Root Phenes Research Articles

IMPACT OF SOIL STERILIZATION FROM DIFFERENT LOCATIONS, WHEAT SEEDS CLEANING AND THEIR INTERACTIONS ON WEED CONTROL, AND YIELD AND YIELD COMPONENTS

IMPACT OF SOIL STERILIZATION FROM DIFFERENT LOCATIONS, WHEAT SEEDS CLEANING AND THEIR INTERACTIONS ON WEED CONTROL, AND YIELD AND YIELD COMPONENTS

Diversity, Variance, and Stability of Root Phenes of Peanut (Arachis hypogaea L.).

Root phenes are associated with the absorptive efficiency of water and fertilizers. However, there are few reports on the genetic variation and stability of peanut (Arachis hypogaea L.) root architecture under different environments. In this study, the diversity, variance and stability of root phenes of 89 peanut varieties were investigated with shovelomics (high throughput phenotyping of root system architecture) for two years in both field and laboratory experiments. The root phenes of these peanut genotypes presented rich diversity; for example, the value of total root length (TRL) ranged from 347.84 cm to 1013.80 cm in the field in 2018, and from 55.14 cm to 206.22 cm in the laboratory tests. The root phenes of different genotypes varied differently; for example, the coefficient of variation (CV) of TRL ranged from 24.0 to 83.5 across the two-year field test. Field and laboratory evaluations were highly correlated, especially on lateral root density (LRD) and root angle (RA), and the quadrant graph analysis of LRD and RA implied that 69.7% of the roots belong to the same type. These not only further reflect root phenes stability through different environment but also demonstrate that some root phenes identified at early stage can indicate their status at later growth stage. In addition, root phenes showed a strong correlation with shoot growth, especially root dry weight (RDW), TRL and（nodule number）NN. Thus, laboratory tests in combination with field shovelomics can efficiently screen and select genotypes with contrasting root phenes to optimize water and nutrient management.

Comparative phenomics of root architecture and anatomy in Phaseolus species

Comparative phenomics of root architecture and anatomy in <i>Phaseolus</i> species

Multi‐objective optimization of root phenotypes for nutrient capture using evolutionary algorithms

SUMMARYRoot phenotypes are avenues to the development of crop cultivars with improved nutrient capture, which is an important goal for global agriculture. The fitness landscape of root phenotypes is highly complex and multidimensional. It is difficult to predict which combinations of traits (phene states) will create the best performing integrated phenotypes in various environments. Brute force methods to map the fitness landscape by simulating millions of phenotypes in multiple environments are computationally challenging. Evolutionary optimization algorithms may provide more efficient avenues to explore high dimensional domains such as the root phenotypic space. We coupled the three‐dimensional functional–structural plant model, SimRoot, to the Borg Multi‐Objective Evolutionary Algorithm (MOEA) and the evolutionary search over several generations facilitated the identification of optimal root phenotypes balancing trade‐offs across nutrient uptake, biomass accumulation, and root carbon costs in environments varying in nutrient availability. Our results show that several combinations of root phenes generate optimal integrated phenotypes where performance in one objective comes at the cost of reduced performance in one or more of the remaining objectives, and such combinations differed for mobile and non‐mobile nutrients and for maize (a monocot) and bean (a dicot). Functional–structural plant models can be used with multi‐objective optimization to identify optimal root phenotypes under various environments, including future climate scenarios, which will be useful in developing the more resilient, efficient crops urgently needed in global agriculture.

Root system size and root hair length are key phenes for nitrate acquisition and biomass production across natural variation in Arabidopsis.

The role of root phenes in nitrogen (N) acquisition and biomass production was evaluated in 10 contrasting natural accessions of Arabidopsis thaliana L. Seedlings were grown on vertical agar plates with two different nitrate supplies. The low N treatment increased the root to shoot biomass ratio and promoted the proliferation of lateral roots and root hairs. The cost of a larger root system did not impact shoot biomass. Greater biomass production could be achieved through increased root length or through specific root hair characteristics. A greater number of root hairs may provide a low-resistance pathway under elevated N conditions, while root hair length may enhance root zone exploration under low N conditions. The variability of N uptake and the expression levels of genes encoding nitrate transporters were measured. A positive correlation was found between root system size and high-affinity nitrate uptake, emphasizing the benefits of an exploratory root organ in N acquisition. The expression levels of NRT1.2/NPF4.6, NRT2.2, and NRT1.5/NPF7.3 negatively correlated with some root morphological traits. Such basic knowledge in Arabidopsis demonstrates the importance of root phenes to improve N acquisition and paves the way to design eudicot ideotypes.

Integrated root phenotypes for improved rice performance under low nitrogen availability.

Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional–structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L‐type and S‐type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct‐seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct‐seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding.

Phenotyping cowpea for seedling root architecture reveals root phenes important for breeding phosphorus efficient varieties

AbstractCowpea (Vigna unguiculata L. Walp.) is a key climate‐resilient legume for food security, especially in sub‐Saharan Africa. Cowpea yields are limited by edaphic stresses including drought and low phosphorus (P) availability. Identifying genotypes with advantageous root phenotypes can facilitate breeding for improved yield in marginal environments. We evaluated 50 elite genotypes from African and U.S. sources for seedling root architecture and root hair length and density. Significant genotypic variation was detected for all phenes, and high heritability was observed for architectural phenotypes including primary root length (77%), basal root number (72%), and taproot branching density (67%). Moderate heritability was detected for root hair length and density among different root classes (34 to 63%), which were positively associated with each other. Principal component analysis identified three clusters, primarily defined by seed dimension and seedling root architecture. Genotypes were identified with longer root hairs (TVu‐7778, Vita7, and Sanzi) and longer taproots (IT96D‐610, IT98K‐111‐1, and IT97K‐499‐35), as potential parents. Root phenotypes, grain, and fodder yield were assessed on a subset of 20 genotypes under contrasting P availability in the field. Some seedling root phenotypes were significantly related to mature plant dry fodder weight (taproot hair density) and to grain yield (lateral root hair density) under low P. Root hairs are positively related to plant productivity under low P. We suggest selection for longer primary roots, as more basal and lateral root roots may be beneficial for cowpea in drought and low P environments. These findings suggest seedling root phenotypes can support cowpea breeding for suboptimal environments.

Investigation of soil nutrients and associated rhizobacterial communities in different sugarcane genotypes in relation to sugar content

BackgroundPlant microbiomes and soil are bridged by rhizobacteria, maintaining and improving plant health and growth in different aspects. This study was conducted in the field station of the Guangxi University, Fusui, China. We investigated soil nutrients, root morphology and rhizosphere bacterial composition, and community structures in 18 sugarcane genotypes concerning sugar content under the same environmental condition.ResultsMost of the rhizosphere microbiomes of these genotypes exhibited similar bacterial compositions. However, the evaluated genotypes harbored a significant effect and difference in the abundance of operational taxonomic units and bacterial composition in the rhizosphere compartments. Alpha diversity analysis on the rhizosphere microbiome showed a significant difference in the bacterial diversity (Shannon index, p < 0.001) and OTU richness (Chao1, p < 0.001). The principal coordinate analysis (PCoA) and hierarchical cluster analysis revealed that the genotype replicated samples grouped, indicating their similarity. Besides, these genotypes also differed significantly in terms of root structure and soil properties. A significant genotypic effect (p < 0.05) was found in the root traits except for rooting depth. The soil chemical properties were significantly different among the evaluated genotypes. Furthermore, sucrose content was strongly correlated with the total root length (TRL) and rooting depth. Genotypes (FN-1702, GUC-3, ZZ-13, ZZ-10, ZZ-6) were the best performing and distinct in bacterial diversity, root structure, soil parameters and sucrose content.ConclusionThe results showed a closely related and highly conserved bacterial community of the rhizosphere microbiome. The rhizosphere microbiome diversity and related bacterial communities were highly associated with the relevant plant taxa, probably at the order level. As a result, it is possible to conclude that the host genotype and the same environmental condition influenced the rhizosphere microbiome via root phenes. Future research regarding plant phenes and microbiome functional groups could be considered an essential factor.Graphic abstract

Root Traits Related with Drought and Phosphorus Tolerance in Common Bean (Phaseolus vulgaris L.)

Roots are key organs for water and nutrient acquisition and transport. Therefore, root phenes that are associated with adaptation to low phosphorus (P) environments could enhance top-soil exploration, while deeper allocation is important for acquiring water and mobile nutrients. The understanding of interactions among root phenes can help in the development of common bean (Phaseolus vulgaris L.) genotypes adapted to drought and low fertility through genetic improvement. Two experiments (pot and field) were conducted at the Agricultural Research Institute of Mozambique to assess the contribution of root phenes to common bean shoot biomass and grain yield under combined stress (drought and low P). The pot study assessed eight genotypes, with four treatments combining water regimes (drought and non-stress) and phosphorus levels (200 and 25) mg P kg−1 soil. In the field study, 24 common bean genotypes were also grown in high and low phosphorus (40 kg P ha−1 and without P application) under irrigation and limited water. The grain yield from fields under drought and P stress were correlated with the pot data on root traits. The response of root phenes to drought and phosphorus stress appeared to be related to the deep and shallow root systems, respectively. Deep rooted genotypes produced more total root biomass and high taproot lateral branching density, which resulted in high total root length under drought and low P stress, while shallow rooted genotypes had low total root biomass and less taproot lateral branching. Increased shoot biomass and grain yield under drought and low P was associated with higher mean values of taproot lateral branching density and total taproot length. Genotypes SER 125, BFS 81, FBN12111-66 and MER 22 11-28 showed a greater score of tap root branching density in the pot study with the highest grain yield in the field under low P and drought stress. Therefore, these can be recommended for use in low phosphorus and drought stress environment or serve as parents for improving phosphorus use efficiency and drought tolerance in common bean.

Root phenotypic diversity in common bean reveals contrasting strategies for soil resource acquisition among gene pools and races

AbstractAlthough genetic diversity for aboveground traits has been well characterized in common bean (Phaseolus vulgaris L.), little is known about population‐specific variation within this species for root architecture. To assess the diversity of root phenotypes, a total of 196 accessions from a core collection were evaluated in the laboratory and field in Pennsylvania, USA, and Chokwe, Mozambique. Substantial phenotypic variation for 15 root phenes exists among gene pools, races, and genotypes. Principal component analysis revealed that Andean and Mesoamerican gene pools and races have distinct integrated root phenotypes. Unsupervised cluster analyses of root phenes identified five groups with distinct integrated root phenotypes and soil foraging strategies. Although integrated phenotypes associated with adaptation to drought and low P availability were found in both gene pools, phenotypes for drought adaptation were more prevalent among Mesoamerican accessions, whereas phenotypes for adaptation to suboptimal P were more common among Andean accessions. These genotypic differences in root phenotypes reflect contrasting strategies for soil resource acquisition and may possibly have evolved as an adaptation to the edaphic conditions in the environments to which Andean and Mesoamerican gene pools are endemic. This diversity of root architectural strategies for soil exploration can serve as an important resource for breeding programs and hybridization between gene pools may result in the generation of novel root phenotypes with improved soil resource acquisition.

Spatio-Temporal Variation in Water Uptake in Seminal and Nodal Root Systems of Barley Plants Grown in Soil.

The spatial and temporal dynamics of root water uptake in nodal and seminal roots are poorly understood, especially in relation to root system development and aging. Here we non-destructively quantify 1) root water uptake and 2) root length of nodal and seminal roots of barley in three dimensions during 43 days of growth. We developed a concentric split root system to hydraulically and physically isolate the seminal and nodal root systems. Using magnetic resonance imaging (MRI), roots were visualized, root length was determined, and soil water depletion in both compartments was measured. From 19 days after germination and onwards, the nodal root system had greater water uptake compared to the seminal root system due to both greater root length and greater root conductivity. At 29 days after germination onwards, the average age of the seminal and nodal root systems was similar and no differences were observed in water uptake per root length between seminal and nodal root systems, indicating the importance of embryonic root systems for seedling establishment and nodal root systems in more mature plants. Since nodal roots perform the majority of water uptake at 29 days after germination and onwards, nodal root phenes merit consideration as a selection target to improve water capture in barley and possibly other crops.

Multiple Integrated Root Phenotypes Are Associated with Improved Drought Tolerance.

To test the hypothesis that multiple integrated root phenotypes would co-optimize drought tolerance, we phenotyped the root anatomy and architecture of 400 mature maize (Zea mays) genotypes under well-watered and water-stressed conditions in the field. We found substantial variation in all 23 root phenes measured. A phenotypic bulked segregant analysis revealed that bulks representing the best and worst performers in the field displayed distinct root phenotypes. In contrast to the worst bulk, the root phenotype of the best bulk under drought consisted of greater cortical aerenchyma formation, more numerous and narrower metaxylem vessels, and thicker nodal roots. Partition-against-medians clustering revealed several clusters of unique root phenotypes related to plant performance under water stress. Clusters associated with improved drought tolerance consisted of phene states that likely enable greater soil exploration by reallocating internal resources to greater root construction (increased aerenchyma content, larger cortical cells, fewer cortical cell files), restrict uptake of water to conserve soil moisture (reduced hydraulic conductance, narrow metaxylem vessels), and improve penetrability of hard, dry soils (thick roots with a larger proportion of stele, and smaller distal cortical cells). We propose that the most drought-tolerant-integrated phenotypes merit consideration as breeding ideotypes.

Genetic control of root architectural plasticity in maize.

Root phenotypes regulate soil resource acquisition; however, their genetic control and phenotypic plasticity are poorly understood. We hypothesized that the responses of root architectural phenes to water deficit (stress plasticity) and different environments (environmental plasticity) are under genetic control and that these loci are distinct. Root architectural phenes were phenotyped in the field using a large maize association panel with and without water deficit stress for three seasons in Arizona and without water deficit stress for four seasons in South Africa. All root phenes were plastic and varied in their plastic response. We identified candidate genes associated with stress and environmental plasticity and candidate genes associated with phenes in well-watered conditions in South Africa and in well-watered and water-stress conditions in Arizona. Few candidate genes for plasticity overlapped with those for phenes expressed under each condition. Our results suggest that phenotypic plasticity is highly quantitative, and plasticity loci are distinct from loci that control phene expression in stress and non-stress, which poses a challenge for breeding programs. To make these loci more accessible to the wider research community, we developed a public online resource that will allow for further experimental validation towards understanding the genetic control underlying phenotypic plasticity.

A case study on the efficacy of root phenotypic selection for edaphic stress tolerance in low-input agriculture: Common bean breeding in Mozambique

Increasing common bean production, through the development and release of new phosphorus (P) efficient cultivars with improved root phenotypes in Mozambique was made possible by integrated physiology, agroecology, and social science research into a breeding pipeline. Social science research on small-holder farmers identified increased production in low fertility soils and ability to improve soil as primary constraints. Identification of root phenes improving P capture by physiological research enabled breeding to select for specific phene states rather than coarse yield-based metrics. This selection process targeted root phenes such as basal root whorl number (BRWN), basal root growth angle (BRGA) and long, dense root hairs. Agroecological research identified positive impacts of P efficient bean lines for enhanced utilization of rock phosphate, reduced soil erosion, greater biological nitrogen fixation, and acceptable competition with maize in polyculture. Socioeconomic research evaluated factors affecting adoption, dissemination and marketing and assessed the impacts of adoption of the new varieties on food security, farm income, women, children and men in specific rural populations. This case study illustrates how trait-based breeding programs, and specifically root ideotype breeding, can successfully utilize a multidisciplinary approach to release new varieties likely to be accepted by farmers and have broad impact on food security, small-holder farmer income and soil health.

Genotypic variation and nitrogen stress effects on root anatomy in maize are node specific.

Root phenotypes that improve nitrogen acquisition are avenues for crop improvement. Root anatomy affects resource capture, metabolic cost, hydraulic conductance, anchorage, and soil penetration. Cereal root phenotyping has centered on primary, seminal, and early nodal roots, yet critical nitrogen uptake occurs when the nodal root system is well developed. This study examined root anatomy across nodes in field-grown maize (Zea mays L.) hybrid and inbred lines under high and low nitrogen regimes. Genotypes with high nitrogen use efficiency (NUE) had larger root diameter and less cortical aerenchyma across nodes under stress than genotypes with lower NUE. Anatomical phenes displayed slightly hyperallometric relationships to shoot biomass. Anatomical plasticity varied across genotypes; most genotypes decreased root diameter under stress when averaged across nodes. Cortex, stele, total metaxylem vessel areas, and cortical cell file and metaxylem vessel numbers scaled strongly with root diameter across nodes. Within nodes, metaxylem vessel size and cortical cell size were correlated, and root anatomical phenotypes in the first and second nodes were not representative of subsequent nodes. Node, genotype, and nitrogen treatment affect root anatomy. Understanding nodal variation in root phenes will enable the development of plants that are adapted to low nitrogen conditions.

Seedling root architecture and its relationship with seed yield across diverse environments in Phaseolus vulgaris

Seedling root phenotypes may have important impacts on fitness and are more easily measured than mature root phenotypes. We phenotyped the roots of 577 genotypes of common bean (Phaseolus vulgaris), representing the bulk of the genetic diversity for recent cultivars and landraces in this species. Root architectural phenotypes of seedlings germinated for nine days were compared to root architectural phenotypes in the field as well as seed yield across 51 environments with an array of abiotic stresses including drought, nutrient deficiency, and heat, as well as non-stress conditions. We observed repeatability ranging from 0.52–0.57 for measures of root phenotypes in seedlings, significant variation in root phene states between gene pools and races, relationships between seedling and field phenotypes, and varying correlations between seedling root phenes and seed yield under a variety of environmental conditions. Seed yield was significantly related to seedling basal root number in 22% of environments, seedling adventitious root abundance in 35% of environments, and seedling taproot length in 12% of environments. Cluster analysis grouped genotypes by their aggregated seedling root phenotype, and variation in seed yield among these clusters under non-stress, drought, and low fertility conditions was observed. These results highlight the existence and influence of integrated root phenotypes for adaptation to edaphic stress, and suggest root phenes have value as breeding targets under real-world conditions.

Response of maize genotypes with different nitrogen use efficiency to low nitrogen stresses

ObjectivesThis paper aims to compare the property difference of spatial and temporal distribution of different nitrogen use efficiency maize genotypes and discuss the physiological mechanism of nitrogen efficiency of maize. MethodIn this study, phenotype of root crowns of maize in seedling stage (V5), bell stage (V12) and silking stage (R1) was conducted to discover phenes and phene modules related to N acquisition. An image was captured for the whole roots. Custom software was used to measure root phenes including root area, root projected structure length, maximum width of roots, and root angle. The study was conducted to examine the differences in spatial and temporal distribution of maize root at two nitrogen levels (0 and 240 kg hm-2), high efficiency genotype ZHENGDAN958 (ZD958) and low efficiency genotype DANYU13 (DY13) are used in field production. Under the low nitrogen stress conditions, the root area of ZD958 significantly increased after bell stage and exceeds the CK by 20.2% at silking stage. With LN, the root projected structure length of ZD958 was longer than that of CK by 49.4% at silking stage. The low efficiency genotype DY13 had no obvious change at two nitrogen levels. The number of the grain yield and root system biomass of high efficiency genotype ZD958 was remarkably larger than that of low efficiency genotype DY13. ConclusionDuring the whole growth stage, the root dry weight, root area and the root width med of high efficiency genotype ZD958 were larger than that of high efficiency genotype DY13. Besides, under the low nitrogen stress conditions, the width of ZD958 deep soil root tended to become longer which is good for the nitrogen absorption from the deep soil. High efficiency genotype can construct a root system which is in a well-developed and reasonable spatial distribution before blooming, so as to ensure plant nitrogen absorption and biomass generation as well. The root index of the nitrogen responsivity of high efficiency genotype ZD958 was higher than that of low efficiency genotype DY13 before blooming.

Reduced root cortical burden improves growth and grain yield under low phosphorus availability in maize.

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 0.2mm2 less LCA under low phosphorus had 75% less root segment respiration, 54% less root phosphorus content, rooted 20cm deeper, allocated up to four times more roots between 60 and 120cm 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.

Impact of root system architecture on rhizosphere and root microbiome

The root system influences plant fitness, health, and productivity via its phenotypic traits (phenes) such as root length, biomass, density, volume, and surface area. Although these traits differentially impact the release of 20 to 80% of total photosynthates as root exudates, their role in influencing microbial communities in the rhizosphere and root environments is not clear. The root phenes or architecture significantly alter soil biophysical and edaphic properties such as aggregation, structure, pH, moisture, temperature, and nutrient stoichiometry (C:N, C:P, and N:P ratios, etc.). Meantime, the exteriors and interiors of various root types demonstrate a tremendous phenotypic plasticity in their cellular structure, anatomy, cell types, shapes, metabolisms and biochemical profiles. These heterogeneities in the rhizosphere and endosphere create micro-environments and ecological niches for diverse microbial species to foster beneficial rhizospheric interactions. Results from the root systems of some agricultural, forest and model plants suggest that root phenes selectively filter and recruit different microbial communities. However, microbial colonization of root and rhizosphere environments may also occur through vertical transmission. We suggest that plant breeders should nevertheless consider root phenome and biota while developing new cultivars. Linking root phenome to microbiome (or its functional traits) and crop management practices may enhance our understanding of rhizospheric interactions, and their role in developing climate-resilient rhizosphere ecosystems.

Functional implications of root cortical senescence for soil resource capture

Root phenes play a primary role in plant adaptation to edaphic stress. Understanding the functional implications of root phenotypes will enable the development of crop varieties with improved soil resource acquisition. Root cortical senescence (RCS) is a type of programmed cell death in cortical cells of several Poaceae species. Until recently there has been very little attention to the functional implications of RCS for water and nutrient capture. We explore the functional implications of RCS as an adaptive trait for water and nutrient acquisition. The present review summarizes evidence from our own studies and other published work, and provides novel insights into the fitness landscape of RCS. Progress has recently been achieved in understanding the development and physiological implications of RCS. We propose that RCS is a useful trait for water and nutrient acquisition, particularly in edaphic stress conditions. Further research is needed to understand the utility and tradeoffs of RCS in the context of specific environments, management practices, and phenotypic backgrounds. The utility of RCS for improved plant performance under edaphic stress merits investigation in the field. RCS may be a useful breeding target for improved soil resource capture in several major crop species including wheat, barley, and triticale.