Sponsoring Institution
National Institute of Food and Agriculture
Project Status
Funding Source
Reporting Frequency
Accession No.
Grant No.
Project No.
Proposal No.
Multistate No.
Program Code
Project Start Date
Jan 1, 2020
Project End Date
Dec 31, 2023
Grant Year
Project Director
Brown, KA, MA.
Recipient Organization
Performing Department
Plant Science
Non Technical Summary
Sustainably feeding a growing population means that crops need to become more efficient in acquisition of water and nutrients while maintaining or increasing yields. Roots are key to the ability of plants to obtain water and nutrients. Efficient root systems grow roots where they can best acquire limiting resources, and these roots should have minimum cost to the plant in terms of nutrient and carbohydrate content, so that these resources can be diverted to the edible parts of the plant. In this project, we investigate root traits that improve efficiency of root systems and the resiliency of crops in the face of an uncertain environment. For example, drought can occur at any time during the growing season, with implications that vary with the timing, the type of soil, and climatic conditions such as temperature and wind speed. Nitrogen fertilizer is a major cost of production for non-legume crops, but it can be leached below the root zone by rain, making it unavailable to the crop and causing pollution of ground water. Phosphorus is more available in uppermost soil layers, so that root systems must explore shallow soil to get phosphorus while also growing deep roots to get water when drought occurs. Creating designer root systems that are better able to make use of soil resources, i.e. water and nutrients, requires knowledge of the specific root traits that are optimal in various environments along with tools for plant breeders to use in creating cultivars with these traits. We will investigate how crops with various root traits perform under drought and limited nutrient supply, discover new traits that have not previously been considered as breeding targets, create ideotypes, i.e. ideal root systems, based on traits that we show to be useful, and develop new technologies to assess and select for root traits.
Animal Health Component
Research Effort Categories

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
Goals / Objectives
The major goals of this research are to contribute to the development of stress-resilient crops by (1) identifying individual and combined root traits that contribute to crop resilience under abiotic stress, including drought and low nutrient availability, (2) developing tools that permit the selection of useful root traits and trait combinations in breeding programs, (3) investigating the role of root-associated microbes (i.e., the root-microbiome) in modulating root physiological responses under abiotic stresses.Goal 1 Objectives1. Create root ideotypes for resilience to drought and nutrient stress2. Discover new traits with potential value in crop breeding3. Demonstrate the value of root traits and trait combinations in various stress scenarios4. Use simulation modeling to test larger numbers of trait combinations and soil conditions than are possible with empirical researchGoal 2 Objectives1. Develop novel technologies for assessing root traits2. Identify genomic regions responsible for natural variation in root traits of cropsGoal 3 Objectives1. Evaluate microbial-mediated changes in root phenomics under distinct stress conditions2. Explore the potential of root-associate microbiomes in mitigating root abiotic stresses3. Discover root-associate taxa and functions that enhance crop stress resilience
Project Methods
Goal 1. Identifying individual and combined root traits that contribute to crop resilience under abiotic stress, including drought and low nutrient availability. (Brown, Lynch, Duque)Root ideotypes will be created based on existing literature and recent discoveries in the lab. Component traits will be tested in the laboratory (for seedling traits only), greenhouse, and various field environments. Greenhouse experiments will be conducted in mesocosms, which are larger containers that do not significantly constrain root growth and can be designed to simulate progressive drought, nitrogen leaching, and compacted layers. Entire root systems can be recovered from greenhouse mesocosms and subject to detailed analyses of root phenes, including structure and physiology. Field environments are available where low nitrogen and drought stress can be imposed, including rainout shelters at the Penn State research farm and field sites with cooperating researchers in the US and Chile. Traits and trait combinations can be tested in each of these environments using publicly available germplasm. Root architectural traits will be measured using WinRhizo software and shovelomics techniques that were previously developed. Root anatomy will be analyzed from images collected by laser ablation tomography and quantified with image analysis software. Performance will be assessed using plant growth and yield metrics. Measurements of physiological and biochemical processes, such as respiration and photosynthesis rates, elemental concentrations, starch accumulation, and other composition traits will be used to link structure and function. Advanced statistical methods will be used to identify useful integrated phenotypes for various stress conditions. Testing of large numbers of trait combinations will be conducted using OpenSimRoot, a structural-functional plant model with spatially explicit capabilities to simulate growth, water and nutrient uptake of various annual crops under drought, nutrient, and compaction stress. Empirical data will be collected to continue parameterization of OpenSimRoot for additional traits and soil conditions. New traits will be discovered through observation of root structures and behavior under different growth conditions.Goal 2. Developing tools that permit the selection of useful root traits and trait combinations in breeding programs. (Brown, Lynch, Duque, Dini Andreote)X-ray fluorescence will be explored as a method to assess the depth of roots based on elemental composition of leaves. Non-essential elements with non-uniform vertical distribution that can be taken up by roots will create an elemental signature that will indicate the depth of active roots. Elemental signatures will be developed by characterizing elemental profiles with soil depth at various field sites and comparing them with signatures detected in the leaves, quantified with X-ray fluorescence, and confirmed with inductively coupled plasma spectroscopy. New anatomical traits will be assessed using laser ablation tomography (LAT), a system we developed for two and three-dimensional imaging of root anatomy, combined with multispectral imaging to reveal chemical signatures not visible in the original LAT technology. Genomic regions associated with natural variation for root traits will be discovered through genome-wide association analysis and quantitative trait loci analysis. Particularly relevant regions will be selected for further dissection including candidate gene testing using mutants and gene editing technologies.Goal 3. Investigating the role of root-associated microbes (i.e., the root-microbiome) in modulating root physiological responses under abiotic stresses. (Brown, Lynch, Dini Andreote)Manipulation of distinct plant genotypes across distinct soil types will be performed to depict the relative influences of these variables on the assembly and dynamics of root-associated microbiomes. Follow-up experiments will test variations of these microbiomes once exposed to controlled abiotic stress conditions. Data collected from these experiments will be linked to plant and root physiological status and serve as baseline information for follow-up in vitro tests. For that, selected plants will be tested with a combination of one or several microbial strains for their roles in mediating changes in root structure and physiology. In addition, distinct plant genotypes exposed to abiotic stresses will be subjected to root exudate collection at different stages of plant development and gradients of stress conditions. Root exudates will be profiled using metabolomics and further used as nutrient sources to enrich specific microbial communities in vitro. The goal is to investigate the extent to which abiotic stresses affect root exudate profiles and, as such, modify the selection of potentially beneficial root-associated microbes. All data analysis will be performed using state-of-the-art bioinformatics tools and statistical methods. The results of this work will be presented at scientific conferences and disseminated through scientific publications in the areas of plant-microbiome and plant microbe-interaction.Results of this project will be disseminated through scientific publications, presentations at scientific conferences, reports to sponsors, and cooperation with journalists to reach a wider audience. Training will be provided to graduate and undergraduate students, who will directly participate in the research including hypothesis generation, experimental design, conducting experiments, and reporting results in various written and spoken forms. Outcomes will be evaluated based on successful publication in high-quality journals, speaking invitations, and influence on the scientific and plant breeding communities.

Progress 01/01/20 to 09/30/20

Target Audience: Crop scientists, plant breeders, seed companies, and technology companies and organizations serving crop industries in the United States and abroad Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Due to COVID restrictions, there were fewer than usual opportunities for students and postdoctoral researchers to attend conferences and workshops. However, before travel restrictions began, one of the postdoctoral researchers presented a talk at the University of Florida, at a conference titled "Big Data in Plant Science" Corteva Agrisciences Plant Science Symposia Series, January 2020.Two graduate students completing their degrees this year presented three seminars each, one of which was at another univerisity. P.I. Lynch presented several seminars via ZOOM, including one in India. How have the results been disseminated to communities of interest?Dr. Duque presented a webinar to the Colombian Association of Plant Breeding and Crop Production and Cenicaña on root and tuber crop phenomics. What do you plan to do during the next reporting period to accomplish the goals?We will continue making progress toward all the goals of the project. Dr. Dini Andreote (new faculty) will continue to set up his new lab and recruit graduate students who will work on Goal 3.

What was accomplished under these goals? Goal 1. Greenhouse and field studies were used to characterize root architecture of sweetpotato, and have revealed genetic variation in root genotypic plasticity in response to drought and low nutrient stress. We have yet to identify root plasticity responses that could confer drought resistance without compromising shape, size and final yield in sweetpotato, since stress affects all potential growing roots.(Duque) In field comparisons of eight cultivars of sweetpotato in Pennsylvania, multi-year field studies were conducted to identify root architectural and anatomical traits associated with better drought tolerance in temperate inbred maize lines of the Wisconsin Diversity panel (Lynch, Brown). No single trait was strongly associated with improved performance under drought. Instead, root traits interact to determine the ability of the root system to access and transport moisture, which is typically more available at depth in terminal drought situations. Two types of analysis were used to identify combinations of root traits, i.e., integrated root phenotypes, that were associated with better performance under terminal drought. In bulked segregant analysis, the root traits of best and worst performing quartiles of genotypes under drought but with similar vigor in well-watered conditions were compared. Cluster analysis is a technique to identify groups of genotypes with similar combinations of root traits. Thick roots with a larger stele, which may be associated with the ability of roots to penetrate hard, drying soil, were found to be valuable in both cluster and bulk segregant analyses. Root systems of the best genotypes and best clusters had steeper crown root angles, anatomical traits that reduce root metabolic cost (fewer and larger cortical cells, more aerenchyma), and negative plasticity (decrease with drought) in metaxylem area, resulting in reduced axial water conductance. Overall, genotypes with water-saving strategies, i.e., with moderated water usage under drought, were superior to those with water-spending strategies, where the plant takes as much water as possible, but for the earliest-flowering genotypes, this did not appear to be as crucial. Earlier flowering genotypes may escape drought to some extent, and due to the shorter growth period, they do not deplete soil moisture to the same extent as late flowering genotypes. Breeders should adjust their ideotypes for root traits based on crop phenology and expected drought scenarios. Common bean (Phaseolus vulgaris) and tepary bean (P. acutifolius) genotypes were compared under drought and well-watered conditions in the greenhouse and field and phenotypic combinations were also tested in silico with OpenSimRoot. As with maize, performance depended on combinations of root traits more than on individual traits. In genotypes with a strong and deep tap root, greater axial water conductance was beneficial under drought, while in shallower rooted genotypes, limited axial conductance and conservation of soil moisture were more beneficial. A comparison of seven leguminous crops revealed a spectrum of phenotypic strategies consistent with these findings, including dimorphic root architectures that co-optimize acquisition of shallow nutrients and deep water (Lynch). Goal 2. Field studies at sites in Arizona and South Africa were used to identify the genetic basis of environmental plasticity of root traits using the Wisconsin Diversity Panel of temperate-adapted maize inbred lines (Lynch, Brown). All of the examined root traits exhibited quantitative variation in trait values and plasticity. A total of 69 unique genes were associated with root architecture traits or their plasticity and 158 genes were associated with root anatomical traits or their plasticity. Broad sense heritability ranged from 0.13 to 0.68 depending on the trait and site. Plasticity traits tended to have lower heritability but fell into the same range, supporting a genetic basis for plasticity. Genes controlling trait values were mostly different from those controlling plasticity in response to drought stress or the different field environments, although a few common genes were discovered, some of which were involved in ethylene, auxin, or abscisic acid (ABA)signaling. These would be the best targets for breeding since they would be the most robust across environments. Phenotypic evaluation of seedlings would be one way to characterize root traits important for yield under stress, provided that these relate to field performance (Lynch). Seedling phenotypes of 577 diverse P. vulgaris genotypes were compared with field performance across 51 environments with a wide range of stresses. Andean, Mesoamerican, Durango, and interspecific gene pools tended to aggregate within the same cluster of integrated phenotypes, suggesting that gene pools are characterized by particular root architectures. Seed yield was significantly related to several seedling traits, including basal root number in 22% of environments and adventitious root number in 35% of environments. Integrated phenotypes with intermediate phene states had the best performance across diverse environments, while more extreme phene states tended to be associated with better performance in particular stress environments but worse performance in others. One trait that was valuable across a range of environments was greater seedling tap root length, which may be related to greater root depth in the field. Goal 3. Nothing to report;new lab being set up.


  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Klein SP, HM Schneider, AC Perkins, KM Brown, JP Lynch. 2020 Multiple integrated root phenotypes are associated with improved drought tolerance. Plant Physiology 183:1011-1025
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Schneider, H, S Klein, M Hanlon, EA Nord, S Kaeppler, K Brown, A Warry, R Bhosale, J Lynch 2020. Genetic control of root architectural plasticity in maize. J Exp Bot 71:3185-3197
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Schneider, H, S Klein, M Hanlon, K Brown, S Kaeppler, J Lynch 2019. Genetic control of root anatomical plasticity in maize. Plant Genome e20003
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Strock, CF, Burridge JD, Niemiec MD, Brown KM and Lynch JP. 2020. Root metaxylem and architecture phenotypes integrate to regulate water use under drought stress. Plant, Cell and Environment
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Oyiga, Benedict C; Palczak, Janina ; Wojciechowski , Tobias; Lynch, Jonathan P.; Naz, Ali A; Leon, Jens; Ballvora, Agim. 2019. Genetic components of root architecture and anatomy adjustments to water-deficit stress in spring barley. Plant, Cell, and Environment 43:692-711. DOI: 10.1111/pce.13683
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Falcon CM, Kaeppler SM, Spalding EP, Miller ND, Haase N, AlKhalifah N, Bohn M, Buckler ES, Campbell DA, Ciampitti I, et al (2020) Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds. Crop Sci 60: 6281. DOI: 10.1002/csc2.20035
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Benes B, Guan K, Lang M, Long SP, Lynch JP, Marshall-Col�n A, Peng B, Schnable J, Sweetlove LJ, Turk MJ (2020) Multiscale computational models can guide experimentation and targeted measurements for crop improvement. Plant J 103: 2131
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Burridge JD, Rangarajan H, Lynch JP (2020) Comparative phenomics of annual grain legume root architecture. Crop Sci 60: 25742593
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Jochua CN, Strock CF, Lynch JP (2020) Root phenotypic diversity in common bean (Phaseolus vulgaris L.) reveals contrasting strategies for soil resource acquisition among gene pools and races. Crop Sci. doi: 10.1002/csc2.20312
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: McFarland BA, AlKhalifah N, Bohn M, Bubert J, Buckler ES, Ciampitti I, Edwards J, Ertl D, Gage JL, Falcon CM, et al (2020) Maize genomes to fields (G2F): 20142017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets. BMC Res Notes 13: 71
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Schneider HM, Lynch JP (2020) Should root plasticity be a crop breeding target? Front Plant Sci 11: 546
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Schneider HM, Postma JA, Kochs J, Pflugfelder D, Lynch JP, van Dusschoten D (2020) Spatio-Temporal Variation in Water Uptake in Seminal and Nodal Root Systems of Barley Plants Grown in Soil. Front Plant Sci 11: 1247
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Strock CF, Lynch JP (2020) Root secondary growth: an unexplored component of soil resource acquisition. Ann Bot 126: 205218
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Vanhees DJ, Loades KW, Bengough AG, Mooney SJ, Lynch JP (2020) Root anatomical traits contribute to deeper rooting of maize under compacted field conditions. J Exp Bot 71: 42434257