Etsushi Kumagai

Genome-wide association mapping for phenotypic plasticity in rice

Phenotypic plasticity of plants in response to environmental changes is important for adapting to changing climate. Less attention has been paid to exploring the advantages of phenotypic plasticity in resource-rich environments to enhance the productivity of agricultural crops. Here, we examined genetic variation for phenotypic plasticity in indica rice (Oryza sativa L.) across two diverse panels: (1) a Phenomics of Rice Adaptation and Yield (PRAY) population comprising 301 accessions; and (2) a Multi-parent Advanced Generation Inter-Cross (MAGIC) indica population comprising 151 accessions. Altered planting density was used as a proxy for elevated atmospheric CO2 response. Low planting density significantly increased panicle weight per plant compared with normal density, and the magnitude of the increase ranged from 1.10 to 2.78 times among accessions for the PRAY population and from 1.05 to 2.45 times for the MAGIC population. Genome-wide-association studies validate three Environmental Responsiveness (ER) candidate alleles (qER1-3) that were associated with relative response of panicle weight to low density. Two of these alleles were tested in 13 genotypes to clarify their biomass responses during vegetative growth under elevated CO2 in Japan. Our study provides evidence for polymorphisms that control rice phenotypic plasticity in environments that are rich in resources such as light and CO2 .

Genetic Variations in Dry Matter Production, Nitrogen Uptake, and Nitrogen Use Efficiency in the AA Genome Oryza Species Grown under Different Nitrogen Conditions

Abstract To clarify the genotypic variation of nitrogen (N) response in the AA genome Oryza species, we investigated dry matter production, N uptake, N and water use efficiencies (NUE and WUE), bleeding sap rate (BR), and root morphological traits at vegetative stage in 6 cultivars and 4 strains of 6 species (O. sativa, O. glaberrima, O. barthii, O. nivara, O. meridionalis, and O. rufipogon) grown under standard N (SN) and low N (LN) conditions. Some wild Oryza strains and O. glaberrima showed high dry matter production under both N conditions. In most plants, total dry weight decreased and root dry weight increased under the LN condition, resulting in decreased top-root ratio. In japonica cultivars of O. sativa, however, these traits were unaffected by the N condition. There were no significant differences in WUE with plant species or N conditions. In all plants, however, NUE was higher in the LN than SN condition, and was conspicuously high in most wild Oryza species and O. glaberrima. Some of them showed increased capacity of nitrate-N (NO3-N) uptake under the LN condition. In cultivars and strains with a high NUE, root dry weight, root surface area, and BR were also higher under the LN condition. These results suggest that a high NUE is associated with the development of a root system, increased BR, and probably increased capacity of NO3-N uptake. This study revealed the presence of superior wild Oryza strains for growth under LN that may be a promising genetic resource for low N-input agriculture.

Effects of elevated CO2 concentration on growth and photosynthesis of Chinese yam under different temperature regimes

Abstract Chinese yam (‘yam’) was grown at different carbon dioxide concentrations ([CO2]), namely, ambient and elevated (ambient + 200 μmol mol−1), under low- and high-temperature regimes in summer and autumn, separately. For comparison, rice was also grown under these conditions. Mean air temperatures in the low- and high-temperatures were respectively 24.1 and 29.1 °C in summer experiment and 20.2 and 24.9 °C in autumn experiment. In summer experiment, yam vine length, leaf area, leaf dry weight (DW), and total DW were significantly higher under elevated [CO2] than ambient [CO2] in both temperature regimes. Additionally, number of leaves, vine DW, and root DW were significantly higher under elevated [CO2] than under ambient [CO2] in the low-temperature regime. In autumn experiment, tuber DW was significantly higher under elevated [CO2] than under ambient [CO2] in the high-temperature regime. These results demonstrate that yam shows positive growth responses to elevated [CO2]. Analysis of variance revealed that significant effect of [CO2] × air temperature interaction on yam total DW was not detected. Elevated-to-ambient [CO2] ratios of all growth parameters in summer experiment were higher in yam than in rice. The results suggest that the contribution of elevated [CO2] is higher in yam than in rice under summer. Yam net photosynthetic rate was significantly higher under elevated [CO2] than under ambient [CO2] in both temperature regimes in summer. Elevated [CO2] significantly affected on the rate in yam but not in rice in both experiments. These findings indicate that photosynthesis responds more readily to elevated [CO2] in yam than in rice.

Finlay-Wilkinson's regression coefficient as a pre-screening criterion for yield responsiveness to elevated atmospheric CO2 concentration in crops.

The rising atmospheric CO2 concentration ([CO2 ]) can increase crop productivity, but there are likely to be intraspecific variations in the response. To meet future world food demand, screening for genotypes with high [CO2 ] responsiveness will be a useful option, but there is no criterion for high [CO2 ] responsiveness. We hypothesized that the Finlay-Wilkinson regression coefficient (RC) (for the relationship between a genotypes yield versus the mean yield of all genotypes in a specific environment) could serve as a pre-screening criterion for identifying genotypes that respond strongly to elevated [CO2 ]. We collected datasets on the yield of 6 rice and 10 soybean genotypes along environmental gradients and compared their responsiveness to elevated [CO2 ] based on the regression coefficients (i.e. the increases of yield per 100 µmol mol-1 [CO2 ]) identified in previous reports. We found significant positive correlations between the RCs and the responsiveness of yield to elevated [CO2 ] in both rice and soybean. This result raises the possibility that the coefficient of the Finlay-Wilkinson relationship could be used as a pre-screening criterion for [CO2 ] responsiveness.

Leaf Photosynthesis and Its Genetic Improvement from the Perspective of Energy Flow and CO2 Diffusion

Abstract Single-leaf photosynthesis is a fundamental process in plant biomass production, and is a major research topic in crop physiology. This paper reviews the recent achievements of research on the physiological determinants of the photosynthetic capacity from the perspective of energy flow and CO2 diffusion. Measurement of chlorophyll fluorescence is a popular method to diagnose the function of photosystem II, and is useful to assess the susceptibility to photoinhibition and allocation of energy, which are keys to improving both stress resistance and photosynthetic productivity. Mesophyll conductance (gm) is the conductance to CO2 diffusion from intercellular airspaces to the chloroplast, and was long thought to be determined by leaf anatomical properties. However, recent studies showed that environmental conditions affect g m. It is possible that g m is affected by the gating of the CO2-permeable aquaporins (cooporins). Stomatal morphology is revealed to be an important factor affecting gas exchange both in crop plants and inArabidopsis thaliana.The knowledge of the stomatal differentiation in Arabidopsis will be applicable to various crops. gm, stomatal conductance (gs) and leaf nitrogen content are the main factors to cause difference in leaf photosynthesis among rice lines, and recent activities are conducted to find genes to manipulate these factors. Although the association of leaf photosynthesis with crop productivity still has a large ‘missing link’, these achievements strongly suggest that the leaf photosynthetic capacity can be genetically improved in crop species.

Probabilistic Risk Assessment of the Rice Cropping Schedule for Central Hokkaido, Japan

AbstractA framework for the probabilistic risk assessment of the rice (Oryza sativa L.) cropping schedule (PRARCS) is presented. The method accounts for interannual meteorological variation, as opposed to the traditional cultivation schedule planning method, which is based on the seasonal change in long-term average air temperature. PRARCS uses an arbitrary developmental index model to estimate the timing of the heading stage, which is required to assess the risks of cold or heat damage and productivity. All results of risk assessment and productivity are linked to transplanting date as the most important cultivation practice for irrigated rice paddies. The results of assessments using PRARCS at Iwamizawa, central Hokkaido, Japan, indicated that for the current climate the optimal transplanting period is the end of May, and this corresponds to the actual transplanting dates used and the increasing risks and decreasing productivity with earlier or later transplanting. Assessment using projected climatic da...

Effects of elevated CO2 concentration on bulbil germination and early seedling growth in Chinese yam under different air temperatures

Abstract The present study investigated the effects of elevated carbon dioxide concentration ([CO2]) and air temperature on the germination of seed bulbils and the seedling vigour of two Chinese yam lines. Plants were grown under two [CO2] levels, ambient and elevated (ambient + 200 μmol mol−1), and two mean air temperature regimes, 22.2 °C (ambient + 1.4 °C) and 25.6 °C (ambient + 5.2 °C). Elevated [CO2] did not affect bulbil germination under both air temperature regimes. During the early growth stage, the dry weight (DW) of leaves, vines, shoots, roots, belowground parts (roots + tubers) and whole plants were higher under elevated [CO2] than ambient [CO2] for both lines under the low- and high-temperature regimes. The values of vigour indexes (index I = germination % × seedling length and index II = germination % × seedling DW) were also higher under elevated [CO2] than ambient [CO2] for both lines. These results indicated that Chinese yam seedlings respond positively to elevated [CO2] during the early growth stage. The above:belowground DW ratios were lower under elevated [CO2] than ambient [CO2] in seedlings with very small new tubers for both yam lines, indicating that elevated [CO2] strongly affected the root growth in the early growth stage. The DWs of post-treatment seed bulbils were higher in the elevated [CO2] under both air temperature regimes. The results showed that Chinese yam used a smaller amount of the reserves in seed bulbils under elevated [CO2] than under ambient [CO2].

Effects of elevated atmospheric CO2 concentration on morphology of leaf blades in Chinese yam

ABSTRACT The effects of elevated carbon dioxide concentration on the morphology of leaf blades in two Chinese yam lines under different temperature conditions were determined. Plants were grown under two [CO2] levels, ambient (about 400 µmol mol−1) and elevated (ambient + 200 µmol mol−1) in the daytime, and two mean air temperature regimes, approximately ambient temperature (22.2°C) and high temperature (25.6°C). The palisade layer was thicker under elevated [CO2] than under ambient [CO2] in both temperature regimes, and the whole yam leaf blade was thicker under elevated [CO2] than under ambient [CO2] in the approximately ambient temperature regime. The numbers of chloroplasts per palisade cell and spongy cell as well as per unit profile area of palisade cell, number of starch grains per chloroplast, profile area of the starch grain, and starch-to-chloroplast area ratio in both palisade and spongy cells were higher under elevated [CO2] than under ambient [CO2] in both temperature regimes. Furthermore, the stomatal density on the abaxial side of the leaf blade in Chinese yam was greater under elevated [CO2] than under ambient [CO2] under both temperature regimes, and stomatal-pore length was higher under elevated [CO2] than under ambient [CO2] in the approximately ambient temperature regime. These results indicate that elevated [CO2] positively affects the photosynthetic apparatus. The results of this study provide information for understanding the response characteristics of the leaf blade under elevated [CO2] and a possible explanation for the positive photosynthetic responses of Chinese yam to elevated [CO2] in our previous study. List of Abbreviations:[CO2]: carbon dioxide concentration