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研究内容

植物ゲノム・遺伝学研究室

わたしたちの研究

わたしたちの研究の目的

 植物はそれぞれ数億〜数千億文字に相当する膨大なゲノム情報をもっていますが、そのすべてが大事な情報であるとは限りません。そこで、わたしたちはさまざまな植物種について膨大なゲノム情報を収集・整理し、その種にとって本当に大事な部分(遺伝子など)がどこにあるかを調べる研究を行っています。さらに、ゲノムや遺伝子の情報を利用して新しい品種を効率よく作り出す方法の開発を進めています。

わたしたちの研究の特徴

 わたしたちは、これまで25種類を超える様々な植物を対象に有用な遺伝子や特徴的な目印(マーカー)を見つけだしてきました。また、トマトやイチゴ、カーネーションなど作物のゲノム解読も行っています。さらに、膨大なゲノム情報から遺伝子を効率的に見つけ出すための解析手法の開発にも取り組んでいます。これらの成果をもとに、国内外の公的機関や企業と共同研究を行い、迅速な品種改良を可能にする育種技術の開発など、ゲノム情報を産業に役立てるための取り組みを行っています。

応用が期待される分野

 ある植物と別の植物、あるいは異なる品種の塩基配列を比較することで、それぞれの植物の特徴を決めている遺伝子をしぼりこむことができます。また、特徴的な遺伝子の働きを明らかにすることによって、病気や干ばつに強い農産物を育種するための基礎的な知識が得られます。このように、ゲノム情報を利用した新たな育種技術が開発できれば、これまでにない優れた性質を持つ新たな品種を作り出すことや、10年以上かかるといわれる品種の育成期間を短縮することが期待されます。また、ゲノム情報を比較することで、長い地球の歴史のなかで植物がどのように進化してきたかを推測し、現在地球に存在する植物の関係を詳細に知ることができます。

研究テーマ

  1. 有用植物の全ゲノム解読
  2.  ゲノム情報が十分でない有用植物の全ゲノム解読を行い、ゲノム解析と育種を行うための基盤を整備します。千葉県が生産額1位(平成26年度)のサツマイモのほか、キク、マメ科3種に取り組みます。また、植物の全ゲノムを安く速く解読するための技術開発を行います。

  3. 有用植物のDNAマーカーと遺伝子型解析技術の開発
  4.  イチゴ、トマト、インゲン、クズ等の有用植物を対象に、全ゲノムを高密度でカバーするDNAマーカーの開発を行います。また、効率良いゲノム再解読法を確立し、有用植物のハプロタイプ地図の作成に取り組みます。

  5. ゲノム情報を活用した育種技術法の開発
  6.  有用形質とマーカーを対応させるための新たな遺伝解析や有用遺伝子領域の高精度なマッピング法を開発するとともに、遺伝子組換え体作出技術の効率化に取り組みます。また、ヤハズエンドウを用いて野生種が栽培種になるまでの過程を模擬実験します。

  7. 大規模配列解析による網羅的な遺伝子機能推定
  8.  トマトやイチゴの果実などで発現している有用遺伝子の網羅的な解析による遺伝子機能の推定を行うために、RNA-seqやマイクロアレイ技術による遺伝子発現解析を行います。また、SNPs(一塩基の変異による多様性)の遺伝子機能への影響を推定するために、SNPsに意味付けする方法の確立に取り組みます。

  9. 育種機関と連携したDNAマーカー選抜の実施
  10. 千葉県農林総合研究センターをはじめとする公的研究機関や種苗会社に所属する育種研究者と協力し、DNAマーカーの開発や、それらを用いた優良個体の選抜を行います。落花生のオレイン酸含量やイチゴの果実表面色の選抜などを行い、付加価値の高い品種の開発に貢献します。

植物ゲノム応用研究室

研究室メンバー

磯部 祥子 室長 sisobe at kazusa.or.jp
(兼)平川 英樹 主任研究員 hh at kazusa.or.jp
白澤 健太 研究員 shirasaw at kazusa.or.jp
七夕 高也 特別研究員 tanabata at kazusa.or.jp
永野 聡一郎 特任研究員 nagano at kazusa.or.jp
林 篤司 特任研究員 ahayashi at kazusa.or.jp

発表論文リスト

2014
Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases.
Asamizu E, Ichihara H, Nakaya A, Nakamura Y, Hirakawa H, Ishii T, Tamura T, Fukami-Kobayashi K, Nakajima Y, Tabata S.
Plant Cell Physiol. 55(1): e8 (2014)

Regulatory change in cell division activity and genetic mapping of a tomato (Solanum lycopersicum L.) elongated-fruit mutant.
Chusreeaeom K, Ariizumi T, Asamizu E, Okabe Y, Shirasawa K, Ezura H.
Plant Biotech (2014) in press

Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai).
Terakami S, Nishitani C, Kunihisa M, Shirasawa K, Sato S, Tabata S, Kurita K, Kanamori H, Katayose Y, Takada N, Saito T, Yamamoto T.
Tree Genet Genomics 10:853-863 (2014)

A novel tomato mutant, Solanum lycopersicum elongated fruit1 (Slelf1), exhibits an elongated fruit shape caused by increased cell layers in the proximal region of the ovary.
Chusreeaeom K, Ariizumi T, Asamizu E, Okabe Y, Shirasawa K, Ezura H
Mol Genet Genomics 289(3):399-409 (2014)

Sequence analysis of the genome of carnation (Dianthus caryophyllus L.).
Yagi M, Kosugi S, Hirakawa H, Ohmiya A, Tanase K, Harada T, Kishimoto K, Nakayama M, Ichimura K, Onozaki T, Yamaguchi H, Sasaki N, Miyahara T, Nishizaki Y, Ozeki Y, Nakamura N, Suzuki T, Tanaka Y, Sato S, Shirasawa K, Isobe S, Miyamura Y, Watanabe A, Nakayama S, Kishida Y, Kohara M, Tabata S.
DNA Res. 21(3):231-41(2014)

Dissection of the octoploid strawberry genome by deep-sequencing of Fragaria species.
Hirakawa H, Shirasawa K, Kosugi S, Tashiro K, Nakayama S, Yamada M, Kohara M, Watanabe A, Kishida Y, Fijishiro T, Tsuruoka H, Minami C, Sasamoto S, Kato M, Nanri K, Komaki A, Yanagi T, Guoxin Q, Maeda F, Ishikawa M, Kuhara S, Sato S, Tabata S, Isobe S
DNA Res. 21(2):169-81(2014)

Development of NILs from heterogeneous inbred families for validating the rust resistance QTLs in peanut (Arachis hypogaea L.).
Yeri SB, Shirasawa K, Pandey MK, Gowda MVC, Sujay V, Shriswathi M, Nadaf HL, Motagi BN, Lingaraju S, Bhat ARS, Varshney RK, Krishnaraj PU, Bhat RS
Plant Breed 133: 80-85. (2014)

2013
Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.).
Yagi M, Yamamoto T, Isobe S, Hirakawa H, Tabata S, Tanase K, Yamaguchi H, Onozaki T.
BMC Genomics 14: 734. (2013)

Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato.
Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H, Isobe S, Tabata S.
DNA Res. 20(6): 593-603. (2013)

Genome-wide SNP genotyping to infer the effects on gene functions in tomato.
Hirakawa H, Shirasawa K, Ohyama A, Fukuoka H, Aoki K, Rothan C, Sato S, Isobe S, Tabata S.
DNA Res. 20(3): 221-233. (2013)

Analysis of a tomato introgression line, IL8-3, with increased Brix content.
Ikeda H, Hiraga M, Shirasawa K, Nishiyama M, Kanahama K, Kanayama Y.
Scientia Horticulturae 153: 103-108. (2013)

Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes.
Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SC, Thudi M, Pandey MK, Rami JF, Foncéka D, Gowda MV, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S.
DNA Res. 20(2): 173-184. (2013)

Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability.
Isobe SN, Hirakawa H, Sato S, Maeda F, Ishikawa M, Mori T, Yamamoto Y, Shirasawa K, Kimura M, Fukami M, Hashizume F, Tsuji T, Sasamoto S, Kato M, Nanri K, Tsuruoka H, Minami C, Takahashi C, Wada T, Ono A, Kawashima K, Nakazaki N, Kishida Y, Kohara M, Nakayama S, Yamada M, Fujishiro T, Watanabe A, Tabata S.
DNA Res. 20(1): 79-92. (2013)

Development of Capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence.
Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi M, Nagata N, Isobe S, Tabata S.
Mol Breed. 31(1): 101-110. (2013)

Marker-assisted backcrossing selection for high O/L ratio in cultivated peanut.
Koilkonda P, Kuwata C, Fukami M, Shirasawa K, Aoki K, Tabata S, Hasegawa M, Kiyoshima H, Suzuki S, Sasamoto S, Kurabayashi A, Tsuruoka H, Wada T, Isobe S
In “Translational Genomics for Crop Breeding: Volume 2 - Improvement for Abiotic Stress, Quality and Yield Improvement”, Wiley-Blackwell, Ed by Varshney R, Tuberosa R, pp 177-192 (2013)

Structural analyses of the tomato genome.
Sato S, Shirasawa K, Tabata S.
Plant Biotechnology 30(3): 257-263. (2013)

DNA marker applications to molecular genetics and genomics in tomato.
Shirasawa K, Hirakawa H.
Breed Sci. 63 (1): 21-30. (2013)

Genome-wide SNP marker development and QTL identification for genomic selection in red clover.
Isobe S, Boller B, Klimenko I, Kolliker S, Rana JC, Sharma TR, Shirasawa K, Hirakawa H, Sato S, Tabata S
In "Breeding Strategy for Sustainable Forage and Turf Grass Improvement", Springer Netherlands, Ed by Barth S, Milbourne D, pp 29-36. (2013)

Red Clover.
Isobe S, Kölliker R, Boller B, Ridy H.
Genetics, Genomics and Breeding of Forage Crops. CRC Press. FL, NY and UL. ISBN 978-1482208108 220-249. (2013)

2012
Upgraded genomic information of Jatropha curcas L.
Hirakawa H., Tsuchimoto S., Sakai H., Nakayama S., Fujishiro T., Kishida Y., Kohara M., Watanabe A., Yamada M., Aizu T., Toyoda A., Fujiyama A., Tabata S., Fukui K., Sato S.
Plant Biotechnology 29: 123-130. (2012)

Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology.
Tanase K., Nishitani C., Hirakawa H., Isobe S., Tabata S., Ohmiya A., Onozaki T.
BMC Genomics. 13: 292. (2012)

Mapping of Micro-Tom BAC-end sequences to the reference tomato genome reveals possible genome rearrangements and polymorphisms.
Asamizu E, Shirasawa K, Hirakawa H, Sato S, Tabata S, Yano K, Ariizumi T, Shibata D, Ezura H.
Int J Plant Genomics 437026. (2012)

In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut.
Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, Takahashi C, Tsuruoka H, Wada T, Isobe S.
BMC Plant Biol. 12(1): 80. (2012)

The tomato genome sequence provides insights into fleshy fruit evolution.
The Tomato Genome Consortium
Nature 485: 635-641. (2012)

Comparative Genetic Mapping and Discovery of Linkage Disequilibrium Across Linkage Groups in White Clover (Trifolium repens L.).
Isobe SN, Hisano H, Sato S, Hirakawa H, Okumura K, Shirasawa K, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, , Kohara M, Tabata S.
G3 (Bethesda). 2(5): 607-617. (2012)

Availability of Micro-Tom mutant library combined with TILLING in molecular breeding of tomato fruit shelf-life.
Okabe Y, Asamizu E, Ariizumi T, Shirasawa K, Tabata S, Ezura H.
Breeding Sci. 62: 202-208. (2012)

Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets.
Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, Asamizu E, Yamaguchi H, Ohyama A.
Theor Appl Genet. 125: 47-56. (2012)

Characterization of active miniature inverted-repeat transposable elements in the peanut genome.
Shirasawa K, Hirakawa H, Tabata S, Hasegawa M, Kiyoshima H, Suzuki S, Sasamoto S, Watanabe A, Fujishiro T, Isobe S.
Theor Appl Genet. 124(8): 1429-1438. (2012)

Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp.
Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Suzuki S, , Hasegawa M, Kiyoshima H, Isobe S.
Mol Breed. 30(1): 125-138. (2012)

Integration of linkage and chromosome maps of red clover (Trifolium pratense L.).
Kataoka R, Hara M, Kato S, Isobe S, Sato S, Tabata S, Ohmido N.
Cytogenet Genome Res. 137(1): 60-69. (2012)

QTL analysis for resistance to bacterial wilt (Burkholderia caryophilli) in carnation (Dainthus caryophyllus) using an SSR-based genetic linkage map.
Yagi M, Kimura T, Yamamoto T, Isobe S, Tabata S, Onozaki T.
Mol Breeding 30: 495-509. (2012)

Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.).
Wang H, Penmetsa RV, Yuan M, Gong L, Zhao Y, Guo B, Farmer AD, Rosen BD, Gao J, Isobe S, Bertioli DJ, Varshney RK,Cook DR, He G.
BMC Plant Biol. 12: 10. (2012)

The integral membrane protein SEN1 is required for symbiotic nitrogen fixation in Lotus japonicus nodules.
Hakoyama T, Niimi K, Yamamoto T, Isobe S, Sato S, Nakamura Y, Tabata S, Kumagai H, Umehara Y, Brossuleit K,Petersen TR, Sandal N, Stougaard J, Udvardi MK, Tamaoki M, Kawaguchi M, Kouchi H, Suganuma N.
Plant Cell Physiol. 53: 225-236. (2012)

Will genomic selection be a practical method for plant breeding?
Nakaya A, and. Isobe S.
Annals of Botany 110(6): 1303-1316. (2012)

Genome-wide SNP marker development and QTL identification for genomic selection in red clover.
Isobe S, Boller B , Klimenko I, Kölliker S2, Rana JC, Sharma TR,Shirasawa K,Hirakawa H, Sato Sand Tabata S.
In: Breeding strategies for sustainable forage and turf grass improvement. Barth S, Milbourne D (ed). Springer, DOI 10.1007/978-94-007-4555-1 (2012)

2011
An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae.
Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S.
DNA Res. 18(4): 221-232. (2011)

SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz).
Sraphet S, Boonchanawiwat A, Thanyasiriwat T, Boonseng O, Tabata S, Sasamoto S, Shirasawa K, Isobe S, Lightfoot DA, Tangphatsornruang S, Triwitayakorn K.
Theor Appl Genet. Apr. 122(6): 1161-1170. (2011)

Survey of the genetic information carried in the genome of Eucalyptus camaldulensis.
Hirakawa H, Nakamura Y, Kaneko T, Isobe S, Sakai H, Kato T, Hibino T, Sasamoto S, Watanabe A, Yamada M, Nakayama S, Fujishiro T, Kishida Y, Kohara M, Tabata S, Sato S. et al.
Plant Biotechnology 28: 471-480. (2011)

Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1.
Fukai E., Soyano T., Umehara Y., Nakayama S., Hirakawa H., Tabata S., Sato S., Hayashi M.
Plant J. 69, 720-730. (2011)

The genome of the mesopolyploid crop species Brassica rapa.
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z. Brassica rapa Genome Sequencing Project Consortium.
Nat Genet. 43(10): 1035-1039. (2011)

Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.
Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima K, Minami C, Muraki A, Nakazaki N, Takahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shin-i T, Minakuchi Y, Kohara Y, Fujiyama, A Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagena JA, Wada N, Kohinata T, Atefeh A, Yuasa S, Matsunaga S, Fukui K.
DNA Res. 18(1): 65-76. (2011)

The first genetic maps for subterranean clover (Trifolium subterraneum L.) and comparative genomics with T. pratense L. and Medicago truncatula Gaertn. to identify new molecular markers for breeding.
Ghamkhar K, Isobe S, Nichols PGH, Faithfull T, Ryan MH, Snowball R, Sato S and Appels R.
Molecular Breeding. 5: 1-14. (2011)

Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.).
Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN, Gowda MV, Radhakrishnan T, Bertioli DJ, Knapp SJ, Varshney RK.
Theor Appl Genet. 122(6): 1119-1132. (2011)

2010
SNP discovery and linkage map construction in cultivated tomato.
Shirasawa K, Isobe S, Hirakawa H, Asamizu E, Fukuoka H, Just D, Rothan C, Sasamoto, S, Fujishiro T, Kishida Y. et al.
DNA Res. 17: 381-391. (2010)

Mapping candidate QTLs related to plant persistency in red clover.
Klimenko I, Razgulayeva N, Gau M, Okumura K, Nakaya A, Tabata S, Kozlov N.N., and Isobe S.
Theor Appl Genet. 120: 1253-1263. (2010)

Molecular genetic linkage map of Soybean. Genetics, Genomics and Breeding of Soybean.
(K. Bilyeu, M.B. Rathaparkhe and C. Kole ed.)
Isobe, S., and Tabata, S.
CRC press. FL, NY and UK ISBN 978-1-57808-681-8. Pp71-91. (2010)

Structural analyses of the genomes in legumes.
Sato S, Isobe S and Tabata S.
Curr Opin Plant Biol. 13: 146-152. (2010)

2009
Construction of a consensus linkage map for red clover (Trifolium pratense L.).
Isobe S, Kolliker R, Hisano H, Sasamoto S, Wada T, Klimenko I, Okumura K, Tabata S.
BMC Plant Biol. 9: 57. (2009)

2007
Genotype matrix mapping: searching for quantitative trait Loci interactions in genetic variation in complex traits.
Isobe S, Nakaya A and Tabata S.
DNA Res. 14: 217-225. (2007)

Quantitative trait locus analysis of multiple agronomic traits in the model legume Lotus japonicus.
Gondo T, Sato S, Okumura K, Tabata S, Akashi R and Isobe S.
Genome 50: 627-637. (2007)

Characterization of the soybean genome using EST-derived microsatellite markers.
Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K and Tabata S.
DNA Res. 14: 271-281. (2007)