start-ver=1.4 cd-journal=joma no-vol=70 cd-vols= no-issue=2 article-no= start-page=231 end-page=240 dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=2020 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification en-subtitle= kn-subtitle= en-abstract= kn-abstract=In this study, DNA markers were developed for discrimination of strawberry (Fragaria × ananassa L.) cultivars based on retrotransposon insertion polymorphisms. We performed a comprehensive genomic search to identify retrotransposon insertion sites and subsequently selected one retrotransposon family, designated CL3, which provided reliable discrimination among strawberry cultivars. Through analyses of 75 strawberry cultivars, we developed eight cultivar-specific markers based on CL3 retrotransposon insertion sites. Used in combination with 10 additional polymorphic markers, we differentiated 35 strawberry cultivars commonly cultivated in Japan. In addition, we demonstrated that the retrotransposon-based markers were effective for PCR detection of DNA extracted from processed food materials, whereas a SSR marker was ineffective. These results indicated that the retrotransposon-based markers are useful for cultivar discrimination for processed food products, such as jams, in which DNA may be fragmented or degraded. en-copyright= kn-copyright= en-aut-name=HirataChiharu en-aut-sei=Hirata en-aut-mei=Chiharu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=WakiTakamitsu en-aut-sei=Waki en-aut-mei=Takamitsu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShimomuraKatsumi en-aut-sei=Shimomura en-aut-mei=Katsumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=WadaTakuya en-aut-sei=Wada en-aut-mei=Takuya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TanakaSeiya en-aut-sei=Tanaka en-aut-mei=Seiya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=IkegamiHidetoshi en-aut-sei=Ikegami en-aut-mei=Hidetoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=UchimuraYousuke en-aut-sei=Uchimura en-aut-mei=Yousuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=HirashimaKeita en-aut-sei=Hirashima en-aut-mei=Keita kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=NakazawaYoshiko en-aut-sei=Nakazawa en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=OkadaKaori en-aut-sei=Okada en-aut-mei=Kaori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=NamaiKiyoshi en-aut-sei=Namai en-aut-mei=Kiyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= affil-num=1 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=2 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=3 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=4 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=5 en-affil=Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University kn-affil= affil-num=6 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=7 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=8 en-affil=Fukuoka Agriculture and Forestry Research Center kn-affil= affil-num=9 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=10 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=11 en-affil=Tochigi Prefectural Agricultural Experiment Station kn-affil= affil-num=12 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=13 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Fragaria × ananassa kn-keyword=Fragaria × ananassa en-keyword=high-throughput sequencing kn-keyword=high-throughput sequencing en-keyword=PCR product kn-keyword=PCR product en-keyword=processed foods kn-keyword=processed foods en-keyword=retrotransposon insertion polymorphisms kn-keyword=retrotransposon insertion polymorphisms END start-ver=1.4 cd-journal=joma no-vol=26 cd-vols= no-issue=5 article-no= start-page=399 end-page=409 dt-received= dt-revised= dt-accepted= dt-pub-year=2019 dt-pub=20190803 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato en-subtitle= kn-subtitle= en-abstract= kn-abstract=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 (similar to 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 F-1 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 F-1 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. en-copyright= kn-copyright= en-aut-name=SasaiRumi en-aut-sei=Sasai en-aut-mei=Rumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TabuchiHiroaki en-aut-sei=Tabuchi en-aut-mei=Hiroaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShirasawaKenta en-aut-sei=Shirasawa en-aut-mei=Kenta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KishimotoKazuki en-aut-sei=Kishimoto en-aut-mei=Kazuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SatoShusei en-aut-sei=Sato en-aut-mei=Shusei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=OkadaYoshihiro en-aut-sei=Okada en-aut-mei=Yoshihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KuramotoAkihide en-aut-sei=Kuramoto en-aut-mei=Akihide kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KobayashiAkira en-aut-sei=Kobayashi en-aut-mei=Akira kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=IsobeSachiko en-aut-sei=Isobe en-aut-mei=Sachiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=3 en-affil=Kazusa DNA Research Institute kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=5 en-affil=Graduate School of Life Science, Tohoku University kn-affil= affil-num=6 en-affil=Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=7 en-affil=Graduate School of Agriculture, Kyoto University kn-affil= affil-num=8 en-affil=Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization kn-affil= affil-num=9 en-affil=Kazusa DNA Research Institute kn-affil= affil-num=10 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=11 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=sweetpotato kn-keyword=sweetpotato en-keyword=GWAS kn-keyword=GWAS en-keyword=QTL mapping kn-keyword=QTL mapping en-keyword=polyploids kn-keyword=polyploids en-keyword=marker-assisted breeding kn-keyword=marker-assisted breeding END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140616 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform en-subtitle= kn-subtitle= en-abstract= kn-abstract=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 2024 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. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=YamamotoAyaka en-aut-sei=Yamamoto en-aut-mei=Ayaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShindoAkiko en-aut-sei=Shindo en-aut-mei=Akiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=2 en-affil= kn-affil=Faculty of Agriculture, Okayama University affil-num=3 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=4 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University en-keyword=DNA fingerprinting kn-keyword=DNA fingerprinting en-keyword=high-throughput sequencing kn-keyword=high-throughput sequencing en-keyword=molecular marker kn-keyword=molecular marker en-keyword=retrotransposon kn-keyword=retrotransposon en-keyword=sweet potato kn-keyword=sweet potato END start-ver=1.4 cd-journal=joma no-vol=57 cd-vols= no-issue=5 article-no= start-page=245 end-page=252 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140625 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site en-subtitle= kn-subtitle= en-abstract= kn-abstract=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 × 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. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=FujiiNobuyuki en-aut-sei=Fujii en-aut-mei=Nobuyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=YamaguchiKentaro en-aut-sei=Yamaguchi en-aut-mei=Kentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=IkeoKazuho en-aut-sei=Ikeo en-aut-mei=Kazuho kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=NakazawaYoshiko en-aut-sei=Nakazawa en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=WakiTakamitsu en-aut-sei=Waki en-aut-mei=Takamitsu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=HirashimaKeita en-aut-sei=Hirashima en-aut-mei=Keita kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=UchimuraYosuke en-aut-sei=Uchimura en-aut-mei=Yosuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=2 en-affil= kn-affil=Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems affil-num=3 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=4 en-affil= kn-affil=Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems affil-num=5 en-affil= kn-affil=Biotechology Division, Tochigi Prefectural Agricultural Experiment Station affil-num=6 en-affil= kn-affil=Biotechology Division, Tochigi Prefectural Agricultural Experiment Station affil-num=7 en-affil= kn-affil=Department of Research Plan and Strategy, Fukuoka Agricultural Research Center affil-num=8 en-affil= kn-affil=Department of Research Plan and Strategy, Fukuoka Agricultural Research Center affil-num=9 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University en-keyword=retrotransposon kn-keyword=retrotransposon en-keyword=primer binding site kn-keyword=primer binding site en-keyword=high-throughput sequencing kn-keyword=high-throughput sequencing en-keyword=polymorphism kn-keyword=polymorphism en-keyword=molecular markers kn-keyword=molecular markers END start-ver=1.4 cd-journal=joma no-vol=185 cd-vols= no-issue= article-no= start-page=57 end-page=62 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140920 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=A rapid and enhanced DNA detection method for crop cultivar discrimination en-subtitle= kn-subtitle= en-abstract= kn-abstract=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. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TakasakiKazuto en-aut-sei=Takasaki en-aut-mei=Kazuto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=FutoSatoshi en-aut-sei=Futo en-aut-mei=Satoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=NiwaKousuke en-aut-sei=Niwa en-aut-mei=Kousuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KawaseMitsuo en-aut-sei=Kawase en-aut-mei=Mitsuo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=AkitakeHiroto en-aut-sei=Akitake en-aut-mei=Hiroto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=2 en-affil= kn-affil=FASMAC Co., Ltd. affil-num=3 en-affil= kn-affil=FASMAC Co., Ltd. affil-num=4 en-affil= kn-affil=Graduate School of Biomedical Engineering, Tohoku University affil-num=5 en-affil= kn-affil=Graduate School of Biomedical Engineering, Tohoku University affil-num=6 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=7 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University en-keyword=Cultivar discrimination kn-keyword=Cultivar discrimination en-keyword=Multiplex PCR kn-keyword=Multiplex PCR en-keyword=Strawberry kn-keyword=Strawberry en-keyword=Practical application kn-keyword=Practical application en-keyword=Retrotransposon kn-keyword=Retrotransposon END start-ver=1.4 cd-journal=joma no-vol=103 cd-vols= no-issue= article-no= start-page=21 end-page=30 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140201 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=コムギ染色体欠損系統を用いた新規活性型レトロトランスポゾン TriRe-1 の分子遺伝学的解析 kn-title=Characterization of a novel retrotransposon TriRe‒1 using nullisomic-tetrasomic lines of hexaploid wheat en-subtitle= kn-subtitle= en-abstract= レトロトランスポゾンは植物ゲノムの主要な構成要素であり,コムギゲノムにおいてはその80オを占める.特に LTR 型レトロトランスポゾンの割合が高く,ゲノムの拡大,配列の多様性およびゲノム構造変異等に大きく寄与し てきたと考えられている.これら配列は自身のコピー配列を複製し増幅するため,ゲノム中には数百,数千に及ぶコ ピー配列をもつ.また,ゲノム進化の過程において多数のファミリーを形成してきた.これら多数のファミリーのう ち,現在でも転移活性を示す活性型ファミリーは,品種間において高い挿入多型を示すことが知られている.このよ うな挿入多型は,連鎖解析および系統解析等各種遺伝解析に利用可能である. 本研究では,コムギにおける新規活性 型レトロトランスポゾンファミリー TriRe-1 の特徴を詳細に解析した.TriRe-1 は転移に必要なタンパク質をコー ドする内部配列をもち,また日本で育成されたコムギ近縁品種間においても高い挿入多型を示したため,現在でも転 移活性を有している,もしくはごく最近まで転移していた可能性が高いと考えられた.一方で,コムギ染色体欠損系 統(ナリソミックテトラソミック系統)を用い,TriRe-1 の挿入箇所を比較解析した.その結果,大部分の挿入箇所 は複数の同祖染色体に存在すると考えられたが,Bゲノムにおいて最も多くの特異的な挿入箇所が同定された.よっ て,Bゲノム祖先種において活発に増幅してきた可能性が示唆された.今回の結果により,新規活性型レトロトラン スポゾン TriRe-1 の品種間挿入多型を利用した DNA マーカー,また,各ゲノム(A,B,Dゲノム)特異的な挿 入箇所を利用したゲノム識別性に優れた DNA マーカーの開発の可能性が期待される. kn-abstract= Retrotransposons constitute the large fraction (~80%) of the wheat genome where numerous and diverse retrotransposon families exist, where especially the long terminal repeat (LTR) retrotransposon family is known to be predominant. Thus, they have been considered to contribute to the genome expansion, sequence diversification and the genome structure alternation in the wheat genome. In addition, the insertion polymorphism of the LTR retrotransposon family among the cultivars has been known to be quite useful for the genetic analysis such as the linkage mapping and the phylogenetic studies. Here, we report the characteristics of a novel active LTR retrotransposon family TriRe‒1, which belongs to the Ty1‒copia group in the hexaploid wheat (Triticum aestivum L.) genome. This retroelement appears to encode all proteins required for the transposition and showed high insertion polymorphism among the hexaploid wheat cultivars, suggesting its potential of transpositional activity with at least recent transposition during wheat evolution. We studied the chromosomal localization of the TriRe‒1 insertion site based on the genome-wide comparative analysis using the nullisomic-tetrasomic lines of the cultivar Chinese Spring. The results showed that although the majority of the TriRe‒1 insertion sites exist across the homoeologous chromosomes of A, B or D genomes, a higher number of insertions in the B genome was detected compared to A or D genome, suggesting a specific amplification in the history of B genome progenitors. In conclusion, a novel LTR retrotransposon TriRe‒1 should be valuable for the development of molecular markers based on insertion polymorphism among the cultivars, and also the genome-specific TriRe‒1 insertion site can be utilized to study evolutional history of wheat genomes. en-copyright= kn-copyright= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name=門田有希 kn-aut-sei=門田 kn-aut-mei=有希 aut-affil-num=1 ORCID= en-aut-name=TakaiTakeru en-aut-sei=Takai en-aut-mei=Takeru kn-aut-name=高井健 kn-aut-sei=高井 kn-aut-mei=健 aut-affil-num=2 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name=田原誠 kn-aut-sei=田原 kn-aut-mei=誠 aut-affil-num=3 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 affil-num=3 en-affil= kn-affil=岡山大学 en-keyword=Retrotransposon kn-keyword=Retrotransposon en-keyword=Wheat kn-keyword=Wheat en-keyword=Molecular markers kn-keyword=Molecular markers en-keyword=Nullisomic-tetrasomic lines kn-keyword=Nullisomic-tetrasomic lines END start-ver=1.4 cd-journal=joma no-vol=272 cd-vols= no-issue=1 article-no= start-page=116 end-page=127 dt-received= dt-revised= dt-accepted= dt-pub-year=2004 dt-pub=20048 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Isolation of a transcriptionally active element of high copy number retrotransposons in sweetpotato genome en-subtitle= kn-subtitle= en-abstract= kn-abstract=

Many plant retrotransposons have been characterized, but only three families (Tnt1, Tto1 and Tos17) have been demonstrated to be transpositionally competent. We followed a novel approach that enabled us to identify an active element of the Ty1-copia retrotransposon family with estimated 400 copies in the sweetpotato genome. DNA sequences of Ty1 -copia reverse transcriptase (RTase) from the sweetpotato genome were analyzed, and a group of retrotransposon copies probably formed by recent transposition events was further analyzed. 3’RACE on callus cDNA amplified transcripts containing long terminal repeats (LTR) of this group. The sequence -specific amplification polymorphism (S-SAP) patterns of the LTR sequence in the genomic DNA were compared between a normal plant and callus lines derived from it. A callus -specific S-SAP product was found into which the retrotransposon detected by the 3’RACE had been transposed apparently during cell culture. We conclude that our approach provides an effective way to identify active elements of retrotransposons with high copy numbers.

en-copyright= kn-copyright= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=AokiTakahiro en-aut-sei=Aoki en-aut-mei=Takahiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=SuzukaShinya en-aut-sei=Suzuka en-aut-mei=Shinya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=YamashitaHiroki en-aut-sei=Yamashita en-aut-mei=Hiroki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TanakaMasaru en-aut-sei=Tanaka en-aut-mei=Masaru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MatsunagaSachi en-aut-sei=Matsunaga en-aut-mei=Sachi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KokumaiShuhei en-aut-sei=Kokumai en-aut-mei=Shuhei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=Okayama University affil-num=2 en-affil= kn-affil=JEOL Limited affil-num=3 en-affil= kn-affil=SK Foods Company, Limited affil-num=4 en-affil= kn-affil=Okayama University affil-num=5 en-affil= kn-affil=National Agricultural Research Center affil-num=6 en-affil= kn-affil=Kabaya Foods Corporation affil-num=7 en-affil= kn-affil=Okayama University en-keyword=retrotransposon kn-keyword=retrotransposon en-keyword=Ipomoea batatas kn-keyword=Ipomoea batatas en-keyword=S-SAP kn-keyword=S-SAP en-keyword=transposition kn-keyword=transposition END start-ver=1.4 cd-journal=joma no-vol=85 cd-vols= no-issue=1 article-no= start-page=99 end-page=108 dt-received= dt-revised= dt-accepted= dt-pub-year=1996 dt-pub=19960201 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=Genotype by Environment Interactions and Parameters for Genotype Responses to Environments in Wheat Breedig Program of Oklahoma kn-title=オクラホマ州の硬質冬小麦の育種における遺伝子型と環境の交互作用と遺伝子型の環境反応性の指標化について en-subtitle= kn-subtitle= en-abstract=著者は、1981・1982年と1985~1988年の二度にわたり、米国オクラホマ州立大学の大学院に留学し、硬質冬小麦(Hard Red Winter Wheat)の育種プロジェクトの下、修士(Master of Science)と博士号(Ph.D.in Crop Science)を取得した。本稿では、同州の硬質冬小麦育種プロジェクトについて触れるとともに、量的形質の選抜に際して最大の課題の一つである遺伝子型と環境の交互作用と、その交互作用をそれぞれの遺伝子型の環境との反応性によって説明しようとする方法(直線回帰分析)を用いて解析した例を紹介する。 kn-abstract=The Wheat breeding program at Oklahoma State University(OSU) is introduced with reference to genotype by environment interactions and linear regression analyses. Oklahoma is the second largest producer of hard red winter wheat in the US. The breeding porgram is conducted by the wheat breeding personnel of the Agronomy Department in collaboration with plant pathologists, entomologists and biochemists of OSU and wheat geneticists of the US Department of Agriculture. The main-stream breeding procedures are F2 or F3 progeny methods, which are modifications of pedigree and bulk breeding methods. The procedures for source population development,selection practice and field trials are discussed. The major objective of the projict is to develop wheat varieties with supperior yield and yield stability. Drought stress is a serious constraint to wheat crop and frequently causes substantial yield reduction in Okrahoma. Other major obstacles to wheat production are disease and insect damage which include leaf rust, mosaic diseses, septoria and green bug. Research and breeding activities to overcome thesse obstacles are briefly reviewed.Genotype by environment interactions are commonly found and cause serious problems in identifying superior genotype over a wide range of environments in the wheat breeding program. Linear regression analyses and other yield stability parameters are proposed to characterize genotype responses to varying environments. The grain yield data from cultivar trials during 1971-1982 were analyzed by an analysis of variance method and linear regression method. The analysis of varince indicated substantial genotype by environment interactions. The linear regression analyses could adequately explain much of the interaction and provided parameters to compare yield responses of genotypes over environments. Other stability parameters were also estimated and their relationships were discussed. The linear regression analyses revealed that selection toward higher average yield over environments favored genotypes adapted for high yeilding environments. en-copyright= kn-copyright= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name=田原誠 kn-aut-sei=田原 kn-aut-mei=誠 aut-affil-num=1 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 en-keyword=wheat kn-keyword=wheat en-keyword=breeding kn-keyword=breeding en-keyword=genotype by environment interaction kn-keyword=genotype by environment interaction en-keyword=linear regression analysis kn-keyword=linear regression analysis en-keyword=stability parameter kn-keyword=stability parameter END start-ver=1.4 cd-journal=joma no-vol=87 cd-vols= no-issue=1 article-no= start-page=133 end-page=139 dt-received= dt-revised= dt-accepted= dt-pub-year=1998 dt-pub=199802 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=エステラーゼ・アイソザイムによるサトイモの系統分類 kn-title=Phylogenetic Analyses of Taro (Colocasia esculenta (L.) Schott) and Related Species based on Esterase Isozymes en-subtitle= kn-subtitle= en-abstract=東アジアを中心に採取したサトイモ(Colocasia esculenta (L) Schott)とその近緑野生種C.gigantea Hook, Alocasia macrorrhiza, A. odora, Xanthosoma sagittifolium (L.) Schott and X. violaceum Schottの84系統について、エステラーゼのアイソザイムの多型を基に類縁関係の推定を行った。UPGMA法によって系統樹を求めたところ、サトイモ69系統は一つの独立したクラスターを形成した。また、ハスイモ(C. gigantea Hook)は、サトイモよりもAlocasia属の種とより近縁であることを示唆する結果を得た。サトイモについて、東アジアの各系統のアイソザイムのバンドパターンを比較したところ、中国雲南省で収集したものは、東アジア各地のサトイモと共通のパターンを示すものが多かったことから、この地域がサトイモ進化に重要な役割を果たしていることが推察された。 kn-abstract=Phylogenetic relationships among the 84 accessions of taro (Colocasia esculenta (L) Schott), C gigantea Hook Alocasia macrorrhiza, A odora, Xanthosoma sagittifolium (L.) Schott and X. violaceum Schott were investigated using isozyme polymorphism of esterase. The phylogenetic tree estimated by the UPGMA analyses revealed that taro accessions formed a single cluster and C. gigantea was more closely related to Alocasia species than to taro. Taro accessions from Yunnan tended to share band patterns with those from various areas, which indicates that the Yunnan area might have been important for taro evolution. en-copyright= kn-copyright= en-aut-name=NguyenViet Xuan en-aut-sei=Nguyen en-aut-mei=Viet Xuan kn-aut-name=グエンヴィエット シュアン kn-aut-sei=グエン kn-aut-mei=ヴィエット シュアン aut-affil-num=1 ORCID= en-aut-name=YoshinoHiromichi en-aut-sei=Yoshino en-aut-mei=Hiromichi kn-aut-name=吉野熙道 kn-aut-sei=吉野 kn-aut-mei=熙道 aut-affil-num=2 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name=田原誠 kn-aut-sei=田原 kn-aut-mei=誠 aut-affil-num=3 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 affil-num=3 en-affil= kn-affil=岡山大学 en-keyword=Colocasia esculenta kn-keyword=Colocasia esculenta en-keyword=phylogeny kn-keyword=phylogeny en-keyword=isozyme kn-keyword=isozyme en-keyword=esterase kn-keyword=esterase END start-ver=1.4 cd-journal=joma no-vol=89 cd-vols= no-issue=1 article-no= start-page=15 end-page=21 dt-received= dt-revised= dt-accepted= dt-pub-year=2000 dt-pub=200002 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=Phylogenetic Pelationships of Taro and Allied Species Based on Restriction Fragment Length Polymorphisms(RFLPs) of Chloroplast DNA kn-title=葉緑体DNAの制限酵素断片長多型(RFLP)を利用したサトイモとその近縁種の類縁関係分析 en-subtitle= kn-subtitle= en-abstract=サトイモ(Colocasia esculenta(L.)Schott)は、有史以前から栽培されており、東南アジアやオセアニアなどで、主食あるいは野菜として利用されている重要な作物である。サトイモの起源地は、野生型の分布及び形態的な多様性によりインドからマレー半島にかけての熱帯地域とされているが、ネパール・中国・オセアニア・沖縄などの地域にも野生型サトイモや、野生化したと思われるサトイモが広く自生している。これらの野生型サトイモは、貴重な遺伝資源であるが、栽培種や野生種との類縁関係については不明な点が多い。本研究では、東アジアで収集されたサトイモとその近縁種について、葉緑体DNAのRFLP分析を行い、それらの類縁関係を調査した。 kn-abstract=Phylogenetic relationshios among 51 accessions of taro (Colocasia esculenta(L.) Schott), C.gigantee Hook, Alocasia macrorrhiza, A.odora, Xanthosoma sagittifolium and Schismatoglottis spp. were investigated using restriction fragment length polymorphisms (RFLPs) of chloroplast DNA. The phylogenetic tree using the Neighbor Joining(NJ) method revealed that Xanthosoma and Schismatoglottis genera were distantly related to Colocasia and Alocasia genera. Among Colocasia and Alocasia accessions, C.esculenta accessions formed a single cluster. However C. gigantea accessions were related DNA among taro accessions were found to be too small to establish significant grouping of the accessions. However, four accessions of taro, which were thought to be inter-generic or inter-specific hybrids, formed an independent cluster. Based on the banding pattern of the RFLP, the plant in genus Colocasia appeared to be the maternal parent of these four accessions. en-copyright= kn-copyright= en-aut-name=OchiaiToshinori en-aut-sei=Ochiai en-aut-mei=Toshinori kn-aut-name=落合利紀 kn-aut-sei=落合 kn-aut-mei=利紀 aut-affil-num=1 ORCID= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name=田原誠 kn-aut-sei=田原 kn-aut-mei=誠 aut-affil-num=2 ORCID= en-aut-name=YoshinoHiromichi en-aut-sei=Yoshino en-aut-mei=Hiromichi kn-aut-name=吉野熙道 kn-aut-sei=吉野 kn-aut-mei=熙道 aut-affil-num=3 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 affil-num=3 en-affil= kn-affil=岡山大学 en-keyword=Colocasia esculenta kn-keyword=Colocasia esculenta en-keyword=chloroplast DNA kn-keyword=chloroplast DNA en-keyword=RFLP analysis kn-keyword=RFLP analysis en-keyword=phylogeny kn-keyword=phylogeny END start-ver=1.4 cd-journal=joma no-vol=96 cd-vols= no-issue=1 article-no= start-page=7 end-page=11 dt-received= dt-revised= dt-accepted= dt-pub-year=2007 dt-pub=200702 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=転移能を有するサツマイモ・レトロトランスポゾン塩基配列から推定される逆転写開始複合体の特徴 kn-title=A Novel Initiation Complex for Reverse Transcription of an Active LTR Retrotransposon in Seeetpotato en-subtitle= kn-subtitle= en-abstract=カルスにおける転移が示されたサツマイモ LTR 型レトロトランスポゾン(Rtsp-1)の塩基配列を調べたところ,逆転写が開始される際,転写された Rtsp-1の RNA と最初の逆転写のプライマーに使われる tRNAMETとの間で,特徴的な逆転写開始複合体を形成し,この複合体が最初の逆転写とその後の過程で必要な逆転写産物(cDNA)の転移などを確実なものとしていることが示唆された.その内容は,1)転写された Rtsp-1の RNA 逆転写開始部位の塩基配列は自身の LTR 配列とステム構造をとること,2)tRNAMETが結合する Rtsp-1の Primer Binding Site 部位には,プライマーの機能を果たす tRNAMETの3'末端の相補配列に加えて,その隣接部位に tRNAMETの5'末端部位と相補的な結合部位が存在するために,tRNAMETの両末端が結合すること,3)Rtsp-1の3'末端側に,tRNAMET及びステム構造に関わる5'LTR の部位との相補配列があり,この3セ末端側が転写開始複合体と結合することにより,ステム構造が崩れて逆転写が開始されると推定されること,4)逆転写が開始された後も,tRNAMETの結合によってRtsp-1の5'末端と3'末端側に近接した状態が保たれることである.Rtsp-1の3セ末端側の転写開始複合体への結合を転写開始の条件とすることにより,最初に合成される cDNA の3'末端への転移が容易となることなどが示唆された. kn-abstract=Sequence analysis of Rtsp-1, an active LTR retrotransposon in the sweetpotato genome,revealed a possible novel Rtsp-1 RNA/tRNAMet complex for initiation of reverse transcription and the first DNA strand transfer. The Rtsp-1 RNA has a primer binding site (PBS) that is partly complementary to the 3’ end of tRNAMet, and possesses an additional sequence complementary to the 5’ end of tRNAMet downstream of the PBS. These additional base-pairings might stabilize the Rtsp-1 RNA/primer complex. In the free form, the 5’ LTR of Rtsp-1 appears to form a stemloop structure apparently preventing the initiation of reverse transcription. While the stemforming site adjacent to the PBS is complementary to the tRNAMet, the other stem-forming site on the LTR complements a region just upstream of the 3’ LTR. Additionally, another region at the 3’ end of the Rtsp-1 RNA shows sequence complementarity to the tRNAMet. As the 3’ end of Rtsp-1 approaches the tRNAMet bound to the PBS, the stem-forming strands dissociate and basepair with their complementary regions in the tRNAMet and the 3’ end of Rtsp-1, respectively. Consequently, the LTR loop opens, allowing reverse transcription to initiate. After the initial reverse transcription stops at the 5’ end of the Rtsp-1 RNA, the synthesized minus strand DNA needs to be transferred to the 3’ end of the RNA to synthesize internal sequences. The Rtsp-1 RNA/tRNAMet complex may have evolved to facilitate this DNA transfer. Similar RNA/tRNA initiation complexes have been reported from reverse transcription in retroviruses and yeast retrotransposons (Ty1 and Ty3). en-copyright= kn-copyright= en-aut-name=TaharaMakoto en-aut-sei=Tahara en-aut-mei=Makoto kn-aut-name=田原誠 kn-aut-sei=田原 kn-aut-mei=誠 aut-affil-num=1 ORCID= en-aut-name=YamashitaHiroki en-aut-sei=Yamashita en-aut-mei=Hiroki kn-aut-name=山下裕樹 kn-aut-sei=山下 kn-aut-mei=裕樹 aut-affil-num=2 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 affil-num=2 en-affil= kn-affil=岡山大学 en-keyword=retrotransposon kn-keyword=retrotransposon en-keyword=reverse transcription kn-keyword=reverse transcription en-keyword=initiation complex kn-keyword=initiation complex en-keyword=retrovirus kn-keyword=retrovirus en-keyword=DNA strand kn-keyword=DNA strand END