Updated on 2025/06/06

写真a

 
NISHIDA Hidetaka
 
Organization
Scheduled update Professor
Position
Professor
External link

Degree

  • 博士（農学） ( 京都大学 )

Research Interests

  • plant genetics

  • plant breeding

  • heading time

  • wheat

  • barley

Research Areas

  • Environmental Science/Agriculture Science / Science in plant genetics and breeding

Education

  • 京都大学大学院   農学研究科 博士課程   農学専攻

    1997.4 - 2002.3

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  • 京都大学大学院   農学研究科 修士課程   農学専攻

    1995.4 - 1997.3

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  • Kyoto University   農学部   農学科

    1991.4 - 1995.3

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Research History

  • Okayama University   Institute of Global Human Resource Development   Professor

    2024

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    Country：Japan

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  • Faculty of Environmental, Life, Natural Science and Technology, Okayama University   Professor

    2023.4 - 2024.3

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    Country：Japan

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  • Okayama University   Faculty of Environmental and Life Sciences   Associate Professor

    2021.4 - 2023.3

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  • Okayama University   The Graduate School of Environmental and Life Science   Associate Professor

    2014.4 - 2021.3

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  • Okayama University   The Graduate School of Environmental and Life Science   Assistant Professor

    2012.4 - 2014.3

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Professional Memberships

Committee Memberships

  • 日本育種学会   総務担当運営委員（総務第一）  

    2022.4 - 2024.3   

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    Committee type：Academic society

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  • 日本育種学会   総務担当運営委員（総務第二）  

    2020.4 - 2022.3   

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    Committee type：Academic society

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  • Chugoku Branch Meeting of Japanese Society of Breeding   Organizer  

    2017.4   

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Papers

  • Molecular polymorphisms of the nuclear and chloroplast genomes among African melon germplasms reveal abundant and unique genetic diversity, especially in Sudan. International journal

    Odirichi Nnennaya Imoh, Gentaro Shigita, Mitsuhiro Sugiyama, Tran Phuong Dung, Katsunori Tanaka, Mami Takahashi, Kazusa Nishimura, Yuki Monden, Hidetaka Nishida, Mashaer Goda, Michel Pitrat, Kenji Kato

    Annals of botany   2025.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    BACKGROUND AND AIMS: Africa is rich in wild species of Cucumis and is considered one of the origins of melon. However, our knowledge of African melon is limited, and genetic studies using melon germplasms with wide geographical coverage are required. Here, we analyzed the genetic structure of African melons, with emphasis on Sudan. METHODS: Ninety-seven accessions of African melon were examined along with 77 reference accessions representing Asian melon and major horticultural groups. Molecular polymorphisms in the nuclear and chloroplast genomes were investigated using 12 RAPD, 7 SSR, and 3 SNP markers. Horticultural traits, including seed size, were measured for 46 accessions, mainly from Sudan. KEY RESULTS: African melons were divided into large and small seed-types based on seed length: large seed-type from Northern Africa and small seed-type from Western and Southern Africa. Both seed types are common in Sudan. Molecular genetic diversity in these geographical populations was as high as in India, the Asian center of melon domestication. Large seed-type from Northern Africa were assigned to Pop4 by structure analysis and had Ib cytoplasm in common with Cantalupensis, Inodorus, and Flexuosus. Small seed-types were highly diversified and geographically differentiated; specifically, Pop1 with Ia cytoplasm in Southern Africa and South Asia, Pop2 with Ia in East Asia, including Conomon and Makuwa, and Pop3 with Ia or Ic in Africa. Sudanese small seed-types were grouped in Pop3, while their cytoplasm type was the mixture of Ia and Ic. Sudanese Tibish had Ic cytoplasm that was unique in Africa, common in Western Africa and Sudan, and also found in wild or feral types. CONCLUSIONS: Melon of Ic lineage, including Tibish, originated from wild melon in the "western Sudan region," and independently of melon with Ia or Ib cytoplasm that originated in Asia. This clearly indicates the polyphyletic origin of melon.

    DOI： 10.1093/aob/mcaf028

    PubMed

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  • Workflow for development of CAPS markers with one type of restriction enzyme to identify citrus cultivars Reviewed

    Kazusa Nishimura, Maho Okuma, Junko Kaneyoshi, Atsu Yamasaki, Kyoka Nagasaka, Kazuki Murata, Yuki Monden, Kenji Kato, Hidetaka Nishida, Tetsuya Nakazaki, Ryohei Nakano

    Tree Genetics & Genomes   20 ( 5 )   2024.8

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    Abstract

    Given the ease of propagating fruit tree species through cloning, the economic viability of their breeding programs hinges on protecting breeders' rights. This necessitates the development of highly accurate DNA markers for cultivar identification. Here, we present a methodology for the rapid design of cleaved amplified polymorphic sequence (CAPS) markers to discriminate newly bred Japanese citrus cultivars from genetically related cultivars. We first compared the performance of ddRAD-seq and MIG-seq in citrus germplasm. The ddRAD-seq libraries generated using EcoRI and HindIII restriction enzymes yielded the highest number of polymorphisms. Subsequently, ddRAD-seq with EcoRI and HindIII was employed to analyze 29 citrus cultivars and thus identify 331,801 genome-wide polymorphisms. A semi-automated bioinformatics pipeline was then utilized to identify candidate CAPS markers, resulting in the discovery of 14,072 potential markers. Of these candidates, 52 were chosen for validation based on their recognition by the PstI restriction enzyme. This evaluation resulted in the development of 11 highly discriminative CAPS markers. Remarkably, a combination of only six such markers was sufficient to differentiate newly bred cultivars from their genetically related parents. The single restriction enzyme employed for these markers facilitates straightforward multiplexing. Finally, a combination of one multiplex marker testing two loci and four singleplex markers was successfully selected that completely discriminated the cultivars other than the bud sports used in this study. The pipeline established here extends beyond citrus and has the potential to simplify marker development and cultivar protection in various plant species.

    DOI： 10.1007/s11295-024-01661-x

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    Other Link： https://link.springer.com/article/10.1007/s11295-024-01661-x/fulltext.html

  • Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East Reviewed

    Gentaro Shigita, Koichiro Shimomura, Tran Phuong Dung, Naznin Pervin Haque, Thuy Thanh Duong, Odirich Nnennaya Imoh, Yuki Monden, Hidetaka Nishida, Katsunori Tanaka, Mitsuhiro Sugiyama, Yoichi Kawazu, Norihiko Tomooka, Kenji Kato

    Theoretical and Applied Genetics   137 ( 7 )   2024.7

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    Abstract

    Key message

    Genotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia.

    Abstract

    The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber.

    DOI： 10.1007/s00122-024-04683-0

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    Other Link： https://link.springer.com/article/10.1007/s00122-024-04683-0/fulltext.html

  • Polyphyletic domestication and inter-lineage hybridization magnified genetic diversity of cultivated melon, Cucumis melo L

    Katsunori Tanaka, Gentaro Shigita, Tran Phuong Dung, Phan Thi Phuong Nhi, Mami Takahashi, Yuki Monden, Hidetaka Nishida, Ryuji Ishikawa, Kenji Kato

    bioRxiv   2024.7

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    Publisher：Cold Spring Harbor Laboratory  

    Abstract

    A total of 212 melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9 mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp.meloand the East Asian subsp.agrestiswere characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence in both nuclear and cytoplasm genomes. In contrast, in South and Southeast Asia, in addition to the Europe/US and East Asian types, recombinant types were also frequently found, indicating unclear genetic differentiation in South and Southeast Asia. Such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types of melon. Seed length was intermediate, between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib in Momordica, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp.agrestisof the Ic type proved to be endemic to Africa, indicating its African origin.

    DOI： 10.1101/2024.06.27.601017

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  • Growth and yield-related traits of near-isogenic wheat lines carrying different alleles at the Vrn-D1 locus Reviewed

    Hiromi Matsuyama, Hiroko Sawada, Masaya Fujita, Masako Seki, Hidetaka Nishida, Kenji Kato

    Plant Production Science   1 - 11   2024.6

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    Publishing type：Research paper (scientific journal)   Publisher：Informa UK Limited  

    DOI： 10.1080/1343943x.2024.2363547

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Books

  • 農業 令和元年（2019）7月号

    西田英隆（ Role： Joint author ,  コムギの起源地を訪ねて ―南コーカサスと中央アジアにおける遺伝資源探索―）

    公益社団法人大日本農会  2019.7 

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  • 科学 2017年10月号

    西田英隆（ Role： Joint author ,  シルクロードを旅した栽培植物：コムギ編）

    岩波書店  2017.7 

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  • 麦の自然史 : 人と自然が育んだムギ農耕

    佐藤 洋一郎, 加藤 鎌司, 河原 太八, 渡部 武, 森 直樹, 辻本 壽, 丹野 研一, 有村 誠, 西田 英隆, 武田 和義, 森川 利信, 冨永 達, 長野 宏子, 大田 正次, 吉村 作治, 笹沼 恒男

    北海道大学出版会  2010  （ ISBN:9784832981904 ）

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    Language：Japanese

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MISC

  • Exploration and comparative analysis of nematode resistance loci in hexaploid sweetpotato with GWAS, QTL mapping, and k-mer based bulk segregation analysis

    栗原未結, 田淵宏朗, 西村和紗, 西田英隆, 加藤鎌司, 門田有希

    育種学研究   26   2024

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  • Identification of genetic region related to the anthocyanin accumulation in sweetpotato storage roots and sequence analysis of the candidate gene

    堀田望未, 岡田吉弘, 神崎浩, 栗原未結, 西村和紗, 西田英隆, 加藤鎌司, 門田有希

    育種学研究   26   2024

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  • High-dense genetic linkage map using multiple-dose markers and random-effect multiple QTL mapping of root-knot nematode resistance in hexaploid sweetpotato

    栗原未結, 田淵宏朗, 加藤鎌司, 西田英隆, 門田有希

    育種学研究   25   2023

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  • Revealing the competition between sweetpotato and southern root knot nematode by transcriptome analysis

    泉谷真, 大畑慎一郎, 田淵宏朗, 西田英隆, 加藤鎌司, 門田有希

    育種学研究   25   2023

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  • Identification and comparative analysis of QTLs related to sweetpotato yield using multiple reference genome sequences

    堀田望未, 岡田吉弘, 栗原未結, 西田英隆, 加藤鎌司, 門田有希

    育種学研究   25   2023

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Presentations

  • The use of a crop development model for genetic analysis of heading date in tetraploid wheat

    Nishimura K., Kawakita S., Monden Y., Kato K., Nakazaki T., Nishida H.

    The 19th Triticeae Meeting Japan  2024.12.21 

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    Event date： 2024.12.21 - 2024.12.22

    Language：Japanese   Presentation type：Poster presentation  

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  • Genetic mapping of mutant genes for heading time in barley using next-generation sequencing

    Takeda S., Okuma M., Mandozai A., Nishimura K., Monden Y., Kato K., Nishida H.

    The 19th Triticeae Meeting Japan  2024.12.21 

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    Event date： 2024.12.21 - 2024.12.22

    Language：Japanese   Presentation type：Poster presentation  

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  • Narrowing down a novel heading-time related QTL located on chromosome 4H and exploration of a causal gene in barley

    M. Okuma, K. Nishimura, Y. Monden, K. Kato, H. Nishida

    16th Chugoku branch meeting of Japanese Society of Breeding  2024.12.14 

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    Event date： 2024.12.14 - 2024.12.15

    Language：Japanese   Presentation type：Oral presentation (general)  

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  • Identification of genetic locus related to carotenoid biosynthesis of storage root of sweetpotato

    N. Horita, Y. Okada, M. Kurihara, K. Nishimura, H. Nishida, K. Kato, Y. Monden

    16th Chugoku branch meeting of Japanese Society of Breeding  2024.12.14 

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    Event date： 2024.12.14 - 2024.12.15

    Language：Japanese   Presentation type：Poster presentation  

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  • Effects of heading time-related genes on internode elongation and young spike development in barley

    C. Nakata, I. Nakatani, Takumi Oka, K. Nishimura, Y. Monden, K. Kato, H. Nishida

    16th Chugoku branch meeting of Japanese Society of Breeding  2024.12.14 

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    Event date： 2024.12.14 - 2024.12.15

    Language：Japanese   Presentation type：Poster presentation  

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Awards

  • Japanese Society of Breeding Best Paper Awards

    2024.9   Japanese Society of Breeding   Elucidation of genetic variation and ppopulation structure of melon genetic resources in the NARO Genbank, and construction of the World Melon Core Collection

    Shigita G., Dung TP, Pervin MN, Duong TT, Imoh ON, Monden Y., Nishida H., Tanaka K., Sugiyama M., Kawazu Y., Tomooka N., Kato K.

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  • Japanese Society of Breeding Best Paper Awards

    2014.3   Japanese Society of Breeding  

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Research Projects

  • オオムギにおける茎葉空間配置の環境応答に関する遺伝機構の解明

    Grant number：22K05585  2022.04 - 2025.03

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    西田 英隆, 加藤 鎌司

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    Grant amount：\4160000 （ Direct expense: \3200000 、 Indirect expense：\960000 ）

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  • フィールド・マルチオミックス解析によるムギ類出穂期不安定性の遺伝学的研究

    Grant number：22H02314  2022.04 - 2025.03

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    加藤 鎌司, 西田 英隆, 塔野岡 卓司, 松山 宏美, 高橋 飛鳥, 島崎 由美, 牧 夏海

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    Grant amount：\17290000 （ Direct expense: \13300000 、 Indirect expense：\3990000 ）

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  • Molecular genetic study on heading time instability in wheat and barley

    Grant number：19H02931  2019.04 - 2022.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    KATO Kenji

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    Grant amount：\17290000 （ Direct expense: \13300000 、 Indirect expense：\3990000 ）

    Heading time is one of the important traits to stably achieve the maximum yield in wheat and barley, but is becoming unstable mainly due to yearly fluctuation of temperature throughout the growing season. In this study, we studied the effect of wheat PCL1 genes and barley PhyC and Ppd-1 genes on heading time and its yearly fluctuation (instability). In wheat, heading was accelerated ca. two weeks and became instable when functional allele of PCL1 was absent, that is, recessive homozygote at three homoeologous loci. In contrast, in plants having at least one functional allele, earliness effect was just a few days. The similar results were also obtained in durum wheat lines developed by introduction of non-functional allele of PCL1 from 'Chogokuwase'. We also identified that additional earliness gene(s) are located on chromosomes 1B, 6A and 6B. In barley, the effect of PhyC and Ppd-H1 on heading time and its instability.

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  • Genetic analysis of heading time unstability in wheat and barley

    Grant number：16H04863  2016.04 - 2019.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    KATO Kenji

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    Grant amount：\16900000 （ Direct expense: \13000000 、 Indirect expense：\3900000 ）

    Growth and yield of crops are significantly affected by changing global environment. Heading time is one of the important traits to achieve the maximum yield in wheat and barley, but is becoming unstable mainly due to yearly fulctuation of temperature throughout the growing season. In this study, we first identified wheat and barley cultivars whose heading time varies largely depending on the year, and then identified the causal gene(s). A wheat breeding line 'Chogokuwase' is an extra early heading line and its heading date is accelerated by warmer temperature in wheat. By map based approach, using segregating populations derived from 'Chogokuwase' x 'Kinuiroha', we identified that the causal gene is PCL1 and triple recessive homozygote become eatra early heading. In barley, HvPhyC mutant allele, which is commonly found in the Japanese early maturity cultivars, proved to cause unstability of heading time depending on the temperature condition during winter.

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  • Map-based cloning and function analysis of a wheat vernalization gene Vrn-D4

    Grant number：26450005  2014.04 - 2017.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    Nishida Hidetaka, KATO Kenji, DUBCOVSKY Jorge, KIPPES Nestor

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    Authorship：Principal investigator  Grant type：Competitive

    Grant amount：\5070000 （ Direct expense: \3900000 、 Indirect expense：\1170000 ）

    In the previous study, a wheat vernalization gene Vrn-D4 was mapped in a centromeric region, 0.09cM interval, of chromosome 5D. In this study, Vrn-D4 was found to be located on the short arm. This new information narrowed further down the Vrn-D4 region. In another analysis, the line with a spring allele Vrn-D4 was found to carry two copies of Vrn-A1, one of which was located on the short arm of chromosome 5D and had specific polymorphisms. Other lines with a spring allele Vrn-D4 also had this Vrn-A1 copy, which confirmed that the causal gene of Vrn-D4 is the Vrn-A1 copy on the short arm of chromosome 5D. Moreover, origin of Vrn-D4 was analyzed.

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Class subject in charge

  • Crop Genetics and Breeding （2024academic year） Second semester  - 火5～6

  • Introduction to Agricultural Sciences （2024academic year） Fourth semester  - 木5～7

  • Course Seminar 2 （2024academic year） 3rd and 4th semester  - 水３

  • Course Seminar 3 （2024academic year） 1st and 2nd semester  - その他

  • Course Seminar 4 （2024academic year） 3rd and 4th semester  - その他

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Social Activities

  • 令和3年度岡山県教育委員会免許法認定講習

    Role(s)：Lecturer

    岡山県  令和3年度岡山県教育委員会免許法認定講習  2021.8.26 - 2021.8.27

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    Type：Certification seminar

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