Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice.

Developing drought-resistant rice (Oryza sativa, L.) is essential for improving field productivity, especially in rain-fed areas affected by climate change. Wild relatives of rice are potential sources for drought-resistant traits. Therefore, we compared root growth and drought response among 22 wild Oryza species, from which Oryza glumaepatula was selected as a promising source for further exploration. A geographically diverse panel of 69 O. glumaepatula accessions was then screened for drought stress-related traits, and 6 of these accessions showed lower shoot dry weight (SDW) reduction, greater percentage of deep roots, and lower stomatal density (STO) under drought than the drought tolerant O. sativa variety, Sahbhagi dhan. Based on whole-genome resequencing of all 69 O. glumaepatula accessions and variant calling to a high-quality O. glumaepatula reference genome, we detected multiple genomic loci colocating for SDW, root dry weight at 30 to 45 cm depth, and STO in consecutive drought trials. Geo-referencing indicated that the potential drought donors originated in flood-prone locations, corroborating previous hypotheses about the coexistence of flood and drought tolerance within individual Oryza genomes. These findings present potential donor accessions, traits, and genomic loci from an AA genome wild relative of rice that, together with the recently developed reference genome, may be useful for further introgression of drought tolerance into the O. sativa backgrounds.

Development of a phenotyping protocol for combined drought and salinity stress at seedling stage in rice.

Introduction: The case of combined drought and salinity stress is increasingly becoming a constraint to rice production, especially in coastal areas and river deltas where low rainfall not only reduces soil moisture levels but also reduces the flow of river water, resulting in intrusion of saline sea-water. A standardized screening method is needed in order to systematically evaluate rice cultivars under combined drought+salinity at the same time because sequential stress of salinity followed by drought or vice-versa is not similar to simultaneous stress effects. Therefore, we aimed to develop a screening protocol for combined drought+salinity stress applied to soil-grown plants at seedling stage. Methods: The study system used 30-L soil-filled boxes, which allowed a comparison of plant growth under control conditions, individual drought and salinity stress, as well as combined drought+salinity. A set of salinity tolerant and drought tolerant cultivars were tested, together with several popular but salinity and drought-susceptible varieties that are grown in regions prone to combined drought+salinity. A range of treatments were tested including different timings of the drought and salinity application, and different severities of stress, in order to determine the most effective that resulted in visible distinction among cultivars. The challenges related to determining a protocol with repeatable seedling stage stress treatment effects while achieving a uniform plant stand are described here. Results: The optimized protocol simultaneously applied both stresses by planting into saline soil at 75% of field capacity which was then allowed to undergo progressive drydown. Meanwhile, physiological characterization revealed that chlorophyll fluorescence at seedling stage correlated well with grain yield when drought stress was applied to vegetative stage only. Discussion: The drought+salinity protocol developed here can be used for screening rice breeding populations as part of a pipeline to develop new rice varieties with improved adaptation to combined stresses.

Disentangling the Roles of Plant Water Status and Stem Carbohydrate Remobilization on Rice Harvest Index Under Drought.

BACKGROUND: Harvest index is an important component of grain yield and is typically reduced by reproductive stage drought stress in rice. Multiple drought response mechanisms can affect harvest index including plant water status and the degree of stem carbohydrate mobilization during grain filling. In this study, we aimed to dissect the contributions of plant water status and stem carbohydrate mobilization to harvest index. Pairs of genotypes selected for contrasting harvest index but similar biomass and days to flowering were characterized at ICAR-RCER, Patna, India and at IRRI, Philippines. RESULTS: Multiple traits were related with harvest index across experiments, including mobilization efficiency at both sites as indicated by groupings in principal component analysis, and plant water status as indicated by direct correlations. Biomass-related traits were positively correlated with harvest index at IRRI but biomass was negatively correlated with harvest index at ICER-RCER, Patna. We observed that some pairs of genotypes showed differences in harvest index across environments, whereas other showed differences in harvest index only under drought. Of all time points measured when all genotypes were considered together, the stem carbohydrate levels at maturity were most consistently (negatively) correlated with harvest index under drought, but not under well-watered conditions. However, in the pairs of genotypes grouped as those whose differences in harvest index were stable across environments, improved plant water status resulted in a greater ability to both accumulate and remobilize stored carbohydrate, i.e. starch. CONCLUSION: By distinguishing between genotypes whose harvest index was improved across conditions as opposed to specifically under drought, we can attribute the mechanisms behind the stable high-harvest index genotypes to be more related to stem carbohydrate remobilization than to plant water status. The stable high-harvest index lines in this study (Aus 257 and Wanni Dahanala) may confer mechanisms to improve harvest index that are independent of drought response and therefore may be useful for breeding improved rice varieties.

Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress.

Drought stress in Southeast Asia greatly affects rice production, and the rice root system plays a substantial role in avoiding drought stress. In this study, we examined the phenotypic and genetic correlations among root anatomical, morphological, and agronomic phenotypes over multiple field seasons. A set of >200 rice accessions from Southeast Asia (a subset of the 3000 Rice Genomes Project) was characterized with the aim to identify root morphological and anatomical phenotypes related to productivity under drought stress. Drought stress resulted in slight increases in the basal metaxylem and stele diameter of nodal roots. Although few direct correlations between root phenotypes and grain yield were identified, biomass was consistently positively correlated with crown root number and negatively correlated with stele diameter. The accessions with highest grain yield were characterized by higher crown root numbers and median metaxylem diameter and smaller stele diameter. Genome-wide association study (GWAS) revealed 162 and 210 significant SNPs associated with root phenotypes in the two seasons which resulted in identification of 59 candidate genes related to root development. The gene OsRSL3 was found in a QTL region for median metaxylem diameter. Four SNPs in OsRSL3 were found that caused amino acid changes and significantly associated with the root phenotype. Based on the haplotype analysis for median metaxylem diameter, the rice accessions studied were classified into five allele combinations in order to identify the most favorable haplotypes. The candidate genes and favorable haplotypes provide information useful for the genetic improvement of root phenotypes under drought stress.

Aus rice root architecture variation contributing to grain yield under drought suggests a key role of nodal root diameter class.

The aus rice variety group originated in stress-prone regions and is a promising source for the development of new stress-tolerant rice cultivars. In this study, an aus panel (~220 genotypes) was evaluated in field trials under well-watered and drought conditions and in the greenhouse (basket, herbicide and lysimeter studies) to investigate relationships between grain yield and root architecture, and to identify component root traits behind the composite trait of deep root growth. In the field trials, high and stable grain yield was positively related to high and stable deep root growth (r = 0.16), which may indicate response to within-season soil moisture fluctuations (i.e., plasticity). When dissecting component traits related to deep root growth (including angle, elongation and branching), the number of nodal roots classified as 'large-diameter' was positively related to deep root growth (r = 0.24), and showed the highest number of colocated genome-wide association study (GWAS) peaks with grain yield under drought. The role of large-diameter nodal roots in deep root growth may be related to their branching potential. Two candidate loci that colocated for yield and root traits were identified that showed distinct haplotype distributions between contrasting yield/stability groups and could be good candidates to contribute to rice improvement.

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Establishment method affects rice root plasticity in response to drought and its relationship with grain yield stability.

By responding to the variable soil environments in which they are grown, the roots of rice crops are likely to contribute to yield stability across a range of soil moistures, nutrient levels, and establishment methods. In this study, we explored different approaches to quantification of root plasticity and characterization of its relationship with yield stability. Using four different statistical approaches (plasticity index, slope, AMMI, and factor analytic) on a set of 17 genotypes including several recently-developed breeding lines targeted to dry direct-seeding, we identified only very few direct relationships between root plasticity and yield stability. However, genotypes identified as having combined yield stability and root plasticity showed higher grain yields across trials. Furthermore, root plasticity was expressed to a greater degree in puddled transplanted trials rather than under dry direct-seeding. Significant interactions between nitrogen and water resulted in contrasting relationships between nitrogen-use efficiency and biomass stability between puddled-transplanted and direct-seeded conditions. These results reflect the complex interaction between nitrogen, drought, and even different types of drought (as a result of the establishment method) on rice root growth, and suggest that although rice root plasticity may confer stable yield across a range of environments, it might be necessary to more narrowly define the targeted environments to which it will be most beneficial.

Ratooning as a management strategy for lodged or drought-damaged rice crops.

Rice (Oryza sativa L.) plants have the ability to develop ratoon tillers if the terminal growing point is lost, such as when the panicle has been aborted, matured, or harvested. We examined postharvest and midseason ratooning as management strategies for damaged rice crops, both in irrigated and rainfed conditions. Genotypic variation was observed in terms of postharvest ratoon tillering, midseason ratoon crop growth after lodging, and midseason ratoon crop growth after drought stress. The genotypic variation in postharvest ratoon tillering was related to stem carbohydrate levels at the time of main crop harvest and was affected by soil moisture levels at the time of main crop harvest. Drought-tolerant varieties did not consistently show improved ratoon crop growth. After lodging, cutting stems at a height of 30 cm produced the highest numbers of ratoon tillers, and the contribution of the ratoon crop to the total harvestable grain yield was highest when the ratoon crop was initiated at earlier growth stages. The highest ratoon grain yields recovered from lodged crops ranged up to 3.58 t ha-1. Total grain yield after drought was improved by trimming the leaves and panicles only in certain conditions and did not appear to be correlated with stem carbohydrate levels. These results suggest that management strategies may be recommended to farmers that exploit the ratooning ability of rice for improved recovery after midseason crop damage.