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沼口 孝司大学院農学研究科 資源生命科学専攻助教
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■ 論文- 2026年08月, Journal of Experimental Botany, 英語[査読有り]研究論文（学術雑誌）
- 2026年, Breeding science, 英語[査読有り]研究論文（学術雑誌）
- Reduced seed shattering is a key yield-improving trait selected during the domestication of the Asian rice, Oryza sativa, from its wild ancestor, O. rufipogon. Three quantitative trait loci, qSH1, sh4, and qSH3, are reported to be involved in the reduced seed-shattering behaviour of cultivated rice. Genotyping surveys of these loci have shown that the sh4 mutation is conserved in all cultivars, whereas the qSH1 mutation is only observed in some japonica cultivars. Furthermore, the qSH3 mutation is observed in indica and japonica cultivars; however, aus cultivars carry a functional allele of wild rice at qSH3, indicating there may be distinct genetic mechanisms in aus for its reduced seed-shattering behaviour independently of qSH1 and qSH3. Through genetic analysis of the segregating populations between an aus cultivar, Kasalath, and wild rice introgression lines carrying the domesticated allele at sh4, we detected three loci associated with the reduced seed-shattering behaviour of Kasalath. Subsequent progeny tests validated their effects on this trait. These findings indicate that there are common and distinct genetic loci governing seed-shattering reduction in rice cultivars, providing novel insights into the complex process of rice domestication. This knowledge may help improve breeding strategies to optimise yield through targeted genetic selection.2025年11月, Molecular genetics and genomics : MGG, 300(1) (1), 108 - 108, 英語, 国際誌[査読有り]研究論文（学術雑誌）
- Springer science and business media LLC, 2025年11月, Plant molecular biology reporter, 44(1) (1), 英語[査読有り]研究論文（学術雑誌）
- 2025年07月, アグリバイオ, 9(7) (7), 13 - 17, 日本語ウメの果実形質に関連する遺伝領域[招待有り]論文集(書籍)内論文
- Japanese society for horticultural science, 2025年, The horticulture journal, 英語[査読有り]研究論文（学術雑誌）
- Japanese Society for Horticultural Science, 2024年, The Horticulture Journal, 93(4) (4), 344 - 352, 英語[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media LLC, 2023年08月, Molecular Genetics and Genomics, 298(6) (6), 1365 - 1375, 英語[査読有り]研究論文（学術雑誌）
- Japanese apricot (Prunus mume) is an important fruit tree in East Asia. ‘Nanko’, the primary cultivar of Japanese apricots, usually suffers from scab, a disease caused by Venturia carpophila. However, there have been few reports on the phenotypic variation in scab resistance/susceptibility and the underlying genetic factors. In this study, we investigated the severity of naturally occurring scabs based on fruit lesions in 108 Japanese apricot accessions over four consecutive years. In each year, both resistant and susceptible accessions were observed, and significant annual correlations were detected among the ratios of diseased fruits (Rt; 0.52–0.76) and among the disease severity indices (Sv; 0.55–0.79). We also conducted a genome-wide association study (GWAS) based on exon-targeted resequencing, and significant peaks were detected in the data from 2017 and 2018. The candidate genes involved in disease resistance are located near nine single-nucleotide polymorphisms. These genes may be associated with the susceptibility of ‘Nanko’ lineages to scab. These findings shed light on the phenotypic and genetic profiles of scab resistance in P. mume and will assist future breeding programs with improving scab resistance.MDPI AG, 2023年07月, Horticulturae, 9(8) (8), 872 - 872, 英語[査読有り]研究論文（学術雑誌）
- Abstract Asian rice (Oryza sativa) was domesticated from O. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci, qSH3 and sh4, are involved in reducing seed shattering in both japonica and indica rice cultivars, while qSH1 and qCSS3 are likely specific to japonica cultivars. In indica cultivars, qSH3 and sh4 fail to explain the degree of seed shattering, as an introgression line (IL) of O. rufipogon W630 carrying domesticated alleles at qSH3 and sh4 still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and the indica cultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC1F2 population between the IL and IR36, we detected two novel loci, qCSS2 and qCSS7 (QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction of qCSS2 and qCSS7 under the presence of qSH3 and sh4 mutations in O. rufipogon W630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. Since qCSS2 and qCSS7 were not detected in previous studies on seed shattering in japonica, their control may be specific to indica cultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree of indica cultivars to maximise their yield.Springer Science and Business Media LLC, 2023年05月, Molecular Genetics and Genomics, 298(4) (4), 943 - 953, 英語[査読有り]研究論文（学術雑誌）
- Asian rice ( Oryza sativa L.) is consumed by more than half of the world's population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice ( Oryza rufipogon Griff.) acquired non-seed-shattering behavior, allowing humans to increase grain yield. Previous studies argued that a reduction in seed shattering triggered by the sh4 mutation led to increased yield during rice domestication, but our experiments using wild introgression lines show that the domesticated sh4 allele alone is insufficient for shattering loss in O . rufipogon . The interruption of abscission layer formation requires both sh4 and qSH3 mutations, demonstrating that the selection of shattering loss in wild rice was not as simple as previously suggested. Here we identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1 , which is conserved in indica and japonica subspecies but absent in the circum -aus group of rice. Through harvest experiments, we further demonstrated that seed shattering alone did not significantly impact yield; rather, yield increases were observed with closed panicle formation controlled by SPR3 and further augmented by nonshattering, conferred by integration of sh4 and qSH3 alleles. Complementary manipulation of panicle shape and seed shattering results in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3 -controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3 , which together led to the loss of shattering.Proceedings of the National Academy of Sciences, 2022年06月, Proceedings of the National Academy of Sciences, 119(26) (26), 英語[査読有り]研究論文（学術雑誌）
- The Kansai Plant Protection Society, 2022年05月, 関西病虫害研究会報, 64, 75 - 80, 日本語[査読有り]研究論文（学術雑誌）
- Japanese Society for Horticultural Science, 2022年, The Horticulture Journal, 91(1) (1), 33 - 41, 英語[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media LLC, 2021年06月, Plant Reproduction, 34(3) (3), 255 - 266, 英語[査読有り]研究論文（学術雑誌）
- Summary Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon‐targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome‐wide single‐nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.Wiley, 2020年11月, The Plant Journal, 104(6) (6), 1551 - 1567, 英語[査読有り]研究論文（学術雑誌）
- ウメ(Prunus mume)はPrunus属の果樹であり,300以上の品種が東アジアを中心に分布しているが,日本の実ウメ,小ウメ,花ウメおよび台湾由来のウメもこれらに含まれる.そこで,日本と台湾のウメの過去の集団動態を推定するために,53品種(実ウメ20品種,小ウメ8品種,花ウメ20品種,台湾5品種)のSSRマーカー20座における遺伝子型のデータセットに基づき,近似ベイズ計算(approximate Bayesian computation)を用いた解析を行った.まず,6つの起こりうる分岐シナリオから最適モデル(事後確率0.501)を推定し,そのモデルの集団動態に関するパラメーターの中央値を算出した.また,ウメの世代時間を7年(生殖可能年齢)と仮定し,世代数を年代に換算した.最適モデルでは,日本と台湾の集団が10360年(95%信頼区間:2079-56910年)前に初めに分岐し,その後3633年(95%信頼区間:1218-12740年)前に日本の集団から花ウメが分かれ,最終的に2387年(95%信頼区間:623-6258年)前に実ウメと小ウメが分化したと推定された.これらの分岐年代は粗く推定されたものであるが,異なった気候条件を伴う地理的隔離により日本と台湾のウメが分化し,その後日本で人の用途に応じて花ウメ,実ウメ,小ウメが最近分化したことを示唆する結果となった.近畿作物・育種研究会, 2020年, 作物研究, 65, 31 - 35, 英語[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media LLC, 2019年06月, Theoretical and Applied Genetics, 132(9) (9), 2615 - 2623, 英語[査読有り]研究論文（学術雑誌）
- 2019年03月, Journal of general plant pathology, 英語[査読有り]研究論文（学術雑誌）
- Elsevier BV, 2019年02月, Scientia Horticulturae, 246, 693 - 699[査読有り]研究論文（学術雑誌）
- Japanese society for horticultural science, 2019年, The horticulture journal, 88(2) (2), 222 - 231, 英語[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media LLC, 2018年04月, Journal of General Plant Pathology, 84(3) (3), 202 - 207[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media LLC, 2018年03月, Tree Genetics & Genomes, 14(2) (2)[査読有り]研究論文（学術雑誌）
- Flower bud development and the timing of blooming are mainly affected by genotype-dependent chilling requirements (CRs) during endodormancy and subsequent heat requirements (HRs) during ecodormancy. However, little information is available regarding the responses of flower buds to temperatures during endodormancy and ecodormancy in japanese apricot. We exposed japanese apricot ‘Nanko’ trees to various temperatures to estimate the CRs and HRs using development index (DVI) models specific for the endodormant (DVIendo) and ecodormant (DVIeco) stages. These models were based on the experimentally determined development rate (DVR). The DVRendo value was calculated as the reciprocal of the chilling time required to break endodormancy. The relationship between the DVRendo value and temperature was estimated using a three-dimensional curve. Our results indicated that 5–6 °C was the most effective temperature for breaking endodormancy in ‘Nanko’ flower buds. Additionally, exposure to −3 °C negatively affected endodormancy release, whereas 15 °C had no effect. We also determined that the DVReco values for temperatures between 5 and 20 °C were the reciprocal values of the time required for blooming after endodormancy release. The values outside this range were estimated using linear functions. The DVI was defined as the sum of the DVR values ranging from 0 to 1. Models for predicting the blooming date were constructed using the functions of sequentially combined DVIendo and DVIeco models. The accuracy of each model was assessed by comparing the predicted and actual blooming dates. The prediction of the model in which DVIeco = 1 corresponded to a 40% blooming level and DVIeco = 0 was set to DVIendo = 0.5 had the lowest root mean square error (RMSE) value (i.e., 3.11) for trees in commercial orchards exposed to different climates. Our results suggest that the developed model may have practical applications.American Society for Horticultural Science, 2017年03月, HortScience, 52(3) (3), 366 - 370[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media LLC, 2013年02月, Nature Genetics, 45(4) (4), 462 - 465[査読有り]研究論文（学術雑誌）
- 日本学術振興会, 科学研究費助成事業, 若手研究, 和歌山県農林水産部(農業試験場、果樹試験場、畜産試験場、林業試験場及び水産試験場), 2018年04月01日 - 2021年03月31日ウメ葉縁えそ病を題材とした果樹ウイルス病害抵抗性に関与する遺伝的因子の同定本研究ではウメのウイルス病害である葉縁えそ病抵抗性に関与する遺伝因子の同定に向け、接ぎ木接種による病徴・ウイルス保毒状況の調査、網羅的発現解析による感受性および非感受性品種間の発現変動遺伝子群の検出ならびにゲノムワイド関連解析（GWAS）による抵抗性に関する遺伝領域の探索を試みた。 その結果、果実収穫用に栽培されている「実ウメ」品種群と比較して、アンズやスモモとの交雑由来の品種群で症状やウイルス保毒濃度ともに少ない傾向が認められた。しかし、その原因因子の解明には至らなかった。今後これらの品種と実ウメとの交雑後代を獲得し、原因因子の遺伝様式解明に引き続き取組む。