Source: TENNESSEE STATE UNIVERSITY submitted to NRP
GENOME WIDE ANALYSIS OF ROOT NODULATION AND ROOT SYSTEM ARCHITECTURE IN SOYBEAN
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1025283
Grant No.
2021-67014-33738
Cumulative Award Amt.
$200,000.00
Proposal No.
2020-03622
Multistate No.
(N/A)
Project Start Date
Jan 15, 2021
Project End Date
Jan 14, 2025
Grant Year
2021
Program Code
[A1152]- Physiology of Agricultural Plants
Recipient Organization
TENNESSEE STATE UNIVERSITY
3500 JOHN A. MERRITT BLVD
NASHVILLE,TN 37209
Performing Department
Agricultural & Environ Sci
Non Technical Summary
Developing crops with better root system architecture and nitrogen use efficiency can lead to resilient crops capable of sustaining productivity in both optimum and stress environments. The increase in soybean global demand and its use in biodiesel and new soy-based products calls for new soybean cultivars that have higher yields, better nutritional values or desirable traits for specific use. The soybean germplasm collection at the USDA is a valuable resource in discovering novel allelic variations. This collection has not been screened extensively for the root nodule and root system architecture traits. We have already established root phenotyping platforms in our laboratory and we are proposing to screen a diverse pool of the USDA soybean collection for nodules and root system architecture traits. Availability of SNP data for this collection will let us run genome-wide analysis and identify QTLs responsible for different root traits. We will then use hairy root transformation to knockout/down some of the candidate genes in the loci identified in earlier reports and new QTLs identified in this project. This project will help us in deciphering the phenotypic variation in soybean root traits. Ultimately, better understanding of the regulatory mechanism controlling these traits can help us in developing resilient crops and a sustainable cropping system.
Animal Health Component
10%
Research Effort Categories
Basic
70%
Applied
10%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011820102050%
2011820108050%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1820 - Soybean;

Field Of Science
1080 - Genetics; 1020 - Physiology;
Goals / Objectives
The long-term goal of this project is to enhance our knowledge in nitrogen use efficiency for soybean and discover mechanisms involved in nodulation.Considering increase in the world population and climate change, developing high yielding and resilient crops is of vital importance. Most of the plant breeding efforts and programs have focused on the aboveground parts of the plants and the root system has been neglected probably due to its hidden nature. Soybean plants acquire 50-70% of their nitrogen needs via nitrogen fixation. Screening the diverse soybean germplasm collection available at USDA can help us identify accessions with better nodulation and shed lights on the regulatory pathways controlling these traits. Water use efficiency in plants relies heavily on their root structure and there is a need to identify such variations in soybean collections as well. With the root phenotyping platform that we have developed here in TSU and the strong team of scientists in this project, our goal isto identify QTLs responsible for traits associated with RSA and nodule formation. Understanding the molecular pathways involved in nodule formation and RSA can help in developing resilient crops and a more sustainable cropping system.
Project Methods
1.1.1 Plant materialsOut of 11,515 USDA soybean accessions in maturity groups II to V, we will select 500 accessions based on the cluster and genetic distance among all the accessions. These accessions will be requested from the USDA?GRIN. This collection has not been screened for nodulation and GWA studies; however, an earlier report has used another set of the USDA collection for RSA with majority from early maturity groups. To avoid duplications, we will remove all of the accessions that were included in those reportsfrom our final list except a small subset which will be used as checks and for comparison of the results. Fifteen seeds from each accession will be pre-germinated in brown germination papers. One week after planting, healthy and uniform seedlings will be inoculated with B. japonicum 110 and transferred to the blotter systemshanging over optimized nutrient solution that is prepared based on previous reports. We will plant only one seedling per blotting unit to avoid root overlaps that might interfere with the RSA analysis. Nodulation and RSA data will be collected using a flatbed scanner and will be processed using open-source RootNav software. For extreme nodulation phenotypes and hairy root transformation assay, we will use the ultrasound aeroponic system to grow the plants for longer period. To address the discrepancy of root development between soil condition and these phenotyping platforms, this panel will be planted in the soil mix inside the greenhouse and also a subset that will be planted and phenotyped in field condition.1.1.2 Genome?wide association analysisThe average nodulation and RSA trait values of the ten biological replicates for 500 accessions will be used for association analysis. Genome?wide association analysis will be performed with GAPIT softwareusing mixed linear model (MLM) and compressed mixed linear model (CMLM) approaches. The SNPs with strong signal associations with a calculated p value (that will be determined by FDR, Bonferroni correction or Permutation test) will be identified for further analysis. Genotypic data from the SoySNP50Karray will be retrieved from SoyBaseand population structure will be calculated using principal component analysis (PCA). Dr. Song and Dr. Valliyodan will assist us in these analyses.

Progress 01/15/21 to 12/13/24

Outputs
Target Audience: Farmers, Especially Soybean Growers Farmers benefit from advancements in soybean breeding, particularly traits that improve root efficiency, nodulation, and nitrogen fixation, which can reduce input costs (e.g., fertilizers) and increase yields. Graduate and Undergraduate Students Directly Involved in the Project Students working on the project gain hands-on experience in cutting-edge genomic techniques, bioinformatics, and field trials, which enhance their education and career prospects. Scientists with Interest in Soybean Research Researchers focused on soybean genetics, plant physiology, and agronomy can utilize findings to advance their own studies, particularly in breeding programs or understanding plant-microbe interactions. Extension Specialists and Agricultural Advisors These professionals bridge the gap between research and farmers, translating complex findings into actionable recommendations for crop management. Policy Makers and Funding Agencies Research outcomes can influence policies on sustainable agriculture and funding priorities for agricultural innovation. Soybean Industry Stakeholders Seed companies, agricultural biotechnology firms, and fertilizer producers have a vested interest in traits that improve crop performance and reduce reliance on external inputs. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Two graduate students and one undergraduate students were enganged in this project and getting trained on soybean root phenotyping How have the results been disseminated to communities of interest? Niraj Ghimire*, Korsi Dumenyo, and Ali Taheri, Genome-Wide Association study for root nodulation in field Soybean. Feb 15, 2024. NAPPN, Purdue University, West Lafayette, IN Niraj Ghimire*, Korsi Dumenyo, and Ali Taheri, Genome-wide association study for root nodulation in field soybean. Nov 18, 2023. Tennessee Academy of Science, Memphis, Tennessee Pallavi Rathore *, Korsi Dumenyo, and Ali Taheri,Genome-wide association study for root system architecture traits in field Soybean [Glycine max (L.) Merr.]. 18 Nov 2023. TennesseeAcademy of Science, Memphis, Tennessee Niraj Ghimire*, Ali Taheri. Korsi Dumenyo. Genome wide analysis of field soybean for root nodulation. 2024 TSU Research Symposium. March 2024 Niraj Ghimire*, Ali Taheri. Korsi Dumenyo. Studying Nodulation Traits in Field Soybean through Genome Wide Association studies. ARD Symposium. April 2024, Nashville, TN Exploring Root System Architecture Traits in Field-Grown Soybean (Glycine max (L.) Merr.) through Genome-Wide Association Analysis. ARD Symposium. April 2024, Nashville, TN Ali Taheri. Genome wide assessment of root system traits in mid to late maturity soybeans. ASPB 2024. Honolulu, HI What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Completed the root nodulation goal of this project on 500 accessions that were ordered from USDA GRIN. Conducted GWAS analysis on these genotypes using TASSEL, FarmCPU and GapIT pipelines. Submitted the paper on root system architechture and GWAS analysis from this work in peer reviewed journal. Rathore, P., Shivashakarappa, K., Ghimire, N.et al.Genome-Wide Association study for root system architecture traits in field soybean [Glycine max(L.) Merr.].Sci Rep14, 25075 (2024). https://doi.org/10.1038/s41598-024-76515-6 Submitted the paper on soybean nodulation on this population that is under review.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Rathore, P., Shivashakarappa, K., Ghimire, N. et al. Genome-Wide Association study for root system architecture traits in field soybean [Glycine max (L.) Merr.]. Sci Rep 14, 25075 (2024). https://doi.org/10.1038/s41598-024-76515-6


Progress 01/15/23 to 01/14/24

Outputs
Target Audience:Farmers specially soybean growers,Graduate and undergraduate students that are directly invoved in the project,Scientists with interest in soybean research. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Two graduate students and one undergraduate students are enganged in this project and getting trained on soybean root phenotyping. How have the results been disseminated to communities of interest?The results were presented in the following conferences: Pallavi Rathore, Taheri Ali, Korsi Dumenyo, Babu Valliyodan, Marc Libault, and Qijian Song. Genome wide analysis of root nodulation and root system architecture in soybean accessions. The North American Plant Phenotyping Network (NAPPN). Feb 2023. Danforth Plant Science Center. MO Niraj Ghimire*, Korsi Dumenyo, and Ali Taheri,Genome-wide association study for root nodulation in field soybean. Nov 18Tennessee Academy of Science, Memphis, Tennessee Pallavi Rathore *, Korsi Dumenyo, and Ali Taheri,Genome-wide association study for root system architecture traits in field Soybean [Glycine max (L.) Merr.]. 18 Nov Tennessee Academy of Science, Memphis, Tennessee What do you plan to do during the next reporting period to accomplish the goals?Complete the nodulation on the remaining soybean accessions Conduct GWAS on nodulation phenotype Prepare and submit manuscripts and final reports to the agency

Impacts
What was accomplished under these goals? Completed the root phenotyping goal of this project on 500 accessions that were ordered from USDA GRIN. Optimized and Conducted GWAS analysis on these genotypes using TASSEL, FarmCPU and GapIT pipelines. Strated soybean nodulation on 500 accessions in multiple batches and have completed 50% oftheir phenotyping.

Publications


    Progress 01/15/22 to 01/14/23

    Outputs
    Target Audience:Students and scientists at Tennessee State University and nearby colleges Changes/Problems:Recruiting graduate student was challenging due to covid restriction. We managed to recruit one and planning to recruit second graduate student for this project in the following semester. What opportunities for training and professional development has the project provided?Two graduate students and one undergraduate students are enganged in this project and getting trained on soybean root phenotyping. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?Complete the root phenotyping for all the soybean accessions. Run the image processing piple and collect the data that is necessary for GWAS study. Prepare CRISPR vectors for targetting come of the candidate genes that are involved in RSA. Finish the GWAS study and analyse the results.

    Impacts
    What was accomplished under these goals? Received the germplasm from USDA GRIN and started the root phenotyping on 100 soybean accessions (1/5 of the total number of accessions). Evaluated multiple piplines and softwares for image analysis.

    Publications


      Progress 01/15/21 to 01/14/22

      Outputs
      Target Audience: Nothing Reported Changes/Problems:Due to the 2020 tornado, our greenhouse facility was completelydestroyed and we are in the processof building new ones. Per conversations with the administration, they will be ready early next semester and we will be able to start our greenhouse experiments soon. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?Conduct the root phenotyping for 500 individual lines in the greenhouse and characterize root traits that are different between these lines.

      Impacts
      What was accomplished under these goals? A panel of soybean lines with diverse background were selected from late maturity groups and ordered from the USDA GRIN website. Student recruitment was carried out for this position and we are hoping that they can join by next semester.

      Publications