Upcycling rice yield trial data using a weather-driven crop growth model.

Efficient plant breeding plays a significant role in increasing crop yields and attaining food security under climate change. Screening new cultivars through yield trials in multi-environments has improved crop yields, but the accumulated data from these trials has not been effectively upcycled. We propose a simple method that quantifies cultivar-specific productivity characteristics using two regression coefficients: yield-ability (ß) and yield-plasticity (α). The recorded yields of each cultivar are expressed as a unique linear regression in response to the theoretical potential yield (Yp) calculated by a weather-driven crop growth model, called as the "YpCGM method". We apply this to 72510 independent datasets from yield trials of rice that used 237 cultivars measured at 110 locations in Japan over 38 years. The YpCGM method can upcycle accumulated yield data for use in genetic-gain analysis and genome-wide-association studies to guide future breeding programs for developing new cultivars suitable for the world's changing climate.

DeepCGP: A Deep Learning Method to Compress Genome-Wide Polymorphisms for Predicting Phenotype of Rice.

Genomic selection (GS) is expected to accelerate plant and animal breeding. During the last decade, genome-wide polymorphism data have increased, which has raised concerns about storage cost and computational time. Several individual studies have attempted to compress the genome data and predict phenotypes. However, compression models lack adequate quality of data after compression, and prediction models are time consuming and use original data to predict the phenotype. Therefore, a combined application of compression and genomic prediction modeling using deep learning could resolve these limitations. A Deep Learning Compression-based Genomic Prediction (DeepCGP) model that can compress genome-wide polymorphism data and predict phenotypes of a target trait from compressed information was proposed. The DeepCGP model contained two parts: (i) an autoencoder model based on deep neural networks to compress genome-wide polymorphism data, and (ii) regression models based on random forests (RF), genomic best linear unbiased prediction (GBLUP), and Bayesian variable selection (BayesB) to predict phenotypes from compressed information. Two datasets with genome-wide marker genotypes and target trait phenotypes in rice were applied. The DeepCGP model obtained up to 99% prediction accuracy to the maximum for a trait after 98% compression. BayesB required extensive computational time among the three methods, and showed the highest accuracy; however, BayesB could only be used with compressed data. Overall, DeepCGP outperformed state-of-the-art methods in terms of both compression and prediction. Our code and data are available at https://github.com/tanzilamohita/DeepCGP.

Diurnal regulation of rice N uptake ability under interrupted N supply.

Plants take up nitrogen (N) both day and night. The diurnal variation in N uptake results from interactions between aboveground and belowground tissues. We examined the long-term effects of interrupted N supply (day only or night only) under hydroponic conditions to test whether plant acclimatisation response to the interrupted N supply differs by day or night. Seedlings experienced 32 days under daytime-fed (DF), night-time-fed (NF), or continuous (CT) N supply. The root N uptake rate (NUR) differed between DF and NF from day 3 of treatment, after which NUR was significantly increased (by up to 82%) in DF and NF plants. The increased NUR during each half-day did not fully compensate for lost access to N during the other half-day, resulting in lower N accumulation by the end of the treatment. The reduction was smaller in DF plants than NF plants. The underlying mechanism of diurnal variation of N uptake is discussed in terms of transpiration demand and gene expression in roots.

Internal transport of CO2 from the root-zone to plant shoot is pH dependent.

We investigated the fate of carbon dioxide (CO2 ) absorbed by roots or internally produced by respiration using gas exchange and stable isotopic labeling. CO2 efflux from detached leaves supplied with bicarbonate/CO2 solutions was followed over six cycles. CO2 effluxes were detected when bicarbonate solution at high pH was used, corresponding to 71-85% of the expected efflux. No CO2 efflux was detected when CO2 solutions at low pH were used but CO2 efflux was subsequently detected as soon as bicarbonate solutions at high pH were supplied. By sealing the leaf and petiole in a plastic bag to reduce diffusion to the atmosphere, a small CO2 efflux signal (14-30% of the expected efflux) was detected suggesting that CO2 in the xylem stream can readily escape to the atmosphere before reaching the leaf. When the root-zones of intact plants were exposed to CO2 solutions, a significant efflux from leaf surface was observed (13% of the expected efflux). However, no signal was detected when roots were exposed to a high pH bicarbonate solution. Isotopic tracer experiments confirmed that CO2 supplied to the root-zone was transported through the plant and was readily lost to the atmosphere. However, little 13 C moved to the shoot when roots were exposed to bicarbonate solutions at pH 8, suggesting that bicarbonate does not pass into the xylem.

Prescreening in large populations as a tool for identifying elevated CO2-responsive genotypes in plants.

Elevated atmospheric CO2 concentration (e[CO2]) can stimulate the photosynthesis and productivity of C3 species including food and forest crops. Intraspecific variation in responsiveness to e[CO2] can be exploited to increase productivity under e[CO2]. However, active selection of genotypes to increase productivity under e[CO2] is rarely performed across a wide range of germplasm, because of constraints of space and the cost of CO2 fumigation facilities. If we are to capitalise on recent advances in whole genome sequencing, approaches are required to help overcome these issues of space and cost. Here, we discuss the advantage of applying prescreening as a tool in large genome×e[CO2] experiments, where a surrogate for e[CO2] was used to select cultivars for more detailed analysis under e[CO2] conditions. We discuss why phenotypic prescreening in population-wide screening for e[CO2] responsiveness is necessary, what approaches could be used for prescreening for e[CO2] responsiveness, and how the data can be used to improve genetic selection of high-performing cultivars. We do this within the framework of understanding the strengths and limitations of genotype-phenotype mapping.

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 .

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 genotype's 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.

Combining mapping of physiological quantitative trait loci and transcriptome for cold tolerance for counteracting male sterility induced by low temperatures during reproductive stage in rice.

Male sterility induced by low temperatures (LTs) during the reproductive stage is a major constraint for temperate zone rice. To detect physiological quantitative trait loci (QTLs), we modeled genotypic variation in the physiological processes involved in low temperature spikelet sterility on the basis of anther length (AL), a proxy for microspore and pollen grain number per anther. The model accounted for 83% of the genotypic variation in potential AL at normal temperature and the ability to maintain AL at LT. We tested the model on 208 recombinant inbred lines of cold-tolerant 'Tohoku-PL3' (PL3) × cold-sensitive 'Akihikari' (AH) for 2 years. QTLs for spikelet fertility (FRT) at LT were detected on chromosomes 5 (QTL for Cold Tolerance at Reproductive stage, qCTR5) and 12 (qCTR12). qCTR12 was annotated with the ability to maintain AL under LTs. qCTR5 was in a region shared with QTLs for culm length and heading date. Genome-wide expression analysis showed 798 genes differentially expressed in the spikelets between the parents at LTs. Of these, 12 were near qCTR5 and 23 were near qCTR12. Gene expression analysis confirmed two candidate genes for qCTR5 (O-methyltransferase ZRP4, Os05g0515600; beta-1,3-glucanase-like protein, Os05g0535100) and one for qCTR12 (conserved hypothetical protein, Os12g0550600). Nucleotide polymorphisms (21 deletions, 2 insertions and 10 single nucleotide polymorphisms) in PL3 were found near the candidate conserved hypothetical protein (Os12g0550600) and upstream in PL3, but not in AH. Haplotype analysis revealed that this gene came from 'Kuchum'. The combination of mapping physiological QTLs with gene expression analysis can be extended to identify other genes for abiotic stress response in cereals.

Phenotypic Plasticity Conditions the Response of Soybean Seed Yield to Elevated Atmospheric CO2 Concentration.

Selection for cultivars with superior responsiveness to elevated atmospheric CO2 concentrations (eCO2) is a powerful option for boosting crop productivity under future eCO2. However, neither criteria for eCO2 responsiveness nor prescreening methods have been established. The purpose of this study was to identify traits responsible for eCO2 responsiveness of soybean (Glycine max). We grew 12 Japanese and U.S. soybean cultivars that differed in their maturity group and determinacy under ambient CO2 and eCO2 for 2 years in temperature gradient chambers. CO2 elevation significantly increased seed yield per plant, and the magnitude varied widely among the cultivars (from 0% to 62%). The yield increase was best explained by increased aboveground biomass and pod number per plant. These results suggest that the plasticity of pod production under eCO2 results from biomass enhancement, and would therefore be a key factor in the yield response to eCO2, a resource-rich environment. To test this hypothesis, we grew the same cultivars at low planting density, a resource-rich environment that improved the light and nutrient supplies by minimizing competition. Low planting density significantly increased seed yield per plant, and the magnitude ranged from 5% to 105% among the cultivars owing to increased biomass and pod number per plant. The yield increase due to low-density planting was significantly positively correlated with the eCO2 response in both years. These results confirm our hypothesis and suggest that high plasticity of biomass and pod production at a low planting density reveals suitable parameters for breeding to maximize soybean yield under eCO2.

Cooling water before panicle initiation increases chilling-induced male sterility and disables chilling-induced expression of genes encoding OsFKBP65 and heat shock proteins in rice spikelets.

In rice (Oryza sativa L.), chilling-induced male sterility increased when plants experienced low water temperature (Tw , 18 °C for 14 d) before panicle initiation. The number of mature pollen grains after chilling at the booting stage (12 °C for 5 d) was only 45% of total pollen grains in low-Tw plants, whereas it was 71% in normal-Tw plants (Tw not controlled; approximately 23 °C under air temperature of 26 °C/21 °C, day/night). Microarray and quantitative PCR analyses showed that many stress-responsive genes (including OsFKBP65 and genes encoding the large heat shock protein OsHSP90.1, heat-stress transcription factors and many small heat shock proteins) were strongly up-regulated by chilling in normal-Tw spikelets, but were unaffected or even down-regulated by chilling in low-Tw spikelets. OsAPX2 and genes encoding some other antioxidant enzymes were also significantly down-regulated by low Tw in chilled spikelets. The levels of lipid peroxidation products (malondialdehyde equivalents) were significantly increased in low-Tw spikelets by chilling. Ascorbate peroxidase activity in chilled spikelets was significantly lower in low-Tw plants than in normal-Tw plants. Our data suggest that an OsFKBP65-related chilling response, which protects proteins from oxidative damage, is indispensable for chilling tolerance but is lost in low-Tw spikelets.

Planting geometry as a pre-screening technique for identifying CO2 responsive rice genotypes: a case study of panicle number.

Identifying CO(2) responsive genotypes is a major target for enhancing crop productivity under future global elevated atmospheric CO(2) concentration ([CO(2)]). However, [CO(2)]-fumigation facilities are extremely expensive and are not easily accessible, and are limited in space for large-scale screening. Hence, reliable donors for initiating [CO(2)]-responsive breeding programs are not in place for crops, including rice. We propose a simple and novel phenotyping method for identifying [CO(2)]-responsive genotypes, and quantify the responsiveness to low planting density over 4-year trials across both temperate and tropical conditions. Panicle number per plant is the key determinant of grain yield and hence was the focus trait across all our trials. In temperate climate, a 3-season field screening using 127 diverse rice genotypes and employing two planting densities (normal and low density) was conducted. Two japonica genotypes were selected based on their higher responsiveness to low planting density as candidates for validating the proposed phenotyping protocol as a pre-screen for [CO(2)]-responsiveness. The approach using the two selected candidates and three standard genotypes was confirmed using a free-air CO(2) enrichment facility and temperature gradient chambers under elevated [CO(2)]. In tropical climate, we grew three rice cultivars, previously identified for their [CO(2)]-responsiveness, at two planting densities. The experiments provided confirmation that responsiveness to low planting density was correlated with that of [CO(2)]-responsiveness across both the temperate and tropical conditions. The planting density would be useful pre-screening method for testing large panels of diverse germplasm at low cost complemented by available CO(2) -control facilities for final validation of candidates from the pre-screens.

Lower responsiveness of canopy evapotranspiration rate than of leaf stomatal conductance to open-air CO2 elevation in rice.

An elevated atmospheric CO2 concentration ([CO2 ]) can reduce stomatal conductance of leaves for most plant species, including rice (Oryza sativa L.). However, few studies have quantified seasonal changes in the effects of elevated [CO2 ] on canopy evapotranspiration, which integrates the response of stomatal conductance of individual leaves with other responses, such as leaf area expansion, changes in leaf surface temperature, and changes in developmental stages, in field conditions. We conducted a field experiment to measure seasonal changes in stomatal conductance of the uppermost leaves and in the evapotranspiration, transpiration, and evaporation rates using a lysimeter method. The study was conducted for flooded rice under open-air CO2 elevation. Stomatal conductance decreased by 27% under elevated [CO2 ], averaged throughout the growing season, and evapotranspiration decreased by an average of 5% during the same period. The decrease in daily evapotranspiration caused by elevated [CO2 ] was more significantly correlated with air temperature and leaf area index (LAI) rather than with other parameters of solar radiation, days after transplanting, vapor-pressure deficit and FAO reference evapotranspiration. This indicates that higher air temperatures, within the range from 16 to 27 °C, and a larger LAI, within the range from 0 to 4 m(2)  m(-2) , can increase the magnitude of the decrease in evapotranspiration rate caused by elevated [CO2 ]. The crop coefficient (i.e. the evapotranspiration rate divided by the FAO reference evapotranspiration rate) was 1.24 at ambient [CO2 ] and 1.17 at elevated [CO2 ]. This study provides the first direct measurement of the effects of elevated [CO2 ] on rice canopy evapotranspiration under open-air conditions using the lysimeter method, and the results will improve future predictions of water use in rice fields.

Food security and climate change: on the potential to adapt global crop production by active selection to rising atmospheric carbon dioxide.

Agricultural production is under increasing pressure by global anthropogenic changes, including rising population, diversion of cereals to biofuels, increased protein demands and climatic extremes. Because of the immediate and dynamic nature of these changes, adaptation measures are urgently needed to ensure both the stability and continued increase of the global food supply. Although potential adaption options often consider regional or sectoral variations of existing risk management (e.g. earlier planting dates, choice of crop), there may be a global-centric strategy for increasing productivity. In spite of the recognition that atmospheric carbon dioxide (CO(2)) is an essential plant resource that has increased globally by approximately 25 per cent since 1959, efforts to increase the biological conversion of atmospheric CO(2) to stimulate seed yield through crop selection is not generally recognized as an effective adaptation measure. In this review, we challenge that viewpoint through an assessment of existing studies on CO(2) and intraspecific variability to illustrate the potential biological basis for differential plant response among crop lines and demonstrate that while technical hurdles remain, active selection and breeding for CO(2) responsiveness among cereal varieties may provide one of the simplest and direct strategies for increasing global yields and maintaining food security with anthropogenic change.

Diurnal and seasonal variations in stomatal conductance of rice at elevated atmospheric CO(2) under fully open-air conditions.

Understanding of leaf stomatal responses to the atmospheric CO(2) concentration, [CO(2)], is essential for accurate prediction of plant water use under future climates. However, limited information is available for the diurnal and seasonal changes in stomatal conductance (g(s)) under elevated [CO(2)]. We examined the factors responsible for variations in g(s) under elevated [CO(2)] with three rice cultivars grown in an open-field environment under flooded conditions during two growing seasons (a total of 2140 individual measurements). Conductance of all cultivars was generally higher in the morning and around noon than in the afternoon, and elevated [CO(2)] decreased g(s) by up to 64% over the 2 years (significantly on 26 out of 38 measurement days), with a mean g(s) decrease of 23%. We plotted the g(s) variations against three parameters from the Ball-Berry model and two revised versions of the model, and all parameters explained the g(s) variations well at each [CO(2)] in the morning and around noon (R(2) > 0.68), but could not explain these variations in the afternoon (R(2) < 0.33). The present results provide an important basis for modelling future water use in rice production.

Acclimation of nitrogen uptake capacity of rice to elevated atmospheric CO2 concentration.

BACKGROUND AND AIMS: Nitrogen (N) is a major factor affecting yield gain of crops under elevated atmospheric carbon dioxide concentrations [CO(2)]. It is well established that elevated [CO(2)] increases root mass, but there are inconsistent reports on the effects on N uptake capacity per root mass. In the present study, it was hypothesized that the responses of N uptake capacity would change with the duration of exposure to elevated [CO(2)]. METHODS: The hypothesis was tested by measuring N uptake capacity in rice plants exposed to long-term and short-term [CO(2)] treatments at different growth stages in plants grown under non-limiting N conditions in hydroponic culture. Seasonal changes in photosynthesis rate and transpiration rate were also measured. KEY RESULTS: In the long-term [CO(2)] study, leaf photosynthetic responses to intercellular CO(2) concentration (Ci) were not affected by elevated [CO(2)] before the heading stage, but the initial slope in this response was decreased by elevated [CO(2)] at the grain-filling stage. Nitrate and ammonium uptake capacities per root dry weight were not affected by elevated [CO(2)] at panicle initiation, but thereafter they were reduced by elevated [CO(2)] by 31-41 % at the full heading and mid-ripening growth stages. In the short-term study (24 h exposures), elevated [CO(2)] enhanced nitrate and ammonium uptake capacities at the early vegetative growth stage, but elevated [CO(2)] decreased the uptake capacities at the mid-reproductive stage. CONCLUSIONS: This study showed that N uptake capacity was downregulated under long-term exposure to elevated [CO(2)] and its response to elevated [CO(2)] varied greatly with growth stage.

Genotypic variation in rice yield enhancement by elevated CO2 relates to growth before heading, and not to maturity group.

Maturity group (based on the number of days to maturity) is an important growth trait for determining crop productivity, but there has been no attempt to examine the effects of elevated [CO(2)] on yield enhancement of rice cultivars with different maturity groups. Since early-maturing cultivars generally show higher plant N concentration than late-maturing cultivars, it is hypothesized that [CO(2)]-induced yield enhancement might be larger for early-maturing cultivars than late-maturing cultivars. To test this hypothesis, the effects of elevated [CO(2)] on yield components, biomass, N uptake, and leaf photosynthesis of cultivars with different maturity groups were examined for 2 years using a free-air CO(2) enrichment (FACE). Elevated [CO(2)] significantly increased grain yield and the magnitude significantly differed among the cultivars as detected by a significant [CO(2)] x cultivar interaction. Two cultivars (one with early and one with late maturity) responded more strongly to elevated [CO(2)] than those with intermediate maturity, resulting mainly from increases in spikelet density. Biomass and N uptake at the heading stage were closely correlated with grain yield and spikelet density over [CO(2)] and cultivars. Our 2 year field trial rejected the hypothesis that earlier cultivars would respond more to elevated [CO(2)] than later cultivars, but it is revealed that the magnitude of the growth enhancement before heading is a useful criterion for selecting rice cultivars capable of adapting to elevated [CO(2)].