Source: PENNSYLVANIA STATE UNIVERSITY submitted to
ROOT CORTICAL CELL FILE NUMBER- A NOVEL TRAIT TO INCREASE DROUGHT TOLERANCE BY REDUCING THE METABOLIC COST OF SOIL EXPLORATION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1001025
Grant No.
2014-67013-21572
Cumulative Award Amt.
$500,000.00
Proposal No.
2013-02682
Multistate No.
(N/A)
Project Start Date
Dec 1, 2013
Project End Date
Nov 30, 2017
Grant Year
2014
Program Code
[A1101]- Plant Health and Production and Plant Products: Biology of Agricultural Plants
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802
Performing Department
Plant Science
Non Technical Summary
We have recently discovered that genetic variation for the number of root cortical cell files (CCFN) in maize is associated with substantial variation in the metabolic costs of soil exploration, and thereby root growth, water acquisition, and yield under drought. The overall objective of this project is to evaluate and develop this trait as a tool to improve drought tolerance in maize and eventually other crops. Specifically, we will: 1. Confirm the physiological utility of CCFN for root growth, soil exploration, and water capture from drying soil in controlled environments. 2. Identify genes underlying natural variation in CCFN and develop stocks that will support mechanistic assessment of its regulation and utility. 3. Evaluate the utility of CCFN for drought tolerance in the field in rainout shelters in PA and a field research facility in AZ. Defining and understanding traits enhancing drought tolerance is of considerable importance for keeping American agriculture competitive while ending world hunger, as well as adapting to climate change, two of NIFA's grand challenges. CCFN could be an entirely new tool for improving drought tolerance of crops. In addition to drought, CCFN may be useful in the acquisition of limiting soil nutrients such as phosphorus and nitrogen. While this project focuses on maize, we have observed variation for CCFN in rice, sorghum, and common bean, so this trait may have broad utility. This project therefore addresses novel scientific issues that are of demonstrable relevance to human welfare.
Animal Health Component
0%
Research Effort Categories
Basic
100%
Applied
0%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2031510101050%
2031510108050%
Knowledge Area
203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants;

Subject Of Investigation
1510 - Corn;

Field Of Science
1010 - Nutrition and metabolism; 1080 - Genetics;
Goals / Objectives
Objectives: We have recently discovered that genetic variation for the number of root cortical cell files (CCFN) in maize is associated with substantial variation in the metabolic costs of soil exploration, and thereby root growth and water acquisition under drought. The overall objective of this project is to evaluate and develop this trait as a tool to improve drought tolerance in maize and eventually other crops. Specifically, we will: Confirm the physiological utility of CCFN for root growth, soil exploration, and water capture from drying soil in controlled environments. Identify genes underlying natural variation in CCFN and develop stocks that will support mechanistic assessment of its regulation and utility. Evaluate the utility of CCFN for drought tolerance in the field in rainout shelters in PA and a field research facility in AZ.
Project Methods
Activity 1. Evaluate the physiological utility of CCFN for drought tolerance in controlled environments. The goal of this objective is to rigorously evaluate the physiological costs and benefits of CCFN and related anatomical traits for water acquisition in drying soil. Greenhouse studies will permit a detailed evaluation of the effect of CCFN on root respiration, root growth, and water uptake. Existing Inbred lines and Recombinant Inbred Lines, in addition to Near Isogenic Lines and transgenics (from activity 2) contrasting for CCFN will be grown in soil mesocosms maintained at field capacity or subjected to progressive drought by irrigating at a fraction of the nonstressed treatment to achieve from 30 to 60 % reduction in shoot growth. Soil water content from representative mesocosms will be tracked with a multiplexed TDR-100 system (Campbell Scientific) placed at various depths in the soil logged by a CR21X (Campbell Scientific). Leaf stomatal conductance and CO2 assimilation will be monitored with a LI 6400 (LI-COR Biosciences). Root depth will be estimated nondestructively in a subset of mesocosms with minirhizotron cameras (BTC100, Bartz Technology Corporation) through transparent horizontal tubes placed throughout the mesocosm. In a typical study plants will be destructively harvested at 14, 28, and 42 days after planting for analysis of tissue water status, biomass, root growth and architecture, leaf area, and root anatomy. The mesocosms have plastic liners that permit the soil column to be removed intact. These columns will be subdivided to determine root length and soil water content with depth. Root length, diameter, and branching will be measured by image analysis (WinRhizo Pro, Regent Instruments). Root anatomical phenotypes will be quantified by image analysis (RootScan) of images gathered from Laser Ablation Tomography. Prior to each harvest a whole-plant carbon budget will be measured as canopy and root CO2 fluxes at mid-day and predawn with a closed-system IRGA (LI-COR 6200), as we have reported previously. Root respiration of distinct segments of the root system will be measured with a LI-COR 6400 IRGA in closed system mode. Leaf water status will be measured as RWC and leaf water potential with a pressure gauge (PMS model 1000). This type of study can be repeated several times per year as needed. If our hypotheses are correct, genotypes with small CCFN will have reduced root respiration, greater root growth and root depth, greater water acquisition, and better growth under drought than genotypes with large CCFN. Activity 2: Analyze genetic natural variation for CCFN. Goal 1: Phenotypic analysis Analysis of constitutive trait expression under non-stress conditions: Approximately 500 lines from the WiDiv association panel have been grown at URBC in 2010, 2011, 2012, and 2013 using two replications per genotype under non-stress conditions. Preliminary analysis of 2010 data is described in the Preliminary Results section. Anatomical measurements from the 2011 grow-out will be completed over the next few months, and analysis of the 2012 and 2013 URBC samples will be completed no later than the end of 2013. The 2010 samples were analyzed by hand-sectioning but all subsequent samples will be analyzed using laser ablation tomography as described above. The 2013 data is expected to be especially useful given the favorable growth conditions and our choice to collect two sub-samples per plot in this season. The trait of focus in this project is CCFN. Following data analysis, outliers will be determined and those images will be manually inspected for accuracy for this trait. In addition, the images of the extreme 5% of the lines will be manually inspected for accuracy to minimize error from the genotypes with most leverage in the analysis. Analysis of plasticity for trait expression under stress: The WiDiv panel will be grown in summer of 2013 and 2014 at ARBC using two replications in non-stress, N stress, and drought stress conditions. Sampling will be described above, and it is anticipated that anatomical data will be available 6 to 9 months following sample collection. CCFN will be evaluated under each regime, and plasticity will be determined as the difference in expression under stress relative to the non-stress control. Goal 2: Candidate gene discovery GWAS analysis is conducted using the Q-K model implemented in GAPIT. For multiple reasons, the most significant SNP is not always in the functional gene, but may be in a gene model adjacent to the causal gene. For this reason, multiple levels of assessment are used to sift through regional candidates (e.g. +/- five annotated gene models). We have developed a microarray-based maize gene atlas - provided to the community via MaizeGDB - and have improved the original data by conducting RNA-seq on the same samples (manuscript accepted - data to become publicly available soon), and expanded it by RNA-seq analysis of additional samples including senescing plants and, most relevant to this project, 24 unique dissected root tissues. The gene atlas is a resource to sort through candidates based on expression on relevant tissues. Expression levels of candidate genes in the WiDiv set is also used as covariate for association analysis as a way to capture causal expression differences that associate with our phenotype but are not due to factors in LD with SNPs in our set. Therefore, the sorting of candidate genes to move forward with is a decision based on combined analysis of genetic prediction, expression variation across tissues and across genotypes, and functional annotation and domain analysis. Goal 3: Candidate gene corroboration and stock development for mechanistic studies The approach to transgenic analysis will be determined based on the predicted expression alteration that will best recapitulate and extend phenotypic variation due to the predicted allelic contrast of the candidate gene. Transgenes will be introduced into HiII and backcrossed into B73 so that comparisons across genes can be accomplished in a uniform genetic background. Transposon lines will be searched for in the publicly available uniform Mu and Ac/Ds sequence tagged resources. Only existing transposon alleles will be used in the scope of the project - we will not have the resources to attempt transposon jumping from nearby launching sites. In addition to the transgenic and transposon lines, we will choose naturally occurring alleles with the largest predicted effect (effect must be at least one cell file), and backcross them into B73 and up to three additional reference inbreds chosen for specific stress tolerance characteristics based on ARBC data. Development of near-isogenic lines will 1) facilitate anatomical and physiological studies of the effect of specific QTL, 2) allow production of phenotypic contrasts independent of the accuracy of our candidate gene predictions, and 3) serve as a resource for high-resolution mapping in the future if additional genetic dissection is required. Activity 3. Evaluate the utility of CCFN for drought tolerance in the field. Existing maize lines and isolines/transgenics generated in activity 2 contrasting for CCFN will be planted with and without progressive drought stress. Plant growth, plant and soil water status, root development, and root respiration will be monitored through time. Plant water status will be measured as midday stomatal conductance (LI-6400), leaf relative water content, and predawn water potential (PMS 1000). Soil water content with depth will be monitored with Dynamax PR2 sensors. Destructive harvests will be used to measure respiration of root segments (LI-6200), root length density and soil water content with depth by soil coring (Giddings), leaf area, plant biomass partitioning, and anatomical analysis (LAT/Rootscan). Fully bordered subplots will be left for determination of yield components.

Progress 12/01/13 to 11/30/17

Outputs
Target Audience:Our primary target audiences are plant biologists and crop breeders Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project supported the PhD training of Jennifer Yang and undergraduate assistants at Penn State and postdoctoral fellow Xia Zhang at Wisconsin. How have the results been disseminated to communities of interest?We have published papers and Lynch presented results at 40 invited talks at universities and research conferences. The Lynch lab web site about root biology gets about 50k visitors per year. What do you plan to do during the next reporting period to accomplish the goals?Follow up on gene discovery activities, better understand this phenotype in maize root crowns.

Impacts
What was accomplished under these goals? We have made substantial progress in all objectives. We have published evidence that decreased CCFN substantially improves the drought tolerance of maize in Africa and the USA. We have also discovered a related yet distinct root phene, cortical cell size (CCS), and have published evidence that it also substantially improves the drought tolerance of maize. We have shown that CCFN and CCS are related to root penetration of hard soil, an important aspect of crop drought tolerance. We have shown that cultivated maize lines over the past 100 years have become more N efficient, in part due to changes in root cortical anatomy. We have shown that root anatomy and architecture interact to determine N capture in maize. We have developed, validated, and advanced an ideotype for improved N and water capture in maize based on our research on root anatomy and architecture. We have identified candidate genes for variation in CCFN that we are now confirming.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: Lynch JP. Rightsizing root phenotypes for drought resistance. J Exp Botany. In Press.
  • Type: Theses/Dissertations Status: Published Year Published: 2017 Citation: Yang, JT. 2017. Integrating Root and Leaf Phenotypes to Enhance Nitrogen Use Efficiency in Maize (Zea Mays L.).


Progress 12/01/15 to 11/30/16

Outputs
Target Audience:Our primary target audiences are plant biologists and crop breeders Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project is supporting the PhD training of Jennifer Yang and undergraduate assistants at Penn State and postdoctoral fellow Xia Zhang at Wisconsin . How have the results been disseminated to communities of interest?We have published papers and Lynch presented results at 15 invited talks at universities and research conferences. The Lynch lab web site about root biology gets about 30k visitors per year. What do you plan to do during the next reporting period to accomplish the goals?Follow up on gene discovery activities, better understand this phenotype in maize root crowns.

Impacts
What was accomplished under these goals? We have made substantial progress in all objectives. We have published evidence that decreased CCFN substantially imprives the drought tolerance of maize in africa and the USA. We have also discovered a related yet distinct root phene, cortical cell size (CCS), and have published evidence that it also substantially improves the drought tolerance of maize. We have shown that CCFN and CCS are related to root penetration if hard soil, an important aspect of crop drought tolerance. We have shown that cultivated maize lines over the past 100 years have become more N efficient, in part due to changes in root cortical anatomy. We have identified candidate genes for variation in CCFN that we are now confirming.

Publications


    Progress 12/01/14 to 11/30/15

    Outputs
    Target Audience:This project will develop several distinct outputs, including: 1- Information regarding the physiological utility of a specific root trait for soil resource acquisition 2- Information regarding the genetic control of this trait in maize The primary target audiences are plant biologists and crop breeders. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project is supporting the PhD training of Jennifer Yang at Penn State and postdoctoral fellow Xia Zhang at Wisconsin. How have the results been disseminated to communities of interest?We have published papers and Lynch presented results at 15 invited talks at universities and research conferences. The Lynch lab web site about root biology gets about 30k visitors per year. What do you plan to do during the next reporting period to accomplish the goals?We are confirming candidate genes by phenotyping mu insertion lines in the candudate genes.

    Impacts
    What was accomplished under these goals? We have made substantial progress in all objectives. We have published evidence that decreased CCFN substantiallyimprives the drought tolerance of maize in africa and the USA. We have also discovered a related yet distinct root phene, cortical cell size (CCS), and have published evidence that it also substantially improves the drought tolerance of maize. We have shown that CCFN and CCS are related to root penetration if hard soil, an important aspect of crop drought tolerance. We have shown that cultivated maize lines over the past 100 years have become more N efficient, in part due to changes in root cortical anatomy. We haveidentified candidate genes for variation in CCFN that we are now confirming.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2015 Citation: York LM, T Galindo Casta�eda, JR Schussler, JP Lynch. 2015. Evolution of maize (Zea mays L.) root architectural and anatomical phenes over the past 100 years corresponds to increased tolerance of nitrogen stress. J Exp. Botany 66:2347-2358.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nord EA, RE Jaramillo, JP Lynch. 2015. Edaphic control of plant response to elevated CO2 in Festuca arundinaceae. Frontiers in Plant Science doi: 10.3389/fpls.2015.00095.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Miguel MA, JA Postma, JP Lynch. 2015. Phene synergism between root hairs and basal root growth angle for phosphorus acquisition in common bean. Plant Physiology, 167:1430-1439.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chimungu JG, KW Loades, JP Lynch 2015 Root anatomical phenes predict root penetration ability and biomechanical properties in maize, J Exp. Botany, 66: 3151-3162.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: York LM, JP Lynch. 2015. Intensive phenotyping of maize (Zea mays L.) root crowns reveals phenes and phene interactions associated with plant growth and N capture. J Exp. Botany, doi:10.1093/jxb/erv241.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Zhan A, H Schneider, JP Lynch. 2015. Reduced lateral root branching density improves drought tolerance in maize. Plant Physiology 168:1603-1615.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bishopp, A, JP Lynch. The hidden half of crop yields. 2015. Nature Plants. doi:10.1038/nplants.2015.117.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Colombi T, Kirchgessner N, Le Mari� C, York LM, Lynch JP, Hund A. 2015. Next generation shovelomics: set up a tent and REST. Plant and Soil 388:1-20.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Zhan A, JP Lynch. 2015. Reduced frequency of lateral root branching improves N capture from low N soils in maize. J Exp. Botany, 66:2055-2065.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Das, A, H Schneider, J Burridge, A Martinez-Ascanio, T Wojciechowski, CN Topp, JP Lynch, JS Weitz, A Bucksch. 2015. Digital Imaging of Root Traits (DIRT): a high-throughput computing and collaboration platform for field-based plant phenomics. Plant Methods, 11:51 DOI: 10.1186/s13007-015-0093-3.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Stelpflug, S.C., R.S. Sekhon, B. Vaillancourt, C.N. Hirsch, C.R. Buell, N. de Leon, and S.M. Kaeppler. 2015. An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development. Plant Genome doi: 10.3835/plantgenome2015.04.0025.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Burton AL, J Johnson, J Foerster, MT Hanlon, SM Kaeppler, JP Lynch, KM Brown. 2015. QTL mapping and phenotypic variation of root anatomical traits in maize (Zea mays L.). Theoretical Applied Genetics, 128:93-106.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chimungu JG, MFA Maliro, PC Nalivata, G Kanyama-Phiri, KM Brown, JP Lynch. 2015. Utility of root cortical aerenchyma under water limited conditions in tropical maize (Zea mays L.). Field Crops Research, 171:86-98.
    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Lynch JP, T Wojciechowski. 2015. Opportunities and challenges in the subsoil: pathways to deeper rooted crops, J Exp. Botany, 66: 2199-2210.


    Progress 12/01/13 to 11/30/14

    Outputs
    Target Audience: This project will develop several distinct outputs, including: 1- Information regarding the physiological utility of a specific root trait for soil resource acquisition 2- Information regarding the genetic control of this trait in maize The primary target audiences are plant biologists and crop breeders. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project is supporting the PhD training of Jennifer Yang at Penn State and postdoctoral fellow Xia Zhang at Wisconsin . How have the results been disseminated to communities of interest? We have published papers and Lynch presented results at 7 invited talks at universities and research conferences. What do you plan to do during the next reporting period to accomplish the goals? We are now investigating whether variation in CCFN is related to N capture. We continue to refine GWAS results to identify major genes controlling this trait.

    Impacts
    What was accomplished under these goals? We have made substantial progress in all objectives. We have published evidence that decreased CCFN substantially imprives the drought tolerance of maize in africa and the USA. We have also discovered a related yet distinct root phene, cortical cell size, and have published evidence that it also substantially improves the drought tolerance of maize. We have identified candidate genes for variation in CCFN that we are now confirming.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2014 Citation: JG Chimungu, KM Brown, JP Lynch. 2014. Large root cortical cell size improves drought tolerance in maize (Zea mays L.). Plant Physiology DOI:10.1104/pp.114.250449
    • Type: Journal Articles Status: Awaiting Publication Year Published: 2014 Citation: AL Burton, J Johnson, J Foerster, MT Hanlon, SM Kaeppler, JP Lynch, KM Brown. 2014. QTL mapping and phenotypic variation of root anatomical traits in maize (Zea mays L.)" Theoretical Applied Genetics, in press
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: JG Chimungu, KM Brown, JP Lynch. Reduced root cortical cell file number improves drought tolerance in maize. Plant Physiology doi:10.1104/pp.114.249037
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Bo Hu, A Henry, KM Brown, JP Lynch. 2014. Root cortical aerenchyma inhibits radial nutrient transport in maize (Zea mays L.). Annals of Botany 113: 181-189.
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Lynch, JP, JG Chimungu, KM Brown. 2014. Root anatomical phenes for water acquisition from drying soil: targets for crop improvement. J Experimental Botany, 65:6155-6166
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Saengwilai P, EA Nord, JG Chimungu, KM Brown JP Lynch. 2014. Root cortical aerenchyma enhances nitrogen acquisition from low nitrogen soils in maize (Zea mays L.) Plant Physiology, 166:726-735
    • Type: Journal Articles Status: Published Year Published: 2014 Citation: Lynch JP. 2014. Root phenes that reduce the metabolic costs of soil exploration: opportunities for 21st century agriculture. Plant, Cell and Environment, doi: 10.1111/pce.12451
    • Type: Journal Articles Status: Awaiting Publication Year Published: 2014 Citation: JG Chimungu, MFA Maliro, PC Nalivata, G Kanyama-Phiri, KM Brown, JP Lynch. Utility of root cortical aerenchyma under water limited conditions in tropical maize (Zea mays L.). Field Crops Research, in press.
    • Type: Journal Articles Status: Awaiting Publication Year Published: 2014 Citation: Lynch JP, T Wojciechowski. Opportunities and challenges in the subsoil: pathways to deeper rooted crops, J Experimental Botany, in press
    • Type: Book Chapters Status: Published Year Published: 2014 Citation: Joseph G. Chimungu, Jonathan P. Lynch 2014 Root Phenes for Improving Nitrogen Acquisition Efficiency. In: Plant Biotechnology: Experience and future prospects, A Ricroch, S Chjopra, SJ Fleischer, eds. Springer.
    • Type: Journal Articles Status: Under Review Year Published: 2014 Citation: Chimungu JG, KW Loades, JP Lynch Root anatomical phenes predict root penetration ability and biomechanical properties in maize. J Exp Botany, submitted