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Outline of our achievements

Laboratory of Plant Genomics and Genetics

About our research

Purpose of our research

 Higher plants harbor large genomes corresponding to several hundred million to several billion nucleotide bases. However, not all of the nucleotide bases in the genome are essential for the vital activity of each species. To elucidate the essential genomic regions, we are continually collecting and analyzing large quantities of genomic information from a variety of higher plants. Furthermore, we have developed methodologies for utilizing the genomic information in plant breeding.

Characteristics of our research

 We have analyzed features of over 25 plant genomes to identify useful genes and DNA markers. In addition, we have achieved de novo whole genome sequencing in several plant species, such as tomato and strawberry. Based on these achievements, we are collaborating with domestic and foreign institutions as well as private companies to develop new breeding technologies.

Expected fields of application

 Gene functions can be predicted by comparing genome sequences across species and germplasms. The gene functions thus discovered can be applied to breeding programs for improving agronomic or industrially important traits, such as stress tolerance and yield, and are expected to generate novel varieties with shortened periods. In addition, the comparison of genome sequences is expected to reveal the evolutional history of plant species.

Our research projects

  1. Plant whole genome sequencing
  2. We have performed de novo whole genome sequencing in plant species for which genomic information has not been accumulated. Re-sequencing is also conducted to investigate diversity in the species.

  3. Gene function analysis
  4. Functions of genes are estimated by performing transcript analysis and mutational analysis. The discovery of whole genome SNPs (single nucleotide polymorphisms) is also pursued in order to isolate the functional SNPs that affect gene actions.

  5. Development of genome manipulation technology
  6. We are developing technology to enable the efficient manipulation of the genome, such as the introduction of multiple genes and regulatory systems for gene expression.

  7. DNA marker development and molecular genetics
  8. To accelerate molecular breeding, we have developed large-scale DNA markers, such as SNPs and microsatellite markers. In addition, we recently began whole genome genotyping, or the so called RAD-seq and GBS techniques, using next generation sequencers. We are also developing methods of statistical analysis specifically for species with complex genome structures, such as polyploid species.

  9. Molecular breeding technologies
  10. Several programs of marker-assisted selection have been performed with the breeders in across Japan and the world. In parallel, we have been developing molecular breeding technologies, such as methods of genomic selection, in conjunction with these plant-breeding specialists and a collaborating statistician. In addition, we are currently developing phenotyping technologies to enhance the efficiency of molecular breeding.


Sachiko Isobe the head of a laboratory sisobe at kazusa.or.jp
Hideki Hirakawa senior researcher hh at kazusa.or.jp
Kenta Shirasawa research staff shirasaw at kazusa.or.jp
Mitsuhiro Kimura research scientist mitsukimu at kazusa.or.jp
Takanari Tanabata research scientist tanabata at kazusa.or.jp
Soichiro Nagano special researcher nagano at kazusa.or.jp
Atsushi Hayashi special researcher ahayashi at kazusa.or.jp


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)

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)

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)

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)

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)

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)

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)