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Traditional rice varieties have been critical for developing improved stress-tolerant rice varieties. Tools to analyze the genome sequences of traditional varieties are accelerating the identification and deployment of genes conferring climate change resilience.

Lowland rice roots have a unique physiological response to drought because of their adaptation to flooded soil. Rice root attributes that facilitate growth under flooded conditions may affect rice response to drought, but the relative roles of root structural and functional characteristics for water uptake under drought in rice are not known. Morphological, anatomical, biochemical, and molecular attributes of soil-grown rice roots were measured to investigate the genotypic variability and genotype×environment interactions of water uptake under variable soil water regimes. Drought-resistant genotypes had the lowest night-time bleeding rates of sap from the root system in the field. Diurnal fluctuation predominated as the strongest source of variation for bleeding rates in the field and root hydraulic conductivity (Lp r) in the greenhouse, and was related to expression trends of various PIP and TIP aquaporins. Root anatomy was generally more responsive to drought treatments in drought-resistant genotypes. Suberization and compaction of sclerenchyma layer cells decreased under drought, whereas suberization of the endodermis increased, suggesting differential roles of these two cell layers for the retention of oxygen under flooded conditions (sclerenchyma layer) and retention of water under drought (endodermis). The results of this study point to the genetic variability in responsiveness to drought of rice roots in terms of morphology, anatomy, and function.

Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.

Levels of gene expression underpin organismal phenotypes 1 , 2 , but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown 1 , 2 . Here we assayed gene expression in rice ( Oryza sativa ) 3 , and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts 4 , 5 . Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions. Overall, more transcripts are conditionally neutral (2.83%) than are antagonistically pleiotropic 6 (0.04%), and transcripts that display lower levels of expression and stochastic noise 7 – 9 and higher levels of plasticity 9 are under stronger selection. Selection strength was further weakly negatively associated with levels of cis -regulation and network connectivity 9 . Our multivariate analysis suggests that selection acts on the expression of photosynthesis genes 4 , 5 , but that the efficacy of selection is genetically constrained under drought conditions 10 . Drought selected for earlier flowering 11 , 12 and a higher expression of OsMADS18 ( Os07g0605200 ), which encodes a MADS-box transcription factor and is a known regulator of early flowering 13 —marking this gene as a drought-escape gene 11 , 12 . The ability to estimate selection strengths provides insights into how selection can shape molecular traits at the core of gene action. Phenotypic selection analysis is used to estimate the type and strength of selection that acts on more than 15,000 transcripts in rice ( Oryza sativa ), which provides insight into the adaptive evolutionary role of selection on gene expression.

Changes in nutrient dose have dramatic effects on gene expression and development. One outstanding question is whether organisms respond to changes in absolute nutrient amount (moles) vs. its concentration in water (molarity). This question is particularly relevant to plants, as soil drying can alter nutrient concentration, without changing its absolute amount. To compare the effects of amount vs. concentration, we expose rice to a factorial matrix varying the dose of nitrogen ( N ) and water ( W ) over a range of combinations, and quantify transcriptome and phenotype responses. Using linear models, we identify distinct dose responses to either N -moles, W -volume, N -molarity ( N / W ), or their synergistic interaction ( N × W ). Importantly, genes whose expression patterns are best explained by N-dose and W interactions ( N / W or N × W ) in seedlings are associated with crop outcomes in replicated field trials. Such N-by-W responsive genes may assist future efforts to develop crops resilient to increasingly arid, low nutrient soils. Scarcity of water and nutrients limit crop yields. Here Swift et al. show that gene expression in rice responds differently to changes in the absolute amount of nitrogen available compared to nitrogen concentration and identify expression profiles associated with crop performance in arid, low-nutrient soils.

Background and AimsFormation of root cortical aerenchyma (RCA) can be induced by nutrient deficiency. In species adapted to aerobic soil conditions, this response is adaptive by reducing root maintenance requirements, thereby permitting greater soil exploration. One trade-off of RCA formation may be reduced radial transport of nutrients due to reduction in living cortical tissue. To test this hypothesis, radial nutrient transport in intact roots of maize (Zea mays) was investigated in two radiolabelling experiments employing genotypes with contrasting RCA.MethodsIn the first experiment, time-course dynamics of phosphate loading into the xylem were measured from excised nodal roots that varied in RCA formation. In the second experiment, uptake of phosphate, calcium and sulphate was measured in seminal roots of intact young plants in which variation in RCA was induced by treatments altering ethylene action or genetic differences.Key ResultsIn each of three paired genotype comparisons, the rate of phosphate exudation of high-RCA genotypes was significantly less than that of low-RCA genotypes. In the second experiment, radial nutrient transport of phosphate and calcium was negatively correlated with the extent of RCA for some genotypes.ConclusionsThe results support the hypothesis that RCA can reduce radial transport of some nutrients in some genotypes, which could be an important trade-off of this trait.

Background and Aims Root hydraulic limitations (i.e. intra-plant restrictions to water movement) may be related to crop performance under drought, and groupings in the hydraulic function of drought-tolerant and drought-susceptible rice (Oryza sativa) varieties have been previously reported. This study aimed to better understand the environmental and physiological relationships with rice root hydraulics under drought. Methods Xylem sap bleeding rates in the field (gsap g-1shoot) were measured on seasonal and diurnal time frames, during which time environmental conditions were monitored and physiological measurements were conducted. Complementary experiments on the effects of vapour pressure deficit (VPD) on root hydraulic conductivity and on transpiration rates of de-rooted tillers were conducted in growth chambers. Key Results The diurnal effects on bleeding rate were more closely related to irradiance than VPD, and VPD effects on root hydraulic conductivity measured on 21-day-old plants were due to effects on plant growth including root surface area, maximum root depth and root:shoot ratio. Leaf osmotic potential was related to the grouping of drought-tolerant and drought-susceptible varieties in rice root hydraulics, and these groupings were independent of differences in phenology. Low single-tiller bleeding rates were observed under high evapo-transpirational demand, higher bleeding rates were observed at more negative leaf osmotic potentials in drought-susceptible varieties, and drought-tolerant and susceptible varieties differed in the VPD-induced increase in transpiration rates of de-rooted tillers. Low root suberin amounts in some of the drought-susceptible varieties may have resulted in higher ion transport, as evidenced by higher sap K+ concentration and higher bleeding rates in those varieties. Conclusions These results provide evidence of the environmental effects on shoots that can influence root hydraulics. The consistent groupings of drought-tolerant and susceptible varieties suggest that traits affecting plant osmotic status may regulate root hydraulic response to drought in rice.

It is widely known that numerous adaptive responses of drought-stressed plants are stimulated by chemical messengers known as phytohormones. Jasmonic acid (JA) is one such phytohormone. But there are very few reports revealing its direct implication in drought related responses or its cross-talk with other phytohormones. In this study, we compared the morpho-physiological traits and the root proteome of a wild type (WT) rice plant with its JA biosynthesis mutant ( , disrupted in the allene oxide cyclase (AOC) gene, for insights into the role of JA under drought. The mutant had higher stomatal conductance, higher water use efficiency and higher shoot ABA levels under severe drought as compared to the WT. Notably, roots of were better developed compared to the WT under both, control and drought stress conditions. Root proteome was analyzed using the Tandem Mass Tag strategy to better understand this difference at the molecular level. Expectedly, AOC was unique but notably highly abundant under drought in the WT. Identification of other differentially abundant proteins (DAPs) suggested increased energy metabolism (i.e., increased mobilization of resources) and reactive oxygen species scavenging in under drought. Additionally, various proteins involved in secondary metabolism, cell growth and cell wall synthesis were also more abundant in roots. Proteome-guided transcript, metabolite, and histological analyses provided further insights into the favorable adaptations and responses, most likely orchestrated by the lack of JA, in the roots. Our results in are discussed in the light of JA crosstalk to other phytohormones. These results together pave the path for understanding the precise role of JA during drought stress in rice.

Drought is a major source of yield loss in the production of rice ( Oryza sativa L.), and cultivars that maintain yield under drought across environments and drought stress scenarios are urgently needed. Root phenotypes directly affect water interception and uptake, so plants with root systems optimized for water uptake under drought would likely exhibit reduced yield loss. Deeper nodal roots that have a low metabolic cost per length (i.e., cheaper roots) via smaller root diameter and/or more aerenchyma and that transport water efficiently through smaller diameter metaxylem vessels may be beneficial during drought. Subsets of the Rice Diversity Panel 1 and Azucena × IR64 recombinant inbred lines were grown in two greenhouse and two rainout shelter experiments under drought stress to assess their shoot, root anatomical, and root architectural phenotypes. Root traits and root trait plasticity in response to drought varied with genotype and environment. The best-performing groups in the rainout shelter experiments had less plasticity of living tissue area in nodal roots than the worst performing groups. Root traits under drought were partitioned into similar groups or clusters via the partitioning-around-medoids algorithm, and this revealed two favorable integrated root phenotypes common within and across environments. One favorable integrated phenotype exhibited many, deep nodal roots with larger root cross-sectional area and more aerenchyma, while the other favorable phenotype exhibited many, deep nodal roots with small root cross-sectional area and small metaxylem vessels. Deeper roots with high theoretical axial hydraulic conductance combined with reduced root metabolic cost contributed to greater shoot biomass under drought. These results reflect how some root anatomical and architectural phenes work in concert as integrated phenotypes to influence the performance of plant under drought stress. Multiple integrated root phenotypes are therefore recommended to be selected in breeding programs for improving rice yield across diverse environments and drought scenarios.

ABSTRACT Salinity is one of the major abiotic stresses affecting rice production, but the levels of salinity in a given field are not constant across the growing season. Since the level of salinity in a rice field can fluctuate, fast recovery from salinity stress may be a useful trait to improve rice productivity in salinity-prone areas. To develop a protocol to screen for salinity recovery, seedling stage hydroponic experiments were conducted to measure salinity recovery over time through both destructive and high-throughput image-based phenotyping. Seven rice varieties were included that had previously been classified as tolerant or susceptible to salinity. Following exposure to seedling stage salinity, plants were transferred to solution with no added salt and allowed to recover. Green leaf area and relative growth rates (RGR) of salinity tolerant varieties and one salinity sensitive variety initiated recovery (i.e. started to increase) after 4 days of salt stress removal and required 6 days to completely recover (i.e. to resume a similar RGR to that observed in the no-salt control treatment), while the other salinity sensitive varieties took more time to recover. An optimal recovery period of 6 days after salt stress removal was identified for screening. Based on RGR and chlorophyll fluorescence values, some salinity sensitive varieties recovered while their Na+ contents remained high. Therefore, salinity tolerance may not necessarily correspond to salinity recovery ability. The protocol optimized here can be scaled up to screen diversity panels and populations and used for genetic mapping of the seedling stage salinity recovery trait.