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NUMAGUCHI KojiGraduate School of Agricultural Science / Department of Bioresource ScienceAssistant Professor
Research activity information
■ Paper- Aug. 2026, Journal of Experimental Botany, English[Refereed]Scientific journal
- 2026, Breeding science, English[Refereed]Scientific journal
- 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.Nov. 2025, Molecular genetics and genomics : MGG, 300(1) (1), 108 - 108, English, International magazine[Refereed]Scientific journal
- Springer science and business media LLC, Nov. 2025, Plant molecular biology reporter, 44(1) (1), English[Refereed]Scientific journal
- Lead, Jul. 2025, アグリバイオ, 9(7) (7), 13 - 17, JapaneseGenomic regions for fruit trait in Japanese apricot[Invited]In book
- Japanese society for horticultural science, 2025, The horticulture journal, English[Refereed]Scientific journal
- Japanese Society for Horticultural Science, 2024, The Horticulture Journal, 93(4) (4), 344 - 352, English[Refereed]Scientific journal
- Springer Science and Business Media LLC, Aug. 2023, Molecular Genetics and Genomics, 298(6) (6), 1365 - 1375, English[Refereed]Scientific journal
- 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, Jul. 2023, Horticulturae, 9(8) (8), 872 - 872, English[Refereed]Scientific journal
- 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, May 2023, Molecular Genetics and Genomics, 298(4) (4), 943 - 953, English[Refereed]Scientific journal
- 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, Jun. 2022, Proceedings of the National Academy of Sciences, 119(26) (26), English[Refereed]Scientific journal
- The Kansai Plant Protection Society, May 2022, Annual Report of The Kansai Plant Protection Society, 64, 75 - 80, Japanese[Refereed]Scientific journal
- Japanese Society for Horticultural Science, 2022, The Horticulture Journal, 91(1) (1), 33 - 41, English[Refereed]Scientific journal
- Springer Science and Business Media LLC, Jun. 2021, Plant Reproduction, 34(3) (3), 255 - 266, English[Refereed]Scientific journal
- 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, Nov. 2020, The Plant Journal, 104(6) (6), 1551 - 1567, English[Refereed]Scientific journal
- Prunus mume Sieb. et Zucc. (conventionally called Japanese apricot, Chinese mei and mume) is a deciduous fruit tree species in the genus Prunus. More than 300 P. mume cultivars are distributed mainly in East Asia, including Japanese fruit, small-fruit and ornamental cultivars and Taiwanese cultivars. In order to estimate demographic history of three Japanese and one Taiwanese subpopulations, approximate Bayesian computation analysis was carried out using 20 SSR genotype datasets of 53 cultivars (20 fruit, 8 small-fruit, 20 ornamental and 5 Taiwanese cultivars). At first, the best fitting model (posterior probability: 0.501) was estimated among six probable scenarios, and median values of demographic parameters were computed. The generation time for P. mume cultivars was assumed to be seven years (full reproductive age) for time conversion. In the best scenario, Japanese and Taiwanese populations had first diverged at 10360 (95% confidence interval (CI): 2079-56910) years ago, followed by the separation of ornamental cultivars among Japanese populations at 3633 (95% CI: 1218-12740) years ago, and final differentiation between fruit and small-fruit cultivars at 2387 (95% CI: 623-6258) years ago. Although the divergence times were roughly estimated, the results suggest that Japanese and Taiwanese populations were separated through the geographic isolation with different climate conditions, and ornamental, fruit and small-fruit cultivars were recently differentiated based on human preference in Japan.Lead, The Society of Crop Science and Breeding in Kinki, Japan, 2020, Journal of Crop Research, 65, 31 - 35, English[Refereed]Scientific journal
- Springer Science and Business Media LLC, Jun. 2019, Theoretical and Applied Genetics, 132(9) (9), 2615 - 2623, English[Refereed]Scientific journal
- Lead, Mar. 2019, Journal of general plant pathology, English[Refereed]Scientific journal
- Elsevier BV, Feb. 2019, Scientia Horticulturae, 246, 693 - 699[Refereed]Scientific journal
- Lead, Japanese society for horticultural science, 2019, The horticulture journal, 88(2) (2), 222 - 231, English[Refereed]Scientific journal
- Springer Science and Business Media LLC, Apr. 2018, Journal of General Plant Pathology, 84(3) (3), 202 - 207[Refereed]Scientific journal
- Springer Science and Business Media LLC, Mar. 2018, Tree Genetics & Genomes, 14(2) (2)[Refereed]Scientific journal
- 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, Mar. 2017, HortScience, 52(3) (3), 366 - 370[Refereed]Scientific journal
- Springer Science and Business Media LLC, Feb. 2013, Nature Genetics, 45(4) (4), 462 - 465[Refereed]Scientific journal
- Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Early-Career Scientists, 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), 01 Apr. 2018 - 31 Mar. 2021Identification of genetic factors associated with resistance to a fruit tree viral disease, mume leaf-edge necrosisViral disease can be a fatal problem in fruit tree cultivation. We tried to reveal genetic factors for resistance to a viral disease in Japanese apricot, mume leaf-edge necrosis. Surveys for symptoms and viral infection in scions grafted to infected rootstocks, transctiptome analysis and genome-wide association study (GWAS) suggested that interspecific hybrids derived from crosses with apricot or Japanese plum was less affected with virses assciated with mume leaf-edge necrosis, compared to varieties for harvesting fruits. However, we could not identify genetic factors for resistance, because all the interspecific hybrids were F1 hybrids which may be heterozygous at candidate loci. The results showed that it is useful to utilize interspecific hybrids to give resistance to viral deseases in Japanese apricot.