植物ゲノム・遺伝学研究室

Identification of resistance locus and characterization of effector genes toward breeding for resistance to Phytophthora infestans.

Arafa RA, Rakha MT, Kamel SM, Soliman NEK, Moussa OM, Shirasawa K

Act Hortic, in press(2020)

Construction of a framework linkage map and genetic dissection of drought- and yield-related QTLs in horsegram (Macrotyloma uniflorum).

Chahota RK, Sharma V, Rana M, Sharma R, Choudhary S, Sharma TR, Shirasawa K, Hirakawa H, Isobe SN

Euphytica 216: 61(2020)

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype.

Nashima K, Shirasawa K, Ghelfi A, Hirakawa H, Isobe S, Suyama T, Wada T, Kurokura T, Uemachi T, Azuma M, Akutsu M, Kodama M, Nakazawa Y, Namai K

DNA Res 10.1093/dnares/dsaa026(2020)

Four genetic loci control compact plant size with yellow pear-shaped fruit in ornamental tomato (Solanum lycopersicum L.).

Safaei M, Olfati JA, Hamidoghli Y, Rabiei B, Yamamoto E, Shirasawa K

Plant Genome 13: e20017(2020)

Genome sequence and analysis of a Japanese radish (Raphanus sativus) cultivar named 'Sakurajima Daikon' possessing giant root.

Shirasawa K, Hirakawa H, Fukino N, Kitashiba H, Isobe S

DNA Res 10.1093/dnares/dsaa010(2020)

The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig (F. carica).

Shirasawa K, Yakushiji H, Nishimura R, Morita T, Jikumaru S, Ikegami H, Toyoda A, Hirakawa H, Isobe S

Plant J 102: 1313-1322(2020)

De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and S. lycopersicum var. cerasiforme, by long-read sequencing..

Takei H, Shirasawa K, Kuwabara K, Toyoda A, Matsuzawa Y, Iioka S, Ariizumi T

DNA Res 10.1093/dnares/dsaa029(2020)

Genetic mapping in autohexaploid sweet potato with low-coverage NGS-based genotyping data.

Yamamoto E, Shirasawa K, Kimura T, Monden Y, Tanaka M, Isobe S

G3 10: 2661-2670(2020)

Chromosome-level de novo genome assemblies of over 100 plant species.

Shirasawa K, Harada D, Hirakawa H, Isobe S, Kole C

Breed Sci, in press(2020)

Advances of whole genome sequencing in strawberry with NGS technologies.

Isobe S, Shirasawa K, Hirakawa H

Hort J 89: 108-114(2020)

Root-knot nematode genetic diversity associated with host compatibility to sweetpotato cultivars.

Asamizu E, Shirasawa K, Hirakawa H, Iwahori H

Mol Plant Pathol doi: 10.1111/mpp.12961(2020)

DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.).

Bhat RS, Rockey J, Shirasawa K, Tilak IS, Patil MPB, Lachagari VBR

BMC Research Notes 13: 20 doi: 10.1186/s13104-020-4883-y.(2020)

Translation of continuous artificial selection on phenotype into genotype during rice breeding programs.

Fujino K, Kawahara Y, Koyanagi K, Shirasawa K

Breed Sci, in press(2020)

Genetic analyses of anthocyanin content using polyploid GWAS followed by QTL detection in the sweetpotato (Ipomoea batatas L.) storage root.

Haque E, Yamamoto E, Shirasawa K, Tabuchi H, Yoon U, Isobe S, Tanaka M

Plant Root 14: 11-21(2020)

Foliar disease resistant and productive mutants from the introgression lines of peanut (Arachis hypogaea).

Joshi P, Jadhav MP, Shirasawa K, Yadawad A, Bhat RS

Plant Breed 139: 148-155(2020)

Identification of genome-wide SNPs among geographically diverse radish accessions.

Kobayashi H, Shirasawa K, Fukino N, Hirakawa H, Akanuma T, Kitashiba H

DNA Res 10.1093/dnares/dsaa001(2020)

Development of high-density genetic linkage maps and identification of loci for chestnut gall wasp resistance in Castanea spp.

Marinoni DT, Nishio S, Valentini N, Shirasawa K, Acquadro A, Portis E, Alma A, Akkak A, Pavese V, Cavalet-Giorsa E, Botta R

Plants 9: 1048(2020)

Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon.

Masuda K, Yamamoto E, Shirasawa K, Onoue K, Kono A, Ushijima K, Kubo Y, Tao R, Henry I, Akagi T

DNA Res 10.1093/dnares/dsaa012(2020)

CURLED LATER1 encoding the largest subunit of the Elongator complex has a unique role in leaf development and meristem function in rice.

Matsumoto H, Yasui Y, Ohmori Y, Tanaka W, Ishikawa T, Numa H, Shirasawa K, Taniguchi Y, Tanaka J, Suzuki Y, Hirano HY

Plant J 104: 351-364(2020)

Genomic insight into the developmental history of southern highbush blueberry populations.

Nishiyama S, Fujikawa M, Yamane H, Shirasawa K, Babiker E, Tao R

Heredity 126: 194-205(2020)

High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography.

Teramoto S, Takayasu S, Kitomi Y, Arai-Sanoh Y, Tanabata T, Uga Y

Plant Methods 16, Article number: 66.(2020)

Genome-wide Association Study of Strawberry Fruit Quality-related Traits Using a MAGIC Population Derived from Crosses Involving Six Strawberry Cultivars.

Wada, T., Tsubone, M., Mori, M., Hirata, C., Nagamatsu, S., Oku, K., Nagano, S., Isobe, S., Suzuki, H., Shimomura, K., Baba, N., Hirashima, K., Sueyoshi, T., Obu, K.-i., Ikegami, H., Uchimura, Y. and Hayashida, T.

The Horticulture Journal, DOI: 10.2503/hortj.UTD-180(2020)

QTL analysis for flowering time in carnation (Dianthus caryophyllus L.).

Yagi M, Shirasawa K, Hirakawa H, Isobe S, Matsuno J, Uno Y, Tanase K, Onozaki T, Yamaguchi H

Sci Hortic 262: 109053(2020)

Transgressive segregation and gene regions controlling thermotolerance of fruit set and pollen germination in Capsicum chinense.

Yamazaki A, Shirasawa K, Hosokawa M

Euphytica 216, 179(2020)

「品種育成」にコミットするゲノム研究とは.

藤野賢治, 白澤健太

育種学研究 22: 68-74(2020)

Detection of Chromosomal Regions for Male Sterility in the Cultivated Strawberry Fragaria × ananassa Duch.

Wada, T., Sueyoshi, T., Hirata, C., Takata, K., Noguchi, Y., Kataoka, S., Isobe, S., Mori, M., Nagamatsu, S., Tanaka, Y. and Shimomura, K.

The Horticulture Journal, DOI: 10.2503/hortj.UTD-136(2020)

RNA-seq Analysis of Meristem Cells Identifies the FaFT3 Gene as a Common Floral Inducer in Japanese Cultivated Strawberry.

Koembuoy, K., Hasegawa, S., Otagaki, S., Takahashi, H., Nagano, S., Isobe, S., Shiratake, K. and Matsumoto, S.

The Horticulture Journal, doi.org/10.2503/hortj.UTD-126(2020)

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

Haque E., Tabuchi H., Monden Y, Suematsu K, Shirasawa K, Isobe S, Tanaka M

Breeding Science　Volume 70 Issue 3(2020)

Developing Transposable Element Marker System for Molecular Breeding

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

Methods Mol Biol. 2020;2107:233-251. doi: 10.1007/978-1-0716-0235-5_11.(2020)

Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies

Ramadan A Arafa , Said M Kamel , Mohamed T Rakha , Nour Elden K Soliman , Olfat M Moussa , Kenta Shirasawa

PLoS One.　2020 Jan 21;15(1):e0221604. doi: 10.1371/journal.pone.0221604. eCollection(2020)

Correction: The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants

Akagi T, Shirasawa K, Nagasaki H, Hirakawa H, Tao R, Comai L, Isabelle M Henry

PLoS Genet. 2020 May 26;16(5):e1008845. (2020)

Mapping of a novel clubroot resistance QTL using ddRAD-seq in Chinese cabbage (Brassica rapa L.).

Laila R, Park JI, Robin AHK, Natarajan S, Vijayakumar H, Shirasawa K, Isobe S, Kim HT, Nou IS

BMC Plant Biol. 19(1): 13. (2019)

A pure line derived from a self-compatible Chrysanthemum seticuspe mutant as a model strain in the genus Chrysanthemum.

Nakano M, Taniguchi K, Masuda Y, Kozuka T, Aruga Y, Han J, Motohara K, Nakata M, Sumitomo K, Hisamatsu T, Nakano Y, Yagi M, Hirakawa H, Isobe SN, Shirasawa K, Nagashima Y, Na H, Chen L, Liang G, Chen R, Kusaba M

Plant Sci. 287: 110174. (2019)

The genome sequence of segmental allotetraploid peanut Arachis hypogaea.

Bertioli DJ, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli SCM, Ren L, Farmer AD, Pandey MK, Samoluk SS, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, El Baidouri M, Guo B, Huang W, Kim KD, Korani W, Lanciano S, Lui CG, Mirouze M, Moretzsohn MC, Pham M, Shin JH, Shirasawa K, Sinharoy S, Sreedasyam A, Weeks NT, Zhang X, Zheng Z, Sun Z, Froenicke L, Aiden EL, Michelmore R, Varshney RK, Holbrook CC, Cannon EKS, Scheffler BE, Grimwood J, Ozias-Akins P, Cannon SB, Jackson SA, Schmutz J

Nat Genet. 51(5): 877-884. (2019)

A reference-grade wild soybean genome

Min Xie, Claire Yik-Lok Chung, Man-Wah Li, Fuk-Ling Wong, Xin Wang, Ailin Liu, Zhili Wang, Alden KY Leung, Tin-Hang Wong, Suk-Wah Tong, Zhixia Xiao, Kejing Fan, Ming-Sin Ng, Xinpeng Qi, Linfeng Yang, Tianquan Deng, Lijuan He, Lu Chen, Aisi Fu, Qiong Ding, Junxian He, Gyuhwa Chung, Sachiko Isobe, Takanari Tanabata, Babu Valliyodan, Henry Nguyen, Steven Cannon, Christine Foyer, Ting-Fung Chan, and Hon-Ming Lam

Nat Commun. 10(1): 1216. (2019)

De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis.

Hirakawa H, Sumitomo K, Hisamatsu T, Nagano S, Shirasawa K, Higuchi Y, KusabaM, Koshioka M, Nakano Y, Yagi M, Yamaguchi H, Taniguchi K, Nakano M, Isobe SN.

DNA Res. 26(3): 195-203. (2019)

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

Okada Y, Monden Y, Nokihara K, Shirasawa K, Isobe S, Tahara M

Plant Cell Rep. 38(11): 1383-1392. (2019)

Current status in whole genome sequencing and analysis of Ipomoea spp.

Isobe S, Shirasawa K, Hirakawa H

Plant Cell Rep.38(11): 1365-1371. (2019)

Genome-wide association study overcomes the genome complexity in autohexaploid chrysanthemum and tags SNP markers onto the flower color genes.

Sumitomo K, Shirasawa K, Isobe S, Hirakawa H, Hisamatsu T, Nakano Y, Yagi M, Ohmiya A

Sci Rep. 9(1): 13947. (2019)

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

Sasai R, Tabuchi H, Shirasawa K, Kishimoto K, Sato S, Okada Y, Kuramoto A, Kobayashi A, Isobe S, Tahara M, Monden Y

DNA Res. 26(5): 399-409. (2019)

Phased genome sequence of an interspecific hybrid flowering cherry, Somei-Yoshino (Cerasus × yedoensis).

Shirasawa K, Esumi T, Hirakawa H, Tanaka H, Itai A, Ghelfi A, Nagasaki H, Isobe S

DNA Res.26(5): 379-389. (2019)

Construction of genetic linkage map and identification of a novel major locus for resistance to pine wood nematode in Japanese black pine (Pinus thunbergii).

Hirao T, Matsunaga K, Hirakawa H, Shirasawa K, Isoda K, Mishima K, Tamura M, Watanabe A

BMC Plant Biol. 19(1): 424. (2019)

Foliar disease resistant and productive mutants from the introgression lines of peanut (Arachis hypogaea).

Pushpesh Joshi, Mangesh P. Jadhav, Kenta Shirasawa, Arati Yadawad, Ramesh S. Bhat

PLANT BREEDING. 139(1): 148-155. (2019)

Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants.

Ghelfi A, Shirasawa K, Hirakawa H, Isobe S

Bioinformatics. 35(21): 4427-4429. (2019)

Evaluation of a new recombinant inbred line mapping population for genetic mapping in groundnut (Arachis hypogaea L.).

Sukruth M, Shirasawa K, Bhat R

Int J Curr Mocrobiol App Sci 8: 2956-2965. (2019)

Impact of Genomics on Capsicum breeding.

Shirasawa K, Ban T, Nagata N, Murakana T

The Capsicum Genome Springer: 209-219. (2019)

Development of DNA marker for distinguishing flesh colour in sweet cherry (Prunus avium L.).

Saito Y, Adachi E, Isuzugawa K, Shirasawa K, Ikenaga M, Sato H

Acta Horticulturae 1235 15-25. (2019)

Development of DNA markers for breeding yellow cherries.

Sato S, Saito Y, Shirasawa K, Ikeda K

Acta Horticulturae 1235 27-32. (2019)

Genomic diversity in old and recent carrot cultivars and breeding populations at a Japanese seed company.

Shibaya T, Kuroda C, Fujii T, Nakayama S, Minami C, Shirasawa K, Isobe S

Acta Horticulturae 1264 249-254. (2019)

QTL analysis and candidate gene SNP for harvest day in sweet cherry (Prunus avium L.).

Isuzugawa K, Shirasawa K, Kurosaka S, Takahashi Y, Saito Y, Adachi E, Ikenaga M, Yamamoto T

Acta Horticulturae 1235 33-40. (2019)

The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants.

Akagi T, Shirasawa K, Nagasaki H, Hirakawa H, Tao R, Comai L, Henry IM

doi: https://doi.org/10.1101/628537

SNP判別PCRによる落花生ahFAD2B遺伝子の変異の判別

渡辺学、桑田主悦、白澤健太、磯部祥子、深見正信

DNA多型　26(1): 77-80. (2019)

アグリゲノム産業研究会-アカデミアと産業会の交流を目指して-

磯部祥子・岩田洋佳・布目司

バイオサイエンスとインダストリー　77(1): 78-80. (2019)

イチゴのDNA分析からわかること

磯部祥子

自費出版書籍. (2019)

倍数性作物におけるNGS利用

田中剛、磯部祥子、門田有希、石川吾郎、瀬々潤

育種学研究　21(1): 55-60. (2019)

Development of AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.)

Mani, G., Shirasawa, K., Varshney, R.K., Pandey, M.K., and Bhat, R.S. 2018

BMC Res. Notes, 11:10

Characterization of Egyptian Phytophthora infestans population using simple sequence repeat markers

Arafa, R.A., Soliman, N.E.K., Moussa, O.M., Kamel, S.M., and Shirasawa, K. 2018

J. Gen. Plant Pathol., Volume 84, Issue 2, pp 104–107

A 3D Shape-Measuring System for Assessing Strawberry Fruits

Kochi, N., Tanabata, T., Hayashi, A., Isobe, S. 2018

International J of Automation Technology, 12(3) pp 395-404

Genome-wide structural mutations among the lines resulting from genetic instability in peanut (Arachis hypogaea L.)

Hake, A.A., Shirasawa, K., Yadawad, A., Nadaf, H.L., Gowda, M.V.C., and Bhat, R.S. 2018

Plant Gene, 13, 1-7.

Derivation of Linear Models for Quantitative Traits by Bayesian Estimation with Gibbs Sampling.

Nakaya, A., Isobe, S. 2017

In: Varshney R., Roorkiwal M., Sorrells M. (eds) Genomic Selection for Crop Improvement. Springer, pp 23-53

Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies

Arafa, R.A., Rakha, M.T., Soliman, N.E.K., Moussa, O.M., Kamel, S.M., and Shirasawa, K. 2017

Plos One, 12, e0189951.

Identification of transposable element markers associated with yield and quality traits from an association panel of independent mutants in peanut (Arachis hypogaea L.)

Hake, A.A., Shirasawa, K., Yadawad, A., et al. 2017

Euphytica, 213, 283.

Marker-assisted backcrossing to develop foliar disease-resistant genotypes in TMV 2 variety of peanut (Arachis hypogaea L.)

Kolekar, R.M., Sukruth, M., Shirasawa, K., et al. 2017

Plant Breed., Volume 136, Issue 6, pages 948–953

Sequence analysis of cultivated strawberry (Fragaria × ananasa Duch.) using microdissected single somatic chromosomes

Yanagi, T., Shirasawa, K., Terachi, M., and Isobe, S. 2017

Plant Methods, 13, 91.

Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.)

Hake, A.A., Shirasawa, K., Yadawad, A., et al. 2017

Plos One, 12, e0186113.

Climate clever clovers: new paradigm to reduce the environmental footprint of ruminants by breeding low methanogenic forages utilising haplotype variation

Kaur, P., Appels, R., Bayer, P. E., Keeble-Gagnere, G., Wang, J., Hideki, H., Shirasawa, K., Vercoe, P., Stefanova, K., Durmic, Z., Nichols, P., Revell, C., Isobe, S. N., Edwards, D., Erskine, W. 2017

Front. Plant Sci., 8, 1463.

Resistance to Phytophthora infestans in tomato wild relatives

Arafa, R.A., Moussa, O.M., Soliman, N.E.K., Shirasawa, K., Kamel, S.M., and Rakha, M.T. 2017

Afr. J. Agric. Res., 12, 2188-2196.

Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Nagano, S., Shirasawa, K., Hirakawa, H., Maeda, F., Ishikawa, M., and Isobe, S.N. 2017

BMC Genomics, 18, 374.

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato

Ohyama, A., Shirasawa, K., Matsunaga, H., et al. 2017

Theor. Appl. Genet., 130, 1601-1616.

The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding

Shirasawa, K., Isuzugawa, K., Ikenaga, M., et al. 2017

DNA Res., 24, 499-508.

A system for distinguishing octoploid strawberry cultivars using high-throughput SNP genotyping

Jung, H.J., Veerappan, K., Natarajan, S., Jeong, N., Hwang, I., Nagano, S., Shirasawa, K., Isobe, S., Nou, I.S. 2017

Trop. Plant Biol., 10, 68-76.

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

Shirasawa, K., Tanaka, M., Takahata, Y., et al. 2017

Sci. Rep., 7, 44207.

Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)

Mori, K., Shirasawa, K., Nogata, H., et al. 2017

Sci. Rep., 7, 41124.

Construction of an SSR and RAD marker-based genetic linkage map for carnation (Dianthus caryophyllus L.)

Yagi, M., Shirasawa, K., Waki, T., et al. 2017

Plant Mol. Biol. Rep., 35, 110.

Challenges to genome sequence dissection in sweetpotato

Isobe, S., Shirasawa, K., and Hirakawa, H. 2017

Breed. Sci., 67, 35-40.

Genetic maps and whole genome sequences of radish.

Shirasawa, K. and Kitashiba, H. 2017

In: Nishio, T. and Kitashiba, H. (eds) Compendium of Plant Genomes The Radish Genome, Springer, Cham, pp. 31-42.

Crop genome research toward genomics-assisted breeding

Shirasawa, K. 2017

Agric. Biotechnol., 1, 76-82.

Development and characterization of a strawberry MAGIC population derived from crosses with six strawberry cultivars.

Wada, T., Oku, K., Nagano, S., Isobe, S. Suzuki, H., Mori, M., Takata, K. Hirata, C., Shimomura, K., Tsubone, M. et al. 2017

Breed Sci, 67(4):370-381

Verification of linkage group using PRINS labeling technique in cultivated strawberry.

Tantivit, K, Isobe, S, Nathewet, P, Okuda, N, Yanagi T. 2017

Acta Horticulturae 1156: VIII International Strawberry Symposium, 10.17660/ActaHortic.2017.1156.22

Effect of insect pollinator on inbreeding versus outbreeding in open pollinated strawberry seeds.

Yanagi, T., Miura, H., Isobe, S., Okuda, N., Yoshida, Y. 2017

Scientia Horticulturae 215 (27):112-116.

Altered regulation of TERMINAL FLOWER 1 causes the unique vernalisation response in an arctic woodland strawberry accession.

Koskela E. A., Kurokura, T., Toivainen, T., Sønsteby, A., Heide, O. M., Sargent, D. J., Isobe S., Jaakola, L., Hilmarsson, H., Elomaa P., Hytönen, T. 2017

New Phytologist DOI: 10.1111/nph.14734

Development of Genome-wide SSR Markers in Horsegram and Their Utilization for Genetic Diversity and Cross-transferability Analysis.

Kaldate, R., Maneet, R., Sharma, R., Hirakawa, H., Kumar, R., Singh, G., Chahota, R. K., Isobe, S. N., Sharma, T., R.

Mol Beed 31:103 (2017)

Development of a Core Collection of Strawberry Cultivars Based on SSR and CAPS Marker Polymorphisms.

Wada, T., Noguchi, Y., Isobe, S., Kunihisa, M., Sueyoshi, T., Shimomura, K. 2017

The Horticulture Journal doi: 10.2503/hortj.MI-142

When the 3rd generation sequencing technologies go marching in.

Isobe, S., Koyanagi, R., Osaki, K. 2017

Ikuysyugakukenkyu, (in Japanese), 19:30-34

Construction of a high-resolution digital map to support citrus breeding using an autonomous multicopter.

Haris, M., Ishii, K., Ziyang, L., Sugiura, T., Qi, M., Watanabe, T., Sukisaki S., Tanabata, T., Isobe, S., Shimizu, T., Yoshioka, T., Nobuhara, H. 2016

ISHS Acta Horticulturae 1135: III International Symposium on Citrus Biotechnology 10.17660/ActaHortic.2016.1135.9

Current SNP genotyping methods for genetics and molecular breeding.

Isobe, S., Kaga, A., Teuzuka, A., Ishikawa, G., Nakamura, T. 2016

Ikuysyugakukenkyu, (in Japanese), 18:21-26

Target amplicon sequencing for genotyping genome-wide single nucleotide polymorphisms identified by whole genome resequencing in peanut

Shirasawa, K., Kuwata, C., Watanabe, M., Fukami, M., Hirakawa, and H., Isobe, S. 2016

Plant Genome, 9, 10.3835/plantgenome2016.06.0052.

The development of a primed in-situ hybridization technique for chromosome labeling in cultivated strawberry (Fragaria × ananassa).

Tantvit, K., Isobe, S., Nathewet, P., Okuda, N., Yanagi, T. 2016

Cytologia 81(4): 439–446

Draft genome sequence of subterranean clover, a reference for genus Trifolium

Hirakawa, H., Kaur, P., Shirasawa, K., Nichols, P., Nagano, S., Appels, R., Erskine, W., Isobe, S.N. 2016

Sci. Rep., 6, 30358.

QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.)

Kolekar, R.M., Sujay, V., Shirasawa, K., et al. 2016

Euphytica, 209, 147-156.

Larg-scale development of simple sequence repeat (SSR) marker using RNA-seq and SSR-enrichment library for Chinese chive (Allium ramosum syn. A. fuberosum).

Tasaki, K., Wakamasu, M., Namai, K., Hirakawa, H., Sasamoto, S., Tsuruoka, H., Minami, C., Isobe, S. 2016

I. DNA polymorphism 24(1):127-133 in Japanese.

Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato

Shirasawa, K., Hirakawa, H., and Isobe, S. 2016

DNA Res., 23, 145-153.

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

Bertioli, D.J., Cannon, S.B., Froenicke, L., Huang, G., Farmer, A.D., Cannon, E.K.S., Liu, X., Gao, D., Clevenger, J., Dash, S., Ren, L., Moretzsohn, M.C., Shirasawa, K., Huang, W., Vidigal, B., Abernathy, B., Chu, Y., Niederhuth, C.E., Umale, P., Araujo, A.C.G., Kozik, A., Kim, K.D., Burow, M.D., Varshney, R.K., Wang, X., Zhang, X., Barkley, N., Guimarães, P.M., Isobe, S., Guo, B., Liao, B., Stalker, H.T., Schmitz, R.J., Scheffler, B.E., Leal-Bertioli, S.C.M., Xun, X., Jackson, S.A., Michelmore, R., Ozias-Akins, P. 2016

Nat. Genet., 48, 438-446.

A simulation-based breeding design that uses whole-genome prediction in tomato

Yamamoto, E., Matsunaga, H., Onogi, A., et al. 2016

Sci. Rep., 6, 19454.

Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato

Shirasawa, K., Hirakawa, H., Nunome, T., Tabata, S., and Isobe, S. 2016

Plant Biotechnol. J., 14, 51-60.

Genomics research and development of genome-based breeding technologies in vegetable crops

Shirasawa, K. 2016

Breed. Res., 18, 124-129.

Identification of QTLs for rust resistane in the peanut wild species Arachis magna and the development of KASP markers for maker assisted selection

Leal-Bertioli, S.C.M., Cavalcante, U., Gouvea, E.G., et al. 2015

G3, 5, 1403-1413.

Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don

Hirakawa, H., Okada, Y., Tabuchi, H., et al. 2015

DNA Res., 22, 171-179.

Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis

Leal-Bertioli, S.C.M., Shirasawa, K., Abernathy, B., et al. 2015

Genetics, 199, 1093-1105.

A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts

Shirasawa, K., Hand, M.L., Henderson, S.T., et al. 2015

Ann. Bot., 115, 567-580.

Development of F1-hybrid Strawberry of Seed Propagation Type Named 'Yotsuboshi'

Mori, T., Kohori, J., Kitamura, H., Inokuchi, T., Kato, I., Sone, K., Ishikawa, M., Maeda, F., Fukami, M., Isobe, S., Sato S. 2015

Hort. Res. (in Japanese) 14 (4)：409–418．

A Novel Phenolic Compound, Chloroxynil, Improves Agrobacterium-Mediated Transient Transformation in Lotus japonicas

Kimura, M., Cutler, S., Isobe, S., 2015

PLOS ONE 10.1371/journal.pone.0131626.

Detection of genome donor species of neglected tetraploid crop Vigna reflex-pilosa (créole bean), and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis)

Chankaew, S., Isemura, T., Isobe, S., et al. 201

Plos One, 9, e104990.

Draft genome sequence of eggplant (Solanum melongena L.): the representative Solanum species indigenous to the Old World

Hirakawa, H., Shirasawa, K., Miyakate, K., et al. 2014

DNA Res., 21, 649-660.

Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba)

El-Rodeny, W., Kimura, M., Hirakawa, H., et al. 2014

Breed. Sci., 64, 252-263.

Identification of the carotenoid modifying gene PALE YELLOW PETAL 1 as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum)

Ariizumi, T., Kishimoto, S., Kakami, R., Maoka, T., Hirakawa, H., Suzuki, Y., Ozeki, Y., Shirasawa, K., Bernillon, S., Okabe, Y., Moing, A., Asamizu, E., Rothan, C., Ohmiya, A., Ezura, H. 2014

Plant J., 79, 453-465.

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

Shirasawa, K., Isobe, S., Tabata, S., and Hirakawa, H. 2014

Breed. Sci., 64, 264-271.

Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea

Sampath, P., Murukarthick, J., Izzah, N.K., Lee, J., Choi, H. I., Shirasawa, K., Choi, B.S., Liu, S., Nou, I. S. Yang, T.J. 2014

Plos One, 9, e94499.

Draft sequences of the radish (Raphanus sativus L.) genome

Kitashiba, H., Li, F., Hirakawa, H., et al. 2014

DNA Res., 21, 481-490.

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. 2014

Tree Genet. Genomics, 10, 853-863.

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., and Ezura, H. 2014

Plant Biotechnol., 31, 149-158.

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., and Ezura, H. 2014

Mol. Genet. Genomics, 289, 399-409.

Sequence analysis of the genome of carnation (Dianthus caryophyllus L.)

Yagi, M., Kosugi, S., Hirakawa, H., et al. 2014

DNA Res., 21, 231-241.

Dissection of the octoploid strawberry genome by deep-sequencing of Fragaria species

Hirakawa, H., Shirasawa, K., Kosugi, S., et al. 2014

DNA Res., 21, 169-181.

Development of NILs from heterogeneous inbred families for validating the rust resistance QTLs in peanut (Arachis hypogaea L.)

Yeri, S.B., Shirasawa, K., Pandey, M.K., et al. 2014

Plant Breed., 133, 80-85.

An Overview of Peanut Genome Structure.

Bertioli, D.J., Araujo, A.C.G., Nielen, S., Heslop-Harrison, P., Guimarães, P.M., Schwarzacher, T., Isobe, S., Shirasawa, K. Leal-Bertioli, S.C.M. 2014

In: Mallikarjuna, N. and Varshney, R.K. (eds) Genetics, Genomics and Breeding of Peanuts, CRC Press, Florida, pp. 114-138.

Breeding of red clover 'Ryokuyu' and its charcteristics.

Okumura, K., Isobe, S., Gau, M., Yamaguchi, H., Sawai, A., Takada, H., Hiroi, K., Uchiyama, K., Matsumura, T., Hayashi, T., Sato, N., Makino, T., Deguchi, K., Yamakawa, M., Sawada, Y., Fujii, H. 2014

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Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.

Qi, X., Li, M.W., Xie, M., Liu, X., Ni, M., Shao, G., Song, C., Kay-Yuen Yim, A., Tao, Y., Wong, F.L., Isobe, S., Wong, C.F., Wong, K.S., Xu, C., Li, C., Wang, Y., Guan, R., Sun, F., Fan, G., Xiao, Z., Zhou, F., Phang, T.H., Liu, X., Tong, S.W., Chan, T.F., Yiu, S.M., Tabata, S., Wang, J., Xu, X., Lam, H.M..

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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., et al. 2013

DNA Res., 20, 593-603.

Genome-wide SNP genotyping to infer the effects on gene functions in tomato

Hirakawa, H., Shirasawa, K., Ohyama, A., et al. 2013

DNA Res., 20, 221-233.

Analysis of a tomato introgression line, IL8-3, with increased Brix content

Ikeda, H., Hiraga, M., Shirasawa, K., Nishiyama, M., Kanahama, K., and Kanayama, Y. 2013

Sci. Hortic., 153, 103-108.

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, D.J., Varshney, R.K., et al. 2013

DNA Res., 20, 173-184.

Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria ×ananassa) and its applicability

Isobe, S.N., Hirakawa, H., Sato, S., et al. 2013

DNA Res., 20, 79-92.

Development of Capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence

Shirasawa, K., Ishii, K., Kim, C., et al. 2013

Mol. Breed., 31, 101-110.

Structural analyses of the tomato genome

Sato, S., Shirasawa, K., and Tabata, S. 2013

Plant Biotechnol., 3, 257-263.

DNA marker applications to molecular genetics and genomics in tomato

Shirasawa, K. and Hirakawa, H. 2013

Breed. Sci., 63, 21-30.

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, 2013

In: Varshney, R. and Tuberosa, R. (eds) Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality, Vol. 2. John Wiley & Sons Ltd, Chichester, pp. 177-192.

Genome-wide SNP marker development and QTL identification for genomic selection in red clover.

Isobe, S., Boller, B., Klimenko, I., et al. 2013

In: Barth, S. and Milbourne, D. (eds) Breeding Strategy for Sustainable Forage and Turf Grass Improvement, Springer, Dordrecht, pp. 29-36.