IAM-naro focuses on a new approach from the field of machine and information research towards the realization of sustainable agriculture. Smart agriculture research is being actively pursued around the world to dramat...
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IAM-naro focuses on a new approach from the field of machine and information research towards the realization of sustainable agriculture. Smart agriculture research is being actively pursued around the world to dramatically improve agricultural productivity and to realize sustainable agriculture. In order to expand smart agriculture technology originated in Japan widely overseas, it is important to promote research and development with an awareness of international standardization.
Key messageGenotyping-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 directio...
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Key messageGenotyping-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 *** 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.
Germination represents the first major transition in plants, and seed dormancy influences germination timing. However, the mechanism by which variations in seed dormancy due to genetic variation or the maternal enviro...
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Germination represents the first major transition in plants, and seed dormancy influences germination timing. However, the mechanism by which variations in seed dormancy due to genetic variation or the maternal environment influence germination timing has not been studied in depth. In this study, the effects of temperature during seed maturation (maternal temperature) and genetic variation on weedy rice seedling emergence in a field environment were evaluated. The experiments were repeated for 4 years using seeds collected from weedy rice groups, which represented different degrees of seed dormancy. The maternal temperature was evaluated via the yearly variation in the field temperature. Genetic variation had a greater effect on seedling emergence during unfavourable seasons than during favourable seasons. A higher maternal temperature delayed seedling emergence during favourable seasons. The notable impact of global warming on seedling emergence has been confirmed over the past 15 years, and this impact will continue even under the sustainable CO2 emission scenario. Maternal effects have long-term effects on seedling emergence at relatively high maternal temperatures, and these effects may increase under global warming.
Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we construc...
Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated 'Asm2sv', identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes.
Genomic prediction is a promising strategy for enhancing crop breeding efficiency. Historical data of breeding and cultivation tests from geographically wide regions presumably contain rich information for training ge...
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Genomic prediction is a promising strategy for enhancing crop breeding efficiency. Historical data of breeding and cultivation tests from geographically wide regions presumably contain rich information for training genomic prediction models. Therefore, it is essential to explore methodologies to effectively handle such data. To improve the prediction accuracy of models using historical data, we incorporated a spatial model to account for spatial structures among field stations, in addition to conventional genomic prediction models. Targeting the rice heading date from historical data across Japan, we first constructed conventional genomic prediction models using genomic and/or meteorological elements as predictors. Next, we obtain the residual terms. Assuming that the residual terms were partly explained by the spatial effects assigned to each field station, a spatial model was applied to the residual terms and the spatial effects were calculated. Our genomic prediction models performed best when the genome, meteorological elements, and genome-meteorology interactions were included (model 3), and they performed second best when the genome and meteorological elements were included (model 2). For these genomic prediction models, residual terms were spatially biased and corrected for spatial effects. For the best model (model 3), the root mean squared errors (RMSE) of genomic prediction combined with spatial effects were approximately 3.6 days under tenfold cross-validation and approximately 5.1 days under leave-one-line-out cross-validation. The inclusion of the spatial effects improved the RMSEs by approximately 15% and 9% for the former and latter, respectively. Lines with highly improved predictions of the spatial effects were developed, mainly in the northern Tohoku region. The spatial effects were heterogeneous and regional patterns were detected. These findings imply that spatial effects are important not only for improving prediction performance but also for di
For producing numerous conidia of Diaporthe destruens, the fungus causing sweet potato foot rot, the fungus was cultured on heat-treated sweet potato leaves placed on an agar medium in natural light at 25 degrees C. A...
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For producing numerous conidia of Diaporthe destruens, the fungus causing sweet potato foot rot, the fungus was cultured on heat-treated sweet potato leaves placed on an agar medium in natural light at 25 degrees C. After 2-3 weeks, numerous pycnidia formed on the leaves and produced numerous droplet-like conidial masses, up to 410 times more conidia than on the medium without the leaves. Abundant conidia can thus be easily prepared to supply experimental studies on disease management.
Purple-fleshed sweetpotato (PFSP) clones containing anthocyanins can be classified into two types based on their aglycone composition: normal peonidin-dominant (Pn-type) and unusual cyanidin-dominant (Cy-type) types. ...
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Purple-fleshed sweetpotato (PFSP) clones containing anthocyanins can be classified into two types based on their aglycone composition: normal peonidin-dominant (Pn-type) and unusual cyanidin-dominant (Cy-type) types. It is unclear how cyanidin dominance is selected in crossbreeding. To improve the breeding scheme, this study investigated the frequency distribution of Cy-type PFSP from three cross combinations. Cross No. 1 was derived by crossing Pn-type purple-fleshed 'Purple Sweet Lord' and orange-fleshed '90IDN-47,' and Cross No.2 was from 'Purple Sweet Lord' and yellow-fleshed 'Miyaakari.' The cyanidin percentage of F1 plants differed significantly between these two crosses and Cross No.1 derived from '90IDN-47' was found to be a superior cross for enhancing Cy-type clones. Cross No.3 was derived from both Cy-type PFSP parents, 'Churakanasa' and 'Kyukei 90,143-4.' In Cross No.3, all F1 plants were classified as Cy-type with a cyanidin content of >= 55%. This result emphasizes the importance of Cy-type PFSP parents as breeding materials.
The hydration state of the alcohols was investigated using the extended molar absorption coefficient, which redefines the molar absorption coefficient as a differential coefficient of concentration. The extended molar...
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The hydration state of the alcohols was investigated using the extended molar absorption coefficient, which redefines the molar absorption coefficient as a differential coefficient of concentration. The extended molar absorption coefficient is a function of the concentration calculated from the difference in absorbance, and is consistent with the conventional molar absorption coefficient, allowing a complete quantitative comparison. The quantitative performance was verified using IR and NIR absorption spectra of aqueous solutions of monovalent alcohols (methanol, ethanol, 1-propanol, 2-propanol, and tert-butanol) that were soluble in water at any mixing ratio. Extended molar absorption coefficient spectra were calculated for the combination bands of water, which were further separated by multivariate curve resolution-alternating least squares (MCR-ALS) into molecular species with different peak wavenumbers: strongly hydrogen-bonded (SHB), weakly hydrogen-bonded (WHB), and free OH species. The number of water species that change when one alcohol molecule increases, i.e., the perturbed hydration number (PHN), was calculated by comparison with the conventional molar absorption coefficient of pure water. The calculated PHN indicates that the numbers of SHB and WHB species are reversed at approximately 20 wt%, and that the free OH species increase at higher alcohol concentrations and are more pronounced for alcohols with bulky alkyl groups. These results provide a quantitative answer to the long-debated question of anomalies in water-alcohol mixing.
In this study, we defined "paste tensile strength" as a gravity-based parameter in the uniaxial tensile direction of the food pastes. The objective was to evaluate the paste tensile strength effect on the pr...
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In this study, we defined "paste tensile strength" as a gravity-based parameter in the uniaxial tensile direction of the food pastes. The objective was to evaluate the paste tensile strength effect on the printability of a screw-based 3D printer. Twenty-one different pastes made of three different agricultural products (pumpkin, potato, and carrot) flakes with water added were extruded in a vertical downward line from a 2 mm-diameter syringe. Paste tensile strength was measured based on the weight or image of a fragment of the paste that fractured spontaneously under its weight, and determined to be in the range of 50-1,420 Pa. This property was, to a certain extent, correlated with the yield stress, consistency index, Young's modulus, hardness, and adherence. Stable 3D-printing was observed in the region where the weight-based paste tensile strength was approximately 500 +/- 150 Pa, independent of the type of food ingredient. It was indicated that the paste tensile strength acts on extrusion stability as a resistance force in the uniaxial tensile direction and contributes to shape stability in conjunction with yield stress. The paste tensile strength defined in this study is expected to serve as a novel evaluation index for screw-based 3D food printers.
Application of organic amendments (OAMs) in paddy fields has several advantages. One such advantage is the supply of essential nutrients to rice plants. However, the application of OAMs enriches microbial respiratory ...
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Application of organic amendments (OAMs) in paddy fields has several advantages. One such advantage is the supply of essential nutrients to rice plants. However, the application of OAMs enriches microbial respiratory substrates as decomposable organic matter, possibly promoting soil reduction and As dissolution after soil submersion. Therefore, this study evaluated the effect of prior aerobic decomposition of organic matter in OAM-mixed soils on the degree of soil reduction and As dissolution under anaerobic soil conditions. The soil used was from a non-polluted paddy field with a light clay texture and a moderate quantity of iron oxides. Rice straw compost and fermented chicken dung (FCD) were mixed with the paddy soil. The OAM-mixed soils were aerobically incubated for 5, 16, or 37 days. Carbon dioxide emissions during the aerobic period indicated that the organic matter in OAMs, especially FCD, was consumed by microbial aerobic respiration. Following aerobic incubation, the soils were anaerobically incubated for 10, 40, or 82 days. The addition of OAMs, particularly FCD, facilitated soil reduction and enhanced As dissolution from anaerobic soils. However, the effect of OAM addition on soil reduction and As dissolution after submersion was considerably weakened by a prolonged aerobic period because of the decrease in easily decomposable organic matter. Our results indicate that applying OAMs to soils earlier and maintaining aerobic conditions for a longer period can be an effective measure to attenuate OAM-enhanced As dissolution in submerged paddy soils. More comprehensive and field-scale investigations with various combinations of OAMs and soils are needed.
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