Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems

Funding: This research was funded by the Generation Challenge Program (GCP) project G3008.06, “Targeting Drought-Avoidance Root Traits to Enhance Rice Productivity under Water-Limited Environments". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems

The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7–40.7 Mb) and on chromosome 8 (20.3–21.9 Mb). Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions

Genotypic Variations in Responses of Lateral Root Development to Transient Moisture Stresses in Rice Cultivars

Soil water regimes under field conditions inevitably tend to fluctuate ranging from drought to waterlogging. Genotypes that adapt better to such changing hydrologic conditions are assumed to have the ability to maintain root system development under such conditions. This study aimed to evaluate the responses of root system development based on lateral root production to transient moisture stresses, and the contribution of the elongation of seminal and nodal root axes and their lateral, root branching, and aerenchyma development in the seminal root axis, to root system development. The seedlings of two aerobic genotypes (UPLRi7 and NSICRc9) and one irrigated-lowland genotype (PSBRc82), and two parental genotypes (Nipponbare and Kasalath) of chromosome segment substitution lines (CSSLs) were grown by hydroponics. The seedlings were exposed to a drought condition by adding polyethylene glycol to the solution for 7 days and then to an O2-deficient stagnant condition for 7 days (drought-to-stagnant condition), or to reverse successive conditions (stagnant-to-drought condition). Under both conditions, the aerobic genotypes showed greater ability to produce lateral roots than the irrigated-lowland genotype. Under the transient stagnant-to-drought condition, the root traits that contributed to greater lateral root production in the aerobic genotypes were faster seminal root elongation that was closely associated with branching of lateral roots, and greater nodal root production. Under transient drought to stagnant condition; these were faster seminal root elongation mediated by higher aerenchyma formation, and greater nodal root production. Kasalath showed much greater ability to produce lateral roots under both transient moisture stress conditions than Nipponbare. This indicates the potential utility of the CSSLs for precise identification of desirable root traits with less genetic confounding

Genotypic variation in rice root system distribution and activity in response to short-term soil drought

In this study, two experiments were conducted to evaluate the genotypic variation of rice root system distribution and root activity in response to short-term drought conditions. Seven rice genotypes were used, of which one (Rexmont) showed the greatest reduction in shoot biomass under drought, and two (Swarna and KDML105) showed the least reduction in shoot biomass under drought in both experiments. In a phytotron experiment (Experiment 1) in which root hydraulic conductivity (Lpr) of 21-day-old rice plants was evaluated in well-watered (control) and dry down (drought) conditions, the Lpr of Swarna, KDML105, and IRAT109 were significantly lower under drought compared to the control. In a field experiment (Experiment 2) conducted in the 2013 wet season at IRRI, stomatal conductance, bleeding rate, and root surface area density (RSAD) at 0-15, 15-30, 30-45, and 45-60 cm soil depths were measured in an irrigated (control) and rainfed (drought) treatments. Swarna, KDML105, and FR13A showed significant reductions in RSAD at 0-30 cm depth under drought in the field compared to the control, while Rexmont and IRAT109 showed no significant changes. In addition, Rexmont and Swarna both maintained higher bleeding rates than the other genotypes. Based on the root hydraulic and architectural traits of contrasting genotypes, we conclude that the bleeding rate did not explain the genotypic variations in the maintenance of shoot biomass, and that reducing shallow root growth and Lpr in response to drought conferred the best ability to maintain shoot biomass under short-term drought conditions