Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation.

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.

Many paths to one goal: Identifying integrated rice root phenotypes for diverse drought environments.

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.