Basic Information

Faculty

• 農学部

Professional Memberships

• THE JAPANESE SOCIETY FOR HORTICULTURAL SCIENCE
• Japanese Society of Breeding
• International Society for Horticultural Science

Academic Degree

• 修士（農学）(京都大学)
• 博士（農学）(京都大学)

Academic Resume (Graduate Schools)

• 京都大学, 大学院農学研究科修士課程農学専攻, 修了
• 京都大学, 大学院農学研究科博士後期課程農学専攻, 修了

Academic Resume (Undergraduate School/Majors)

• 京都大学, 農学部資源生物科学科, 卒業

High School

• High School

  岡山県立倉敷青陵高等学校

Research History

• From May 2019, To Present

  Kyoto University, Graduate School of Agriculture, Assistant Professor
• From Apr. 2018, To Apr. 2019

  Kyoto University, Graduate School of Agriculture, Postdoc
• From Apr. 2016, To Mar. 2018

  日本学術振興会, 特別研究員DC2

ID,URL

• J-Global ID

  201801013623000497

researchmap URL

• https://researchmap.jp/nishiyama020

Research

Research Topics, Overview of the research

• Research Topics

  Genetics, genomics, and breeding of fruit tree species

• Overview of the research

  Dr. Soichiro Nishiyama is working on genetics and breeding science for fruit crops. The current research focus is mainly on persimmon and blueberry.

Research Interests

• 果樹園芸学
• 倍数性
• 遺伝

Research Areas

• Environmental science/Agricultural science, Horticulture

Papers

• Integer programming for selecting set of informative markers in paternity inference.

  Soichiro Nishiyama; Kengo Sato; Ryutaro Tao

  BMC bioinformatics, 08 Jul. 2022, Lead author, Corresponding author

  
• Phenotypic evaluation of shape diversity in persimmon fruit using two- and three-dimensional imaging

  A. Kusumi; Y. Osako; R. Nakano; S. Nishiyama; R. Tao

  Acta Horticulturae, Apr. 2022

  
• Candidate gene analysis for ASTRINGENCY controlling fruit astringency in Diospyros kaki based on mRNA- and small RNA-sequencing analyses

  Y. Fujiwara; S. Nishiyama; N. Onoue; R. Matsuzaki; K. Yonemori; R. Tao

  Acta Horticulturae, Apr. 2022

  
• Genome-Wide Identification of Loci Associated With Phenology-Related Traits and Their Adaptive Variations in a Highbush Blueberry Collection

  Kyoka Nagasaka; Soichiro Nishiyama; Mao Fujikawa; Hisayo Yamane; Kenta Shirasawa; Ebrahiem Babiker; Ryutaro Tao

  Frontiers in Plant Science, 21 Jan. 2022, Corresponding author

  
• Characterization of Tissue-specific Transcriptomic Responses to Seedlessness Induction by Gibberellin in Table Grape

  Soichiro Nishiyama; Daisuke Yoshimura; Akihiko Sato; Keizo Yonemori

  The Horticulture Journal, 2022, Corresponding author

  
• Insights into the Physiological and Molecular Mechanisms Underlying Highbush Blueberry Fruit Growth Affected by the Pollen Source

  Kyoka Nagasaka; Hisayo Yamane; Soichiro Nishiyama; Shu Ebihara; Ryusuke Matsuzaki; Masakazu Shoji; Ryutaro Tao

  The Horticulture Journal, 2022

  
• Characterization of a gene co-expression network associated with mgst, the pollen modifier gene of gametophytic self-incompatibility in sweet cherry (prunus avium l.)

  K. Ono; E. T. Chang; S. Nishiyama; A. Wünsch; R. Tao; K. Ono

  Acta Horticulturae, Jun. 2021

  
• Frequent reversion and continuous size variation in the small fruit mutant 'totsutanenashi' persimmon

  S. Wang; C. L. Tam; I. Naito; S. Nishiyama; R. Tao

  Acta Horticulturae, Jun. 2021

  
• Genomics-based discrimination of 2n gamete formation mechanisms in polyploids: a case study in nonaploid Diospyros kaki ‘Akiou’

  Peng Sun; Soichiro Nishiyama; Hideaki Asakuma; Roeland E Voorrips; Jianmin Fu; Ryutaro Tao

  G3 Genes|Genomes|Genetics, 29 May 2021, Corresponding author

  
• Allelic distribution at SNP loci within bud dormancy-related QTLs in Japanese apricot (Prunus mume) collections

  T. Hsiang; W. Chen; H. Yamane; S. Nishiyama; R. Nakano; R. Tao

  Acta Horticulturae, May 2021

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

  Soichiro Nishiyama; Mao Fujikawa; Hisayo Yamane; Kenta Shirasawa; Ebrahiem Babiker; Ryutaro Tao

  Heredity, Jan. 2021, Lead author, Corresponding author

  
• Functional and expressional analyses of apple FLC-like in relation to dormancy progress and flower bud development.

  Soichiro Nishiyama; Miwako Cecile Matsushita; Hisayo Yamane; Chikako Honda; Kazuma Okada; Yosuke Tamada; Shigeki Moriya; Ryutaro Tao

  Tree physiology, 14 Nov. 2019, Lead author

  
• Changes in cytokinin metabolism in a small fruit mutant of ‘Hiratanenashi’ persimmon (Diospyros kaki Thunb.)

  I. Naito; S. Nishiyama; M. Gao-Takai; H. Yamane; R. Tao

  Acta Horticulturae, 30 Aug. 2018

  
• Comparative Mapping of the ASTRINGENCY Locus Controlling Fruit Astringency in Hexaploid Persimmon (Diospyros kaki Thunb.) with the Diploid D. lotus Reference Genome

  Nishiyama Soichiro; Onoue Noriyuki; Kono Atsushi; Sato Akihiko; Ushijima Koichiro; Yamane Hisayo; Tao Ryutaro; Yonemori Keizo

  HORTICULTURE JOURNAL, Jul. 2018, Lead author

  
• RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

  Takeuchi Takanori; Matsushita Miwako Cecile; Nishiyama Soichiro; Yamane Hisayo; Banno Kiyoshi; Tao Ryutaro

  JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE, May 2018, Lead author

  
• Identification of QTLs controlling chilling and heat requirements for dormancy release and bud break in Japanese apricot (Prunus mume)

  Yuto Kitamura; Tsuyoshi Habu; Hisayo Yamane; Soichiro Nishiyama; Kei Kajita; Takuya Sobue; Takashi Kawai; Koji Numaguchi; Tetsuya Nakazaki; Akira Kitajima; Ryutaro Tao

  Tree Genetics and Genomes, 01 Apr. 2018

  
• Characterization of a gene regulatory network underlying astringency loss in persimmon fruit.

  Soichiro Nishiyama; Noriyuki Onoue; Atsushi Kono; Akihiko Sato; Keizo Yonemori; Ryutaro Tao

  Planta, Mar. 2018, Lead author

  
• Differences in Physiological Characteristics and Gene Expression Levels in Fruits between Japanese Persimmon (Diospyros kaki Thunb.) ‘Hiratanenashi’ and Its Small Fruit Mutant ‘Totsutanenashi’

  羽生剛; 山根久代; 内藤一平; 西山総一郎; 野中亜優美; 河井崇; 山田寿; 田尾龍太郎

  Horticulture Journal, 2016

  
• EFFECT OF ABA TREATMENT ON TANNIN ACCUMULATION AT AN EARLY STAGE OF FRUIT DEVELOPMENT IN PERSIMMON

  S. Nishiyama; K. Yonemori; J. Ueda

  Acta Horticulturae, Jul. 2014

  
• IDENTIFICATION OF PLANT HORMONES IN ENDOSPERM LIQUID OF MANGOSTEEN FRUITS AT YOUNG DEVELOPMENTAL STAGES

  K. Yonemori; S. Nishiyama; C. Yapwattanaphun; J. Ueda

  Acta Horticulturae, Jul. 2014

  
• Development of Molecular Markers Associated with Sexuality in Diospyros lotus L. and Their Application in D-kaki Thunb

  Takashi Akagi; Kei Kajita; Takanori Kibe; Haruka Morimura; Tomoyuki Tsujimoto; Soichiro Nishiyama; Takashi Kawai; Hisayo Yamane; Ryutaro Tao

  JOURNAL OF THE JAPANESE SOCIETY FOR HORTICULTURAL SCIENCE, Jul. 2014

  

Misc.

• 3D-scanner aided quantification of changes in geometric parameters of fruit shape during persimmon fruit development

  久住あかね; 西山総一郎; 田尾龍太郎

  園芸学研究 別冊, 2022

  
• Three-dimensional imaging of persimmon tannin cells by electron microscopy and machine learning

  西山総一郎; 田尾龍太郎; 米森敬三

  園芸学研究 別冊, 2022

  
• The relationship between preference and sensory attributes of blueberry fruit

  平岩尚樹; 山根久代; 西山総一郎; 田尾龍太郎

  園芸学研究 別冊, 2022

  
• Origin and pleiotropy of the fruit size mutation in ‘Hiratanenashi’ bud sports

  西山総一郎; WANG S.; TAM Chun-Lai; 田尾龍太郎

  園芸学研究 別冊, 2021

  
• Genomics-based discrimination of 2n gamete formation mechanisms in polyploids

  西山総一郎; SUN P.; 朝隈英昭; VOORRIPS Roeland; FU Jianmin; 田尾龍太郎

  育種学研究, 2021

  
• Genome wide association study in a southern highbush blueberry population based on polyploid model

  長坂京香; 西山総一郎; 藤川真央; 山根久代; 白澤健太; BABIKER Ebrahiem; 田尾龍太郎

  園芸学研究 別冊, 2021

  
• Application of deep-learning for detection and cultivar classification of persimmon fruits in a field environment

  久住あかね; 大迫祐太朗; 中野龍平; 西山総一郎; 田尾龍太郎

  園芸学研究 別冊, 2021

  
• Highbush blueberry fruit development affected by pollen donor

  長坂京香; 山根久代; 西山総一郎; 海老原脩; 松崎隆介; 庄子雅和; 田尾龍太郎

  園芸学研究 別冊, 2021

  
• Development of a marker set optimization algorithm for identifying pollen parent of seedling

  西山総一郎; 田尾龍太郎

  園芸学研究 別冊, 2021

  
• Identification of candidate genes controlling fruit astringency in persimmon

  藤原陽介; 西山総一郎; 尾上典之; 松崎隆介; 米森敬三; 田尾龍太郎

  園芸学研究 別冊, 2021

  
• Genome-wide association study on agronomic traits in southern highbush blueberry

  西山総一郎; 藤川真央; 山根久代; 白澤健太; BABIKER Ebrahiem; 田尾龍太郎

  園芸学研究 別冊, 2020

  
• Intra-clonal genetic variation in ’Hiratanenashi’ Nonaploid persimmon

  西山総一郎; WANG S.; 田尾龍太郎

  育種学研究, 2020

  
• Genetic Diversity and Population Structure Analysis of Vaccinium Corymbosum Assessed By Double Digest Restriction-Site Associated DNA Sequencing

  Babiker Ebrahiem; Fujikawa Mao; Tao Ryutaro; Yamane Hisayo; Nishiyama Soichiro; Shirasawa Kenta

  HORTSCIENCE, Sep. 2019

  
• トランスクリプトーム解析による日本タイプ完全甘と中国タイプ完全甘のPA蓄積制御メカニズムの比較

  西山総一郎; 尾上典之; 河野淳; 佐藤明彦; 田尾龍太郎; 米森敬三

  園芸学研究 別冊, 2019

  
• カキの果実発達を制御する遺伝子発現ネットワーク

  西山総一郎; 尾上典之; 河野淳; 佐藤明彦; 米森敬三; 田尾龍太郎

  園芸学研究 別冊, 2019

  
• ddRAD-seq法によるハイブッシュブルーベリーの集団構造解析

  藤川真央; BABIKER Ebrahiem; 西山総一郎; 山根久代; 白澤健太; 田尾龍太郎

  園芸学研究 別冊, 2019

  
• カキ甘渋性決定遺伝子座の多様性解析

  西山総一郎; 藏本晃栄; 尾上典之; 河野淳; 佐藤明彦; 米森敬三; 田尾龍太郎

  園芸学研究 別冊, 2018

  
• カキ甘渋性に関する共発現ネットワーク解析

  西山総一郎; 尾上典之; 河野淳; 佐藤明彦; 米森敬三; 田尾龍太郎

  園芸学研究 別冊, 2017

  
• カキ甘渋性決定遺伝子座とシンテニィのあるマメガキゲノム領域の解析

  西山総一郎; 尾上典之; 河野淳; 佐藤明彦; 牛島幸一郎; 山根久代; 田尾龍太郎; 米森敬三

  園芸学研究 別冊, 2017

  
• カキ甘渋性に関するトランスクリプトーム解析

  西山総一郎; 尾上典之; 河野淳; 佐藤明彦; 米森敬三; 田尾龍太郎

  園芸学研究 別冊, 2016

  
• ‘平核無’の小果突然変異体‘突核無’の果実におけるサイトカイニン含量および遺伝子発現の変化

  内藤一平; 西山総一郎; 高居恵愛; 山根久代; 田尾龍太郎

  園芸学研究 別冊, 2016

  
• Comparative genomics of the locus controlling astringency in Diospyros species.

  Nishiyama, S; A. Kono; N. Onoue; A. Sato; K. Ushijima; H. Yamane; R. Tao; K. Yonemori

  Abst. Plant & Animal Genome, 2016

  
• Effectiveness of Molecular Markers for Detecting the Non-astringent Trait of Chinese Persimmon and a Trial to Identify the Gene Conferring Chinese PCNA Trait in 'Luo Tian Tian Shi'

  Keizo Yonemori; Soichiro Nishiyama; Hisayo Yamane; Akihiko Sato

  HORTSCIENCE, Sep. 2015

  
• マメガキを用いたカキの甘渋性決定遺伝子座の比較ゲノム解析

  西山総一郎; 佐藤明彦; 河野淳; 尾上典之; 牛島幸一郎; 山根久代; 田尾龍太郎; 米森敬三

  園芸学研究 別冊, 2015

  

Presentations

• 倍数性果樹のゲノム特性-カキとブルーベリーの育種努力の歴史と展望-

  西山総一郎

  「高次倍数体をどうにかする会」2021冬, 23 Dec. 2021, Invited

  
• Physiological and genetic characterization of ‘Totsutanenashi’, a nonaploid persimmon mutant bearing extremely small size fruit

  Soichiro Nishiyama; Chiho Iwami; Sheng Wang; ChunLai Tam; Ryutaro Tao

  7th International Symposium on Persimmon, 23 Sep. 2021

  
• DNA sequence diversity of the astringency-controlling locus in Diospyros kaki

  Tao, R; A. Kuramoto; S. Nishiyama

  7th International Symposium on Persimmon, 24 Sep. 2021

  
• 高次倍数体のSNP検出

  西山総一郎

  園芸作物バイオインフォマティクス入門3, 10 Sep. 2021, Invited

  
• Characterization of population structure and genetic variation of chilling requirement in southern highbush blueberry

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

  XII International Vaccinium Symposium, 30 Aug. 2021

  
• Genome-wide association mapping of phenology-ralted traits in southern highbush blueberry using ddRAD-seq

  Babiker, E; K. Nagasaka; S. Nishiyama; M. Fujikawa; H. Yamane; R. Tao

  Annual meeting of American Society for Horticultural Science, 05 Aug. 2021

  
• Genetic analysis of proanthocyanidin accumulation in hexaploid persimmon

  Soichiro Nishiyama

  The 4th KU-KUGSA Bilateral Symposium, 05 Dec. 2018, Invited

  
• Genetics of proanthocyanidins accumulation control in persimmon fruit

  Soichiro Nishiyama

  HZAU-NTU-KU Joint Horticulture Symposium, 03 Sep. 2018, Invited

  
• カキ甘渋性の分子制御機構解明にむけて

  西山総一郎

  福井県立大学 生物資源学先端セミナー, 17 Jul. 2018, Invited

  
• Toward isolation of a gene conferring astringency loss in persimmon fruit

  Nishiyama, S; N. Onoue; A. Kono; A. Sato; K. Yonemori; R. Tao

  Plant and Animal Genome XXV, 17 Jan. 2017

  
• Transcriptome analysis for astringency in persimmon fruit

  Nishiyama, S; N. Onoue; A. Kono; A. Sato; K. Yonemori; R. Tao

  The ISHS VI International Symposium on Persimmon, 17 Oct. 2016

  

External funds: Kakenhi

• ゲノミクスと果実フェノミクスに基づく倍数体果樹育種の新展開

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (A))

  Basic Section 39030:Horticultural science-related

  Kyoto University

  西山 総一郎

  From 01 Apr. 2022, To 31 Mar. 2025, Granted

  果樹;カキ;倍数性;ゲノム;機械学習

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21KK0269/
• エピジェネティックなトランスポゾン時空間特異的転移制御による果実発達機構の解明

  Grant-in-Aid for Challenging Research (Exploratory)

  Medium-sized Section 39:Agricultural and environmental biology and related fields

  Kyoto University

  山根 久代

  From 09 Jul. 2021, To 31 Mar. 2024, Granted

  DNAメチル化;エピジェネティクス;果実成熟;トランスポゾン;果樹

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K19113/
• 完全甘ガキ性決定遺伝子の同定と機能解析

  Grant-in-Aid for Early-Career Scientists

  Basic Section 39030:Horticultural science-related

  Kyoto University

  西山 総一郎

  From 01 Apr. 2021, To 31 Mar. 2024, Granted

  果樹;プロアントシアニジン;倍数性;果実品質;ゲノム;ゲノム解析

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K14848/
• 作物科学研究へのパラダイムシフトを誘起するカキ属植物の研究加速化のための基盤形成

  Grant-in-Aid for Challenging Research (Pioneering)

  Medium-sized Section 39:Agricultural and environmental biology and related fields

  Kyoto University

  田尾 龍太郎

  From 01 Apr. 2020, To 31 Mar. 2025, Granted

  果樹;遺伝子情報;機械学習;果実形状;遺伝子機能評価;倍数体

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20K20454/
• カキ果実のプロアントシアニジン蓄積の組織学的解析とその分子生物学的制御機構の解明

  Grant-in-Aid for Scientific Research (C)

  Basic Section 39030:Horticultural science-related

  Ryukoku University

  米森 敬三

  From 01 Apr. 2020, To 31 Mar. 2023, Granted

  タンニン細胞;果樹;カキ;渋味;蓄積制御

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20K06038/
• Establishment of the consumer-oriented breeding system in blueberry based on genomic and cognitive sciences

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Medium-sized Section 39:Agricultural and environmental biology and related fields

  Kyoto University

  田尾 龍太郎

  From 07 Oct. 2019, To 31 Mar. 2024, Granted

  果樹;園芸;嗜好性;栽培化;倍数体

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19KK0156/
• Understanding the mechanism of fruit size control with a focus on a persimmon small fruit mutant

  Grant-in-Aid for Early-Career Scientists

  Basic Section 39030:Horticultural science-related

  Kyoto University

  Soichiro Nishiyama

  From 01 Apr. 2019, To 31 Mar. 2021, Project Closed

  果樹;ゲノム;倍数体;トランスクリプトーム;果実発達;果実品質;倍数性;器官サイズ;全ゲノム解析;枝変わり

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19K15832/
• カキ果実におけるプロアントシアニジン蓄積制御機構解明

  Grant-in-Aid for Research Activity Start-up

  0602:Agricultural and environmental biology and related fields

  Kyoto University

  西山 総一郎

  From 24 Aug. 2018, To 31 Mar. 2020, Project Closed

  園芸学;果実;二次代謝;トランスクリプトーム;ゲノム;倍数性;甘渋性;倍数体ゲノム;フラボノイド

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18H06008/
• カキの特異なプロアントシアニジン蓄積の基盤となる分子遺伝学的機構の解明と応用

  Grant-in-Aid for Scientific Research (B)

  Basic Section 39030:Horticultural science-related

  Kyoto University

  西山 総一郎

  From 01 Apr. 2023, To 31 Mar. 2027, Granted

  果樹;育種;倍数性;二次代謝;ゲノミクス

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23H02202/

Education

Teaching subject(s)

• From 01 Apr. 2023, To 31 Mar. 2024

  Special Laboratory Work in Pomology2

  AC35, Year-long, Graduate School of Agriculture, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Special Laboratory Work in Pomology1

  AC34, Year-long, Graduate School of Agriculture, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Pomology Seminar2

  AB17, Year-long, Graduate School of Agriculture, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Pomology Seminar1

  AB16, Year-long, Graduate School of Agriculture, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Molecular Plant Breeding

  5375, Fall, Faculty of Agriculture, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Seminar in Horticultural Science

  5285, Year-long, Faculty of Agriculture, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Special Laboratory Work in Pomology2

  AC35, Year-long, Graduate School of Agriculture, 5
• From 01 Apr. 2022, To 31 Mar. 2023

  Pomology Seminar1

  AB16, Year-long, Graduate School of Agriculture, 4
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar in Horticultural Science

  5285, Year-long, Faculty of Agriculture, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Special Laboratory Work in Pomology1

  AC34, Year-long, Graduate School of Agriculture, 5
• From 01 Apr. 2022, To 31 Mar. 2023

  Pomology Seminar2

  AB17, Year-long, Graduate School of Agriculture, 4
• From Apr. 2020, To Mar. 2021

  Seminar in Horticultural Science

  Year-long, 農学部
• From Apr. 2020, To Mar. 2021

  Special Laboratory Work in Pomology1

  Year-long, 農学研究科
• From Apr. 2020, To Mar. 2021

  Special Laboratory Work in Pomology2

  Year-long, 農学研究科
• From Apr. 2020, To Mar. 2021

  Pomology Seminar1

  Year-long, 農学研究科
• From Apr. 2020, To Mar. 2021

  Pomology Seminar2

  Year-long, 農学研究科
• From Apr. 2021, To Mar. 2022

  Seminar in Horticultural Science

  Year-long, 農学部
• From Apr. 2021, To Mar. 2022

  Special Laboratory Work in Pomology1

  Year-long, 農学研究科
• From Apr. 2021, To Mar. 2022

  Special Laboratory Work in Pomology2

  Year-long, 農学研究科
• From Apr. 2021, To Mar. 2022

  Pomology Seminar1

  Year-long, 農学研究科
• From Apr. 2021, To Mar. 2022

  Pomology Seminar2

  Year-long, 農学研究科

Administration

Faculty management (title, position)

• From 01 Apr. 2021, To 31 Mar. 2023

  情報セキュリティ・システム委員会　委員