Yoshihiro Kawahara

Profile Information

Affiliation: Research Center for Advanced Analysis, NARO, National Agriculture and Food Research Organization

Degree: Ph.D.(Mar, 2007, Tokyo Metropolitan University)

Researcher number: 30546370
ORCID ID: https://orcid.org/0000-0002-9314-1632
J-GLOBAL ID: 201501011571969481
researchmap Member ID: B000248193

主にイネを対象とした農作物のオミックス解析や関連するデータベース開発を行っています。様々なイネ品種のゲノム配列やトランスクリプトームの比較解析からそれぞれの品種に特徴的な形質に関係する遺伝子を探したり、イネのゲノムアノテーションデータベース「RAP-DB」や遺伝子発現データベース「TENOR」の開発、運用に携わっています。それ以外にも、NGS解析やデータベース構築に関して、様々な研究者の方と共同研究を行っています。

Research Interests

Research Areas

Research History

Oct, 2022 - Present

Research Center for Advanced Analysis, NARO (NAAC), National Agriculture and Food Research Organization
Apr, 2021 - Sep, 2022

Research Center for Advanced Analysis, NARO, National Agriculture and Food Research Organization
Apr, 2016 - Mar, 2021

Institute of Crop Sciences, NARO, National Agriculture and Food Research Organization
Apr, 2014 - Mar, 2016

National Institute of Agrobiological Sciences
Apr, 2009 - Mar, 2014

National Institute of Agrobiological Sciences
Apr, 2008 - Mar, 2009

National Institute of Agrobiological Sciences
Apr, 2007 - Mar, 2008

National Institute of Advanced Industrial Science and Technology
Feb, 2007 - Mar, 2007

Institute of Molecular Evolutionary Genetics, Department of Biology, The Pennsylvania State University

Awards

2021

-, Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding

Yoshihiro Kawahara, Tomoko Endo, Mitsuo Omura, Yumiko Teramoto, Takeshi Itoh, Hiroshi Fujii, Takehiko Shimada
2017

-, Genomic dissection of a ‘Fuji’ apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection

Miyuki Kunihisa, Shigeki Moriya, Kazuyuki Abe, Kazuma Okada, Takashi Haji, Takeshi Hayashi, Yoshihiro Kawahara, Ryutaro Itoh, Takeshi Itoh, Yuichi Katayose, Hiroyuki Kanamori, Toshimi Matsumoto, Satomi Mori, Harumi Sasaki, Takashi Matsumoto, Chikako Nishitani, Shingo Terakami, Toshiya Yamamoto

Papers

Haploid-resolved and chromosome-scale genome assembly in Citrus unshiu and its parental species, C. nobilis and C. kinokuni

Sachiko Isobe, Hiroyoshi Fujii, Kenta Shirasawa, Yoshihiro Kawahara, Tomoko Endo, Takehiko Shimada

Jun 5, 2023
Hands on workshop using “SMART breeding tools”

Sugimoto Kazuhiko, Yonemaru Jun-ichi, Sakai Hiroaki, Kawahara Yoshihiro, Kajiya-Kanegae Hiromi

Breeding Research, advpub, 2023
Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy.

Toshiyuki Imaizumi, Yoshihiro Kawahara, Gabriela Auge

Molecular ecology, 31(24) 6556-6569, Dec, 2022
Artificial selection in the expansion of rice cultivation.

Kenji Fujino, Yoshihiro Kawahara, Kenta Shirasawa

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 135(1) 291-299, Jan, 2022
Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution.

Toshiyuki Imaizumi, Kaworu Ebana, Yoshihiro Kawahara, Chiaki Muto, Hiroyuki Kobayashi, Akira Koarai, Kenneth M Olsen

Communications biology, 4(1) 952-952, Aug 10, 2021
Translation of continuous artificial selection on phenotype into genotype during rice breeding programs

Fujino Kenji, Kawahara Yoshihiro, Koyanagi Kanako O., Shirasawa Kenta

Breeding Science, 2021
Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing

N Tanaka, M Shenton, Y Kawahara, M Kumagai, H Sakai, H Kanamori, J Yonemaru, S Fukuoka, K Sugimoto, M Ishimoto …

Plant and Cell Physiology, Dec 10, 2020
Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat

Behnam Derakhshani, Habtamu Ayalew, Kohei Mishina, Tsuyoshi Tanaka, Yoshihiro Kawahara, Hossein Jafary, Youko Oono

Plants, 9(5) 596-596, May 7, 2020 Peer-reviewed
Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley

Behnam Derakhshani, Hossein Jafary, Bahram Maleki Zanjani, Karim Hasanpur, Kohei Mishina, Tsuyoshi Tanaka, Yoshihiro Kawahara, Youko Oono

PLOS ONE, 15(4) e0230820-e0230820, Apr 16, 2020 Peer-reviewed
Mikan genome database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding

Yoshihiro Kawahara, Tomoko Endo, Mitsuo Omura, Yumiko Teramoto, Takeshi Itoh, Hiroshi Fujii, Takehiko Shimada

Breeding Science, 70(2) 200-211, Apr, 2020 Peer-reviewedLead author
Whole-genome sequencing of the NARO World Rice Core Collection (WRC) as the basis for diversity and association studies

N Tanaka, M Shenton, Y Kawahara, M Kumagai, H Sakai, H Kanamori, J Yonemaru, S Fukuoka, K Sugimoto, M Ishimoto …

Plant and Cell Physiology, doi.org/10.1093/pcp/pcaa019, Feb, 2020 Peer-reviewed
TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data.

Kumagai M, Nishikawa D, Kawahara Y, Wakimoto H, Itoh R, Tabei N, Tanaka T, Itoh T

DNA research : an international journal for rapid publication of reports on genes and genomes, Sep, 2019 Peer-reviewed
Databases for rice omics studies

Takeshi Itoh, Yoshihiro Kawahara, Tsuyoshi Tanaka

Rice Genomics, Genetics and Breeding, 541-554, Mar 15, 2018 Peer-reviewed
Gene expression of rice seeds surviving 13- and 20-month exposure to space environment

Manabu Sugimoto, Youko Oono, Yoshihiro Kawahara, Oleg Gusev, Masahiko Maekawa, Takashi Matsumoto, Margarita Levinskikh, Vladimir Sychev, Natalia Novikova, Anatoly Grigoriev

Life Sciences in Space Research, 11 10-17, Nov 1, 2016 Peer-reviewed
Magnaporthe oryzae Glycine-Rich Secretion Protein, Rbf1 Critically Participates in Pathogenicity through the Focal Formation of the Biotrophic Interfacial Complex

Takeshi Nishimura, Susumu Mochizuki, Naoko Ishii-Minami, Yukiko Fujisawa, Yoshihiro Kawahara, Yuri Yoshida, Kazunori Okada, Sugihiro Ando, Hideo Matsumura, Ryohei Terauchi …

PLOS PATHOGENS, 12(10) e1005921, Oct, 2016 Peer-reviewed
Genomic dissection of a 'Fuji' apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection

Miyuki Kunihisa, Shigeki Moriya, Kazuyuki Abe, Kazuma Okada, Takashi Haji, Takeshi Hayashi, Yoshihiro Kawahara, Ryutaro Itoh, Takeshi Itoh, Yuichi Katayose …

BREEDING SCIENCE, 66(4) 499-515, Sep, 2016 Peer-reviewed
TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice

Yoshihiro Kawahara, Youko Oono, Hironobu Wakimoto, Jun Ogata, Hiroyuki Kanamori, Harumi Sasaki, Satomi Mori, Takashi Matsumoto, Takeshi Itoh

PLANT AND CELL PHYSIOLOGY, 57(1) e7, Jan, 2016 Peer-reviewed
Punctual transcriptional regulation by the rice circadian clock under fluctuating field conditions.

Jun Matsuzaki, Yoshihiro Kawahara, Takeshi Izawa

The Plant cell, 27(3) 633-48, Mar, 2015 Peer-reviewed
Implications of miR166 and miR159 induction to the basal response mechanisms of an andigena potato (Solanum tuberosum subsp andigena) to salinity stress, predicted from network models in Arabidopsis

Ai Kitazumi, Yoshihiro Kawahara, Ty S. Onda, David De Koeyer, Benildo G. de los Reyes

GENOME, 58(1) 13-24, Jan, 2015 Peer-reviewed
Genome-Wide Transcriptome Analysis Reveals that Cadmium Stress Signaling Controls the Expression of Genes in Drought Stress Signal Pathways in Rice

Youko Oono, Takayuki Yazawa, Yoshihiro Kawahara, Hiroyuki Kanamori, Fuminori Kobayashi, Harumi Sasaki, Satomi Mori, Jianzhong Wu, Hirokazu Handa, Takeshi Itoh …

PLOS ONE, 9(5) e96946, May, 2014 Peer-reviewed

Misc.

スマート育種を実現する3種の育種情報ツール "Pedigree Finder", "BRIMASS"および"有用遺伝子カタログとアリルグラフ"—Breeding information tools for "Smart Breeding" : "Pedigree Finder", "BRIMASS" and "Allele graph with catalog of useful genes in agriculture"—特集スマート育種の展開 : 現状と将来展望

米丸淳一, 坂井寛章, 鐘ヶ江弘美, 川原善浩

JATAFFジャーナル = JATAFF journal : 農林水産技術, 10(12) 12-16, Dec, 2022
Investigation of important genes from rice core collections

田中伸裕, MATTHEW Shenton, 川原善浩, 神谷岳洋, 藤原徹, 江花薫子

育種学研究, 24, 2022
Hunting the genes for BLANDING of the premium rice cultivars from Hokkaido

藤野賢治, 藤野賢治, 川原善浩, 白澤健太

飯島藤十郎記念食品科学振興財団年報, 36, 2021
History of rice breeding supposed by genome diversity analysis

白澤健太, 川原善浩, 小柳香奈子, 藤野賢治

育種学研究, 22, 2020
高温登熟耐性の異なる3品種の遺伝子発現プロファイリング

佐藤豊, 川原善浩, 竹久妃奈子

育種学研究, 21, 2019
宿主核に移行するいもち病菌エフェクターの解析

横谷尚起, 南尚子, 西村岳志, 川原善浩, 光原一朗, 西澤洋子, 南栄一

日本植物病理学会大会プログラム・講演要旨予稿集, 2016 52, Mar 3, 2016
情報解析ツールの開発,整備 1 超高速配列決定時代に対応した情報リソース開発(GIR1001)

伊藤剛, 田中剛, 沼寿隆, 坂井寛章, 川原善浩

農林水産省農林水産技術会議事務局研究成果, (515) 80-87, Mar 31, 2014
遺伝子発現情報のプロファイリング 1 イネのトランスクリプトーム解析(RTR0001)

伊藤剛, 松本隆, 大野陽子, 水野浩志, 沼寿隆, 坂井寛章, 川原善浩

農林水産省農林水産技術会議事務局研究成果, (515) 49-57, Mar 31, 2014
リン酸欠乏条件下におけるコムギトランスクリプトーム解析

大野陽子, 小林史典, 川原善浩, 谷澤隆之, 金森裕之, 佐々木晴美, 森聡美, WU J., 伊藤剛, 松本隆 …

育種学研究, 16, 2014
イネ科植物のデータベース:レファレンスから品種間比較へ

伊藤剛, 熊谷真彦, 金重石, 伊藤龍太郎, 川原善浩, 坂井寛章, 李城信, 沼寿隆, 田中剛, 松本隆

日本植物細胞分子生物学会大会・シンポジウム講演要旨集, 31st 58, Aug 20, 2013
A reference rice genome sequence in the 10K Genome Era

Takeshi Itoh, Baltazar A. Antonio, Yoshihiro Kawahara, Tsuyoshi Tanaka, Hiroaki Sakai, Takashi Matsumoto, Takuji Sasaki

Genetics and Genomics of Rice, 5 1-7, Jan 1, 2013
ソルガムの紫斑点病感染で発現誘導される遺伝子群の解析

川東広幸, 水野浩志, 川原善浩, 金森裕之, 南博, 森聡美, 佐々木晴美, 伊藤剛, 松本隆

日本植物細胞分子生物学会大会・シンポジウム講演要旨集, 30th 92, Aug 3, 2012
イネの新たな高精度版ゲノムとRAP‐DB

伊藤剛, 坂井寛章, 沼寿隆, 川原善浩, 田中剛, 松本隆, 佐々木卓治

日本植物生理学会年会要旨集, 53rd 108, Mar 9, 2012
ゲノムワイドな系統解析によるイネ栽培史における遺伝子移入パターンの解明

熊谷真彦, 川原善浩, 呉健忠, 伊藤剛

日本進化学会大会プログラム・講演要旨集(Web), 14th, 2012
Independent domestication of Asian rice cultivars followed by multiple hybridization events

Yang Ching-chia, Yoshihiro Kawahara, Hiroshi Mizuno, Wu Jianzhong, Takashi Matsumoto, Takeshi Itoh

GENES & GENETIC SYSTEMS, 86(6) 439-439, Dec, 2011
Comprehensive expression analysis of the rice retrogenes

Hiroaki Sakai, Hiroshi Mizuno, Yoshihiro Kawahara, Hironobu Wakimoto, Hiroshi Ikawa, Hiroyuki Kawahigashi, Hiroyuki Kanamori, Takashi Matsumoto, Takeshi Itoh, Brandon S. Gaut

GENES & GENETIC SYSTEMS, 86(6) 385-385, Dec, 2011
ソルガムのアノテーション情報がない領域から紫斑点病感染で発現誘導される遺伝子の同定

水野浩志, 川東広幸, 川原善浩, 金森裕之, 南博, 森聡美, 佐々木晴美, 伊藤剛, 松本隆

育種学研究, 13 31, Sep 23, 2011
イネレトロ遺伝子の網羅的発現解析

坂井寛章, 水野浩志, 川原善浩, 脇本泰暢, 伊川浩司, 川東広幸, 金森裕之, 松本隆, 伊藤剛, ガウトブランドン

日本遺伝学会大会プログラム・予稿集, 83rd 61, Aug 31, 2011
Evola:全ヒト遺伝子の分子進化データベース~全転写産物解析による包括的オルソログ解析~

坂手龍一, 松矢明宏, 佐藤慶治, 川原善浩, 山崎千里, 伊藤剛, 五條堀孝, 今西規

生化学, 4P-1011, 2008
Evola:系統樹解析にもとづくH‐InvDBヒト遺伝子のオルソログデータベース

松矢明宏, 松矢明宏, 坂手龍一, 坂手龍一, 川原善浩, 川原善浩, 佐藤慶治, 佐藤慶治, 藤井康之, 藤井康之 …

生化学, 1P-1063, 2007

Books and Other Publications

Rice Genomics, Genetics and Breeding - Databases for Rice Omics Studies

Takeshi Itoh, Yoshihiro Kawahara, Tsuyoshi Tanaka (Role: Joint author)

Springer, Singapore, Feb, 2018 (ISBN: 9789811074608)
次世代シークエンサーＤＲＹ解析教本細胞工学別冊

清水厚志, 坊農秀雅 (Role: Contributor)

学研メディカル秀潤社, Oct, 2015

Presentations

イネ有用遺伝子カタログとアリルグラフ

川原善浩

日本育種学会第142回講演会, Sep 23, 2022
イネ有用遺伝子情報のカタログ構築とその活用について

川原善浩

第39回日本植物バイオテクノロジー学会（堺）大会, Sep 12, 2022 Invited
イネ品種間〜種間多様性情報の整備と他作物への展開

川原善浩, 熊谷真彦

生物多様性のDNA情報学, Apr 28, 2022 Invited
Literature-based curation of gene annotation, genomic variations, and transcriptomics information in RAP-DB

Yoshihiro Kawahara

Database Workshop, The 63rd Annual Meeting of the Japanese Society of Plant Physiologists, Mar 24, 2022 Invited
カンキツのゲノム情報と CAPS マーカー情報をつなぐデータベース: Mikan Genome Database (MiGD)

川原善浩

果樹茶業研究会果樹バイテク研究会, Oct 9, 2019 Invited
イネのリファレンスゲノムと様々な品種の多様性情報のいまとこれから

川原善浩

第2回植物インフォマティクス研究会, Sep 2, 2019 Invited
Extensive update of the rice reference genome by the cutting-edge DNA sequencing technologies

Yoshihiro Kawahara

134th Japanese Society of Breeding, Sep 22, 2018 Invited
The challenges of reference-quality genome assembly of rice cultivars using MinION

Yoshihiro Kawahara

Nanopore Day, Tokyo, Aug 20, 2018 Invited

Professional Memberships

Research Projects

Development of citrus metabolites breeding system based on the genealogy of alleles

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2022 - Mar, 2025
遺伝子近傍保存モジュールによる発現抑制機構の解明と分子育種への利用

科学研究費助成事業, 基盤研究(A), 日本学術振興会, Apr, 2022 - Mar, 2025

吉田均, 黒羽剛, 川原善浩, 牧野能士
Analysis of rice gene Stva that enhances stripe resistance by Stvb

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2021

Hayano-Saito Yuriko
The regulatory DNA Landscape in the rice endosperm

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2017 - Mar, 2020

Kawakatsu Taiji
Time-series Dual RNA-Seq analysis of rice and blast fungus

Grants-in-Aid for Scientific Research, Grant-in-Aid for Young Scientists (B), Japan Society for the Promotion of Science, Apr, 2013 - Mar, 2015

KAWAHARA Yoshihiro