Soil compaction represents a major challenge for modern agriculture. Compaction is intuitively thought to reduce root growth by limiting the ability of roots to penetrate harder soils. We report that ...root growth in compacted soil is instead actively suppressed by the volatile hormone ethylene. We found that mutant
and rice roots that were insensitive to ethylene penetrated compacted soil more effectively than did wild-type roots. Our results indicate that soil compaction lowers gas diffusion through a reduction in air-filled pores, thereby causing ethylene to accumulate in root tissues and trigger hormone responses that restrict growth. We propose that ethylene acts as an early warning signal for roots to avoid compacted soils, which would be relevant to research into the breeding of crops resilient to soil compaction.
Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we ...report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
Background
Root architectural and anatomical phenotypes are important for adaptation to drought. Many rice-growing regions face increasing water scarcity. This study describes drought responses of 11 ...Egyptian rice cultivars with emphasis on plastic root responses that may enhance drought adaptation.
Results
Eleven Egyptian rice cultivars were phenotyped for root architectural and anatomical traits after 6 weeks growth in soil mesocosms under well-watered conditions. Four of these cultivars were more intensively phenotyped under progressive drought stress in mesocosms, using a system where more moisture was available at depth than near the surface. In response to drought stress, all cultivars significantly reduced nodal root number while increasing large lateral root branching density and total lateral root length in the deepest portions of the mesocosm, where moisture was available. Nodal root cross-sectional area, but not stele area, was reduced by drought stress, especially in the basal segments of the root, and the number of late metaxylem vessels was reduced in only one cultivar. Alterations in deposition of lignin were detected by UV illumination from laser ablation tomography, enhanced by digital staining, and confirmed with standard histochemical methods. In well-watered plants, the sclerenchyma and endodermis were heavily lignified, and lignin was also visible throughout the epidermis and cortex. Under drought stress, very little lignin was detected in the outer cell layers and none in the cortex of nodal roots, but lignin deposition was enhanced in the stele. Root anatomical phenes, including cross-section area and metaxylem vessel number and lignin deposition varied dramatically along large lateral root axes under drought stress, with increasing diameter and less lignification of the stele in successive samples taken from the base to the root apex.
Conclusions
Root architectural and anatomical traits varied significantly among a set of Egyptian cultivars. Most traits were plastic, i.e. changed significantly with drought treatment, and, in many cases, plasticity was cultivar-dependent. These phenotypic alterations may function to enhance water uptake efficiency. Increased large lateral root branching in the deep soil should maintain water acquisition, while water transport during drought should be secured with a more extensively lignified stele.
We tested the hypothesis that reduced root cortical cell file number (CCFN) would improve drought tolerance in maize (Zea mays) by reducing the metabolic costs of soil exploration. Maize genotypes ...with contrasting CCFN were grown under wellwatered and water-stressed conditions in greenhouse mesocosms and in the field in the United States and Malawi. CCFN ranged from six to 19 among maize genotypes. In mesocosms, reduced CCFN was correlated with 57% reduction of root respiration per unit of root length. Under water stress in the mesocosms, genotypes with reduced CCFN had between 15% and 60% deeper rooting, 78% greater stomatal conductance, 36% greater leaf CO₂ assimilation, and between 52% to 139% greater shoot biomass than genotypes with many cell files. Under water stress in the field, genotypes with reduced CCFN had between 33% and 40% deeper rooting, 28% lighter stem water oxygen isotope enrichment (δ¹⁸O) signature signifying deeper water capture, between 10% and 35% greater leaf relative water content, between 35% and 70% greater shoot biomass at flowering, and between 33% and 114% greater yield than genotypes with many cell files. These results support the hypothesis that reduced CCFN improves drought tolerance by reducing the metabolic costs of soil exploration, enabling deeper soil exploration, greater water acquisition, and improved growth and yield under water stress. The large genetic variation for CCFN in maize germplasm suggests that CCFN merits attention as a breeding target to improve the drought tolerance of maize and possibly other cereal crops.
Several root anatomical phenes affect water acquisition from drying soil, and may therefore have utility in breeding more drought-tolerant crops. Anatomical phenes that reduce the metabolic cost of ...the root cortex (‘cortical burden’) improve soil exploration and therefore water acquisition from drying soil. The best evidence for this is for root cortical aerenchyma; cortical cell file number and cortical senescence may also be useful in this context. Variation in the number and diameter of xylem vessels strongly affects axial water conductance. Reduced axial conductance may be useful in conserving soil water so that a crop may complete its life cycle under terminal drought. Variation in the suberization and lignification of the endodermis and exodermis affects radial water conductance, and may therefore be important in reducing water loss from mature roots into dry soil. Rhizosheaths may protect the water status of young root tissue. Root hairs and larger diameter root tips improve root penetration of hard, drying soil. Many of these phenes show substantial genotypic variation. The utility of these phenes for water acquisition has only rarely been validated, and may have strong interactions with the spatiotemporal dynamics of soil water availability, and with root architecture and other aspects of the root phenotype. This complexity calls for structural–functional plant modelling and 3D imaging methods. Root anatomical phenes represent a promising yet underexplored and untapped source of crop breeding targets.
Root anatomical phenes affecting the metabolic cost of soil exploration and root hydraulic conductance represent a promising yet underexplored source of breeding targets for crops with greater drought tolerance.
New roots for agriculture: exploiting the root phenome Lynch, Jonathan P.; Brown, Kathleen M.
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
06/2012, Volume:
367, Issue:
1595
Journal Article
Peer reviewed
Open access
Recent advances in root biology are making it possible to genetically design root systems with enhanced soil exploration and resource capture. These cultivars would have substantial value for ...improving food security in developing nations, where yields are limited by drought and low soil fertility, and would enhance the sustainability of intensive agriculture. Many of the phenes controlling soil resource capture are related to root architecture. We propose that a better understanding of the root phenome is needed to effectively translate genetic advances into improved crop cultivars. Elementary, unique root phenes need to be identified. We need to understand the ‘fitness landscape’ for these phenes: how they affect crop performance in an array of environments and phenotypes. Finally, we need to develop methods to measure phene expression rapidly and economically without artefacts. These challenges, especially mapping the fitness landscape, are non-trivial, and may warrant new research and training modalities.
We present a method to visually score 10 root architectural traits of the root crown of an adult maize plant in the field in a few minutes. Phenotypic profiling of three recombinant inbred line (RIL) ...populations of maize (Zea mays L.; B73xMo17, Oh43xW64a, Ny821xH99) was conducted in 2008 in a silt loam soil in Pennsylvania and in a sandy soil in Wisconsin, and again in 2009 in Pennsylvania. Numbers, angles and branching pattern of crown and brace roots were assessed visually at flowering. Depending on the soil type in which plants were grown, sample processing took from three (sand) to 8 min (silt-loam). Visual measurement of the root crown required 2 min per sample irrespective of the environment. Visual scoring of root crowns gave a reliable estimation of values for root architectural traits as indicated by high correlations between measured and visually scored trait values for numbers (r ² = 0.46-0.97), angles (r ² = 0.66-0.76), and branching (r ² = 0.54-0.88) of brace and crown roots. Based on the visual evaluation of root crown traits it was possible to discriminate between populations. RILs derived from the cross NY821 x H99 generally had the greatest number of roots, the highest branching density and the most shallow root angles, while inbred lines from the cross between OH43 x W64a generally had the steepest root angles. The ranking of genotypes remained the same across environments, emphasizing the suitability of the method to evaluate genotypes across environments. Scoring of brace roots was better correlated with the actual measurements compared to crown roots. The visual evaluation of root architecture will be a valuable tool in tailoring crop root systems to specific environments.
Root phenes and phene states that reduce the metabolic cost of soil exploration may improve plant growth under low phosphorus availability. We tested the hypothesis that under low phosphorus, reduced ...living cortical area (LCA) would increase soil exploration, phosphorus capture, biomass, and grain yield. Maize genotypes contrasting in LCA were grown in the field and in greenhouse mesocosms under optimal and suboptimal phosphorus regimes. Percent LCA in nodal roots ranged from 25% to 67%. Plants with 0.2 mm2 less LCA under low phosphorus had 75% less root segment respiration, 54% less root phosphorus content, rooted 20 cm deeper, allocated up to four times more roots between 60 and 120 cm depth, had between 20% and 150% more biomass, 35–40% greater leaf phosphorus content, and 60% greater grain yield compared with plants with high LCA. Low‐LCA plants had up to 55% less arbuscular mycorrhizal colonization in axial roots, but this decrease was not correlated with biomass or phosphorus content. The LCA components cortical cell file number and cortical cell size were important for biomass and phosphorus content under low phosphorus. These results are consistent with the hypothesis that root phenes that decrease the metabolic cost of soil exploration are adaptive under phosphorus stress.
Living cortical area of maize root tissue is reduced under suboptimal phosphorus availability through the production of aerenchyma. Using greenhouse and field‐grown maize genotypes with contrasting living cortical area, we tested the hypothesis that plants with reduced living cortical area would have decreased respiratory carbon and phosphorus demand, greater soil exploration, and greater phosphorus capture. Genotypes with reduced living cortical area had reduced root segment respiration and phosphorus content, greater shoot biomass, phosphorus content, and grain yield under suboptimal phosphorus availability. Our results support the hypothesis that reduced living cortical area may have adaptive value under suboptimal phosphorus availability.
Root cortical aerenchyma (RCA) reduces root respiration in maize by converting living cortical tissue to air volume. We hypothesized that RCA increases drought tolerance by reducing root metabolic ...costs, permitting greater root growth and water acquisition from drying soil. To test this hypothesis, recombinant inbred lines with high and low RCA were observed under water stress in the field and in soil mesocosms in a greenhouse. In the field, lines with high RCA had 30% more shoot biomass at flowering compared with lines with low RCA under water stress. Root length density in deep soil was significantly greater in the high RCA lines compared with the low RCA lines. Mid-day leaf relative water content in the high RCA lines was 10% greater than in the low RCA lines under water stress. The high RCA lines averaged eight times the yield of the low RCA lines under water stress. In mesocosms, high RCA lines had less seminal root respiration, deeper rooting, and greater shoot biomass compared with low RCA lines under water stress. These results support the hypothesis that RCA is beneficial for drought tolerance in maize by reducing the metabolic cost of soil exploration.
Regulation of transcript structure generates transcript diversity and plays an important role in human disease
. The advent of long-read sequencing technologies offers the opportunity to study the ...role of genetic variation in transcript structure
. In this Article, we present a large human long-read RNA-seq dataset using the Oxford Nanopore Technologies platform from 88 samples from Genotype-Tissue Expression (GTEx) tissues and cell lines, complementing the GTEx resource. We identified just over 70,000 novel transcripts for annotated genes, and validated the protein expression of 10% of novel transcripts. We developed a new computational package, LORALS, to analyse the genetic effects of rare and common variants on the transcriptome by allele-specific analysis of long reads. We characterized allele-specific expression and transcript structure events, providing new insights into the specific transcript alterations caused by common and rare genetic variants and highlighting the resolution gained from long-read data. We were able to perturb the transcript structure upon knockdown of PTBP1, an RNA binding protein that mediates splicing, thereby finding genetic regulatory effects that are modified by the cellular environment. Finally, we used this dataset to enhance variant interpretation and study rare variants leading to aberrant splicing patterns.
PDF
