Faculty Profiles - MONDEN Yuki

Papers - MONDEN Yuki

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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

PubMed

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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

PubMed

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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

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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

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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

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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

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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

Scopus

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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

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