Aims Growth reductions and yield losses from drought could be mitigated by developing rice genotypes with more efficient root systems. We examined spatiotemporal responses to drought in order to determine whether roots developing in upper vs. deeper soil layers respond differently to drought stress. Methods Root anatomical and architectural phenotypes of two rice genotypes, Azucena (drought tolerant) and IR64 (drought susceptible), were measured weekly in well-watered and vegetative-stage drought stress treatments in solid medium with stratified moisture availability. Basal and apical segments were collected from older, deeper nodal roots and apical segments from younger, shallow roots for assessment of anatomy and lateral rooting phenotypes. The relationship between root anatomy and root respiration rates was tested in solution culture and solid medium. Results Compared to IR64, Azucena had deeper root systems and larger diameter roots in both treatments but reduced its living tissue area in response to drought, while IR64 roots exhibited less plasticity in root diameter. Root respiration rates were positively correlated with root diameter and living tissue area, providing evidence that root anatomy affects the metabolic cost of tissues. In response to drought, Azucena showed reduced theoretical axial hydraulic conductance in shallow roots and at the base of deep roots but slightly greater conductance at the tip of deep roots, while IR64 displayed low plasticity in metaxylem phenotypes. Conclusion We propose that the plasticity of root phenotypes in Azucena contributes to its drought tolerance by reducing the metabolic cost of soil exploration and improving the efficiency of water transport.

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.

Background Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus, indica, temperate japonica, and tropical japonica). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets. Results We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice and Arabidopsis. Conclusions Root hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.

Root anatomical traits show significant variation among rice, Oryza sativa L., genotypes and are of interest for improving adaptation to a variety of edaphic, hydrological and nutritional environments in which rice is grown. However, they are difficult to measure and the genetic controls of these traits are not well understood in rice. We conducted genome-wide association (GWA) analyses using moderate- and high-density SNP panels on a diverse rice population to identify genomic regions and candidate genes that control root anatomical traits. We identified 28 genomic regions for metaxylem vessel area and number, root cross-sectional area, stele area, and aerenchyma area. One genomic region associated with metaxylem vessel number and two regions associated with three root thickness-related traits, stele area, root cross-sectional area and metaxylem vessel area, were supported by chromosome-specific GWA using a high-density SNP panel and are regarded as highly significant regions controlling trait variation. Candidate genes in these regions were related to cell differentiation, elongation and division, and secondary cell wall formation. For genomic regions identified in the indica subpopulation, haplotype variation and root anatomical phenotypes were associated with geographic distributions of the accessions, notably the presence of alternate alleles conferring larger diameter roots, stele, and metaxylem vessels in accessions from the indica 2 and indica 3 subgroups originating largely in south and southeast Asia. The identification of genomic regions and candidate genes related to root anatomical traits in a diverse panel of rice varieties deepens our understanding of trait variation and genetic architecture and facilitates the incorporation of favorable alleles into breeding populations.