, we constructed a genetic linkage map based on retrotransposon insertion polymorphisms using a mapping population derived from a cross between 'Purple Sweet Lord' (PSL) and '90IDN-47' cultivars. High-throughput sequencing and subsequent data analyses identified many Rtsp-1 retrotransposon insertion sites, and their allele dosages (simplex, duplex, triplex, or double-simplex) were determined based on segregation ratios in the mapping population. Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively. Interestingly, most of these insertions (similar to 90%) were present in a simplex manner, indicating their utility for linkage map construction in polyploid species. Additionally, our approach led to savings of time and labor for genotyping. Although the number of markers herein was insufficient for map-based cloning, our trial analysis exhibited the utility of retrotransposon-based markers for linkage map construction in sweetpotato.

DOI： 10.1270/jsbbs.65.145

パインアップルにおけるレトロトランスポゾン挿入多型マーカー開発と品種識別への適用

奈島賢児, 寺上伸吾, 國久美由紀, 西谷千佳子, 正田守幸, 竹内誠人, 浦崎直也, 太郎良和彦, 門田有希, 田原誠, 山本俊哉

DNA多型 23 ( 1 ) 29 - 33 2015

シイタケ(Lentinula edodes)におけるレトロトランスポゾン挿入多型を利用したHigh-Throughput な品種判定マーカーの開発

湯浅まり恵, 門田有希, 田原誠

DNA多型 23 ( 1 ) 34 - 38 2015

Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform Reviewed

Yuki Monden, Ayaka Yamamoto, Akiko Shindo, Makoto Tahara

DNA RESEARCH 21 ( 5 ) 491 - 498 2014.10

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS

In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2,024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships.

DOI： 10.1093/dnares/dsu015

A rapid and enhanced DNA detection method for crop cultivar discrimination Reviewed

Yuki Monden, Kazuto Takasaki, Satoshi Futo, Kousuke Niwa, Mitsuo Kawase, Hiroto Akitake, Makoto Tahara

JOURNAL OF BIOTECHNOLOGY 185 57 - 62 2014.9

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

In many crops species, the development of a rapid and precise cultivar discrimination system has been required for plant breeding and patent protection of plant cultivars and agricultural products. Here, we successfully evaluated strawberry cultivars via a novel method, namely, the single tag hybridization (STH) chromatographic printed array strip (PAS) using the PCR products of eight genomic regions. In a previous study, we showed that genotyping of eight genomic regions derived from FaRE1 retrotransposon insertion site enabled to discriminate 32 strawberry cultivars precisely, however, this method required agarose/acrylamide gel electrophoresis, thus has the difficulty for practical application. In contrast, novel DNA detection method in this study has some great advantages over standard DNA detection methods, including agarose/acrylamide gel electrophoresis, because it produces signals for DNA detection with dramatically higher sensitivity in a shorter time without any preparation or staining of a gel. Moreover, this method enables the visualization of multiplex signals simultaneously in a single reaction using several independent amplification products. We expect that this novel method will become a rapid and convenient cultivar screening assay for practical purposes, and will be widely applied to various situations, including laboratory research, and on-site inspection of plant cultivars and agricultural products. (C) 2014 The Authors. Published by Elsevier B.V.

DOI： 10.1016/j.jbiotec.2014.06.013

Application of iPBS in high-throughput sequencing for the development of retrotransposon-based molecular markers Reviewed

Yuki Monden, Kentaro Yamaguchi, Makoto Tahara

Current Plant Biology 1 40 - 44 2014.8

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier

Retrotransposons are major components of higher plant genomes, and long terminal repeat (LTR) retrotransposons are especially predominant. Thus, numerous LTR retrotransposon families with high copy numbers exist in most plant genomes. As the integrated copies of these retrotransposons are genetically inherited, their insertion polymorphisms among crop cultivars have been used as functional molecular markers such as inter-retrotransposon amplification polymorphism (IRAP), retrotransposon microsatellite amplification polymorphism (REMAP), retrotransposon-based insertion polymorphism (RBIP) and sequence-specific amplification polymorphism (S-SAP). However, the effective use of these methods requires suitable LTR sequences showing high insertion polymorphism among crop cultivars. Recently, we conducted an efficient screening of LTR retrotransposon families that showed high insertion polymorphism among closely related strawberry cultivars using a next-generation sequencing platform. This method focuses on the primer binding site (PBS), which is adjacent to the 5' LTR sequence and is conserved among different LTR retrotransposon families. Construction of a sequencing library using the PBS motif allowed us to identify a large number of LTR sequences and their insertion sites throughout the genome. The LTR sequences identified by our method showed high insertion polymorphism among closely related strawberry cultivars, and these families should thus be useful in the development of molecular markers for phylogenetic and genetic diversity studies. This article briefly describes the general aspects of retrotransposon-based molecular markers and also outlines our method for screening LTR sequences suitable for genetic analyses.(. http://www.ddbj.nig.ac.jp/).

DOI： 10.1016/j.cpb.2014.09.001

mPing: The bursting transposon Reviewed

Ken Naito, Yuki Monden, Kanako Yasuda, Hiroki Saito, Yutaka Okumoto

BREEDING SCIENCE 64 ( 2 ) 109 - 114 2014.6

Language：English Publisher：JAPANESE SOC BREEDING

Though transposable elements (TEs) have been considered as an efficient source of evolution, it has never been possible to test this hypothesis because most of TE insertions had occurred millions of years ago, or because currently active TEs have very few copies in a host genome. However, mPing, the first active DNA transposon in rice, was revealed to hold a key to answer this question. mPing has attained high copy numbers and still retained very high activity in a traditional rice strain, which enabled direct observation of behavior and impact of a bursting TE. A comprehensive analysis of mPing insertion sites has revealed it avoids exons but prefers promoter regions and thus moderately affects transcription of neighboring genes. Some of the mPing insertions have introduced possibly useful expression profile to adjacent genes that indicated TE's potential in de novo formation of gene regulatory network.

DOI： 10.1270/jsbbs.64.109

Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site Reviewed

Yuki Monden, Nobuyuki Fujii, Kentaro Yamaguchi, Kazuho Ikeo, Yoshiko Nakazawa, Takamitsu Waki, Keita Hirashima, Yosuke Uchimura, Makoto Tahara

GENOME 57 ( 5 ) 245 - 252 2014.5

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：CANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESS

Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5' LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria x ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a "unique" insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars.

DOI： 10.1139/gen-2014-0031

Characterization of a novel retrotransposon TriRe-1 using nullisomic-tetrasomic lines of hexaploid wheat

Yuki Monden, Takeru Takai, Makoto Tahara

岡山大学農学部学術報告 103 21 - 30 2014

新規活性型レトロトランスポゾンTriRe-1の挿入多型を利用した、High-throughputなコムギ品種判定マーカーの開発

門田有希, 高井健, 田原誠, 梅野佑太, 中村遼太

DNA 多型 22 ( 1 ) 60 - 65 2014

活性型レトロトランスポゾンを利用したアントシアニン含有紫サツマイモ品種識別用DNAマーカーの開発

門田有希, 山本彩加, 田原誠

DNA多型 ( 21 ) 47 - 54 2013

イチゴにおけるレトロトランスポゾン品種識別マーカーの開発

秋竹広翔, 田原誠, 門田有希, 高崎一人, 布藤聡

DNA多型 ( 21 ) 64 - 72 2013

Physical mapping of two novel photoperiod sensitivity genes, se14 and se15, using mPing SCAR markers Reviewed

ASAMI Takehito, OKUMOTO Yutaka, SAITO Hiroki, YUAN Qingbo, MONDEN Yuki, TERAISHI Masayoshi, TSUKIYAMA Takuji, TANISAKA Takatoshi

作物研究 ( 54 ) 85 - 89 2009.11

High Potential of a Transposon mPing as a Marker System in japonica x japonica Cross in Rice Reviewed

Y. Monden, K. Naito, Y. Okumoto, H. Saito, N. Oki, T. Tsukiyama, O. Ideta, T. Nakazaki, S. R. Wessler, T. Tanisaka

DNA Research 16 ( 2 ) 131 - 140 2009.1

mPingを含んで転写される遺伝子の同定 Reviewed

稲垣春香, 築山拓司, 門田有希, Shanta Karki, 奥本裕, 中崎鉄也, 寺石政義, 谷坂隆俊

作物研究 54 75 - 80 2009

Up regulation of a rice transposon Ping in active strain EG4

Yuki Monden, Ken Naito, Takuji Tsukiyama, Yutaka Okumoto, Takatoshi Tanisaka

Journal of crop research 54 119 - 123 2009

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