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
Sep 1, 2015
Project End Date
Aug 31, 2019
Grant Year
Project Director
Kalavacharla, V.
Recipient Organization
DOVER,DE 19901
Performing Department
Agriculture & Natural Resource
Non Technical Summary
Common bean (Phaseolus vulgaris L.) is the most important grain legume in the world and is a $1.2 billion crop in the United States. Common bean and other legumes are affected greatly by many biotic and abiotic stresses, and specifically common bean yields are negatively impacted by the bean rust fungal pathogen Uromyces appendiculatus, which may cause losses from 18-100%. We plan to use cutting-edge molecular genetics and epigenomics techniques to better understand the resistance and susceptibility mechanisms to this important disease. Differences in DNA methylation and gene expression will be compared among a rust-resistant wild type, susceptible wild type, and two susceptible mutants derived from the resistant wild type. This work builds on our previous common bean molecular genetics and genomics work in the area of disease resistance and comparative genomics along with the development of a reference DNA methylome project that is underway. This project will help us determine the effect of genome mutations affecting disease resistance on global DNA methylation and transcription simultaneously, under normal and biotic stress conditions. Additionally, the proposed project will also contribute to understanding of disease resistance mechanisms in soybean (Glycine max) and lima bean (Phaseolus lunatus) which are closely related legumes of economic significance in the United States. This project will further allow for the training of researchers from many levels at Delaware State University, the University of Arkansas-Pine Bluff, and at Mayville State University.
Animal Health Component
Research Effort Categories

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
Goals / Objectives
Objective 1: Develop reference leaf methylomes and transcriptomes from four genotypes of common bean.Objective 2: Develop biotic stressed leaf methylomes and transcriptomes from four genotypes of fungal rust-infected common bean and determine the methylomic and transcriptomic changes between resistant and susceptible genotypes.Objective 3: Expand the reach of the project through development of community genomics resources and integrated research-education and outreach programs.
Project Methods
Objective 1:Genotypes and Growth Conditions: Bean genotypes that will be used for reference methylome work are the cultivar Sierra (resistant wild type), the cultivar Olathe (susceptible wild type), and two susceptible mutants derived from Sierra via fast-neutron-bombardment, crg and ur3-Δ3. We will follow current protocols from the PI's laboratory in achieving these steps. Germinated seeds will be planted in a growth chamber, with day/night temperatures of 28/20°C and 14/10 h photoperiod. Two-week-old plant primary leaves will be collected and stored in a -80?C freezer until DNA and RNA isolation.Whole Genome Bisulfite Sequencing: DNA isolation from leaves will be conducted using a cetyl trimethylammonium bromide (CTAB) method. Extracted DNA will be used for whole genome bisulfite sequencing. Bisulfite conversion of genomic DNA will be performed using the EZ DNA Methylation-Lightning™ Kit from Zymo Research™. Unmethylated cytosines (C) undergo deamination and are ultimately sequenced as thymines (T), whereas 5-methylcytosines (5mC) are unaffected by bisulfate conversion and remain sequenced as cytosines (C). The resulting bisulfite-converted DNA will then be prepared with an Illumina® HiSeq SBS Kit and sequenced on an Illumina® HiSeq 2500 platform at the sequencing center at the Delaware Biotechnology Institute (DBI) in Newark, DE, where the PI is an affiliated faculty. Reads will then be mapped back to the reference genome (G19833,!info?alias=Org_Pvulgaris). Bioinformatic analysis will be conducted using Integrative Genomics Viewer (IGV, 29) and the CLC Workbench software that is used for sequence analyses.Transcriptome Sequencing (RNA-Seq): RNA will be extracted from leaves with TRIzol® reagent, from Life Technologies™, according to the manufacturer's instructions. Extracted RNA will then be prepared for Illumina® sequencing with a TruSeq® RNA Sample Preparation Kit v2 and sequenced on an Illumina® HiSeq 2500 platform. Reads will then be mapped back to the reference genome (G19833, Phytozome). Bioinformatic analysis will be conducted using IGV as well as CLC Genomics Workbench.Validation Using Real-Time PCR (RT-PCR): As a confirmation that the RNA-seq data accurately reflects transcript levels, selected genes will be verified using real-time PCR (RT-PCR). Some genes that will be incorporated as a control include Cytochrome P450, WRKY7, and other randomly selected genes that show significant differential expression in the transcriptome results.The same RNA that will be submitted for RNA-seq will be reverse-transcribed using with Oligo dT using Superscript III First Strand Synthesis System (Life Technologies, 18080-051) according to manufacturer's instructions. Real-time PCR (RT-PCR) will be conducted on a 7500 Real-time PCR system Applied Biosystems platform with Power SYBR®Green PCR master mix (Applied Biosystems, 4309155). The ΔΔCT method will be used to analyze differential expression, in reference to the constitutively expressed gene cons7.Bioinformatic analysis: In addition to IGV and CLC Genomics Workbench mentioned above, Eukaryotic Orthologous Groups (KOG) Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis will also be used. KOG analysis will be used to determine the classification of genes that are of significant differences in expression, as determined by RNA-seq analysis.These research protocols are well established in the PI and Co-PI's laboratories.Objective 2:All of the above procedures and analyses methods described in Objective 1 will be conducted for Objective 2, except that in this case, we are inoculating the plants with bean rust. Two-week-old plant primary leaves will be rust-inoculated with a solution of water, approximately 20,000 spores per milliliter, and 0.01% Tween 20 along with appropriate mock-inoculated control plants.Bioinformatic analysis: Bioinformatic analysis of the resulting data will be carried out as per the procedures described above, and the unstressed reference transcriptome and methylome data from Objective 1, will be compared to the stressed data from Objective 2. This analysis will reveal differences between plants treated with bean rust, as well as the differences between resistant and susceptible genotypes with regards to DNA methylation and gene expression.Objective 3:Students from high schools, undergraduate and graduate students will work with the PI and Co-PIs and research associate to develop and interpret the data generated by the first two objectives. Students and technical staff will work together to communicate the results at conferences and in publications. Epigenomics Web Site and Databases: In order to develop a portal so that collaborators, as well as external community members, can access project details, we will implement a common bean epigenenomics web site at DSU. Personnel from the DSU Center for Integrated Biological and Environmental Research will be involved in developing, maintaining and updating the web site. Previous and future results can be maintained on this portal.

Progress 09/01/17 to 08/31/18

Target Audience:Undergraduate students, graduate students, high school students Changes/Problems:As described earlier, the delay in our accomplishments is because of delay in funding received, as well as, mainly, the problems with inoculation needing the collaborative efforts of our USDA-ARS colleagues. We plan to complete this in the upcoming year. What opportunities for training and professional development has the project provided?Undergraduate students working in the laboratory (whether funded or not funded by the project) have been exposed to the goals of the grant. Since biotic stress is known to cause methylation changes in some systems, our goal is to test this in the bean-bean rust system 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?We will complete analyzing the data from the methylation analysis. Next the transcriptome data will be analyzed and publications will be prepared from this work.

What was accomplished under these goals? From Objective 1:The reference leaf methylomes and transcriptomes from genotype Sierra was first developed; this has been analyzed and is being used as a reference for Objective 2. We will be analyzing the data from the methylome sequencing first, and subsequently, we will analyze the data from the inoculated samples.


    Progress 09/01/16 to 08/31/17

    Target Audience:We have exposed high school students, and undergraduate students to the reasearch that is being conducted in this project and other bean projects in the research group. We strongly feel that understanding of the importance of plants and their related pathogens and pests, and means to control this through the use of classical genetics, molecular genetics, and genomics techniques is very useful to generate interest in food security. Changes/Problems:As indicated in the last report, we were delayed in carrying out the inoculations at DSU due to environmental conditions which made successful inoculations difficult. Therefore, we reached out to our USDA-ARS collaborator for the rust inoculations, which was successful, and then we have been taking time to carefully prepare the materials at hand for the integrated BS-seq and RNA-seq work. Nothing major has changed with the approach. What opportunities for training and professional development has the project provided?Through the project we have opened our research group to provide training for individuals in plant-pathogen interactions, as well as molecular genetics and genomics methodologies. The staff involved in the project have presented their work at professional conferences that has allowed us to keep up to date with cutting edge protocols. How have the results been disseminated to communities of interest?We have presented our work through conferences as well as publications that are open-access. What do you plan to do during the next reporting period to accomplish the goals?We are submitting our high quality DNA for Sodium bisulfite-sequencing (BS-seq). Meanwhile, we are training on methylation analyses using the bioinformatics software CLC Bio. Additionally, we plan to conduct transcriptome library prepration and sequencing from the same tissues used for BS-seq.

    What was accomplished under these goals? Objective 1: We have completed developing the reference methylome and transcriptome from the resistant genotype, Sierra which is the parental material for the susceptible mutants that were proposed to be used in the project. Objective 2: We have completed inocuations of the leaves from Sierra, Olathe (naturally susceptible), and crg and ur3 mutant. High quality DNA has been isolated and these are being submitted for Sodium Bisulfite treatment andlibrary preparation and sequencing. Objective 3: The community genomics resources development is ongoing. We have submitted various sets of transcriptome, and epigenomic data to NCBI and we have completed discussions with other bean genomics and bioinformatics researchers who have database resources for hosting of our data for access to the bean community and beyond. Additionally, we continue to invite high school and middle school students and teachers to observe our work and invite student internships at the undergradaute and high school level.


      Progress 09/01/15 to 08/31/16

      Target Audience:The project was discussed and contents were exposed to undergraduate and graduate students as well as visitors to the Molecular Genetics & Epigenomics laboratory at DSU as well as collaborating laboratories at UAPB and MSU. Changes/Problems:Our goal was to initiate the biotic stressed sample work but due to lack of successful inoculation of our bean plants due to environmental conditions, we have decided to send our bean seed to our USDA-ARS collaborator in Beltsville (discussions initated and in progress). This ARS laboratory routinely works with bean rust, therefore, we hope to be able to complete Obj 2, and at the same time collect samples for completing Obj 1. An important step for us was to understand methylome generation and how to analyze this information; by reviewing current literature in common bean, legumes, and in other model plants, we were able to successfully generate a Sierra (bean Meso-American genotype)methylome; this will be used as a model as we develop the reference and biotic stressed methylomes for the project. What opportunities for training and professional development has the project provided?The staff member that has been working on this project has become proficient in analyses of methylome data. Undergraduate students working on the project have become proficient in molecular biology methods related to the project. How have the results been disseminated to communities of interest?We are in the process of preparing a poster for presentation at the 2017 International Plant & Animal Genome Conference in San Diego. What do you plan to do during the next reporting period to accomplish the goals?We plan to inoculate our bean plants with the biotic stress (rust), and collect samples for our reference and stress samples; we will then process these samples according to the procedures that we have developed, sequence the methylomes; We will also recruit undergraduate students to help us in the project.

      What was accomplished under these goals? Obj 1 and Obj 2: Reference and biotic stressedleaf methylomes and transcriptomes from four genotypes of common bean; These are in progress; since the release of the common bean genome, we have focused the first year on a better understanding and development of a DNA methylation map for common bean in the parental genotype Sierra. This is important as this has served as the first report of the methylome of a Meso-American common bean variety compared to the previously published methylome of G19833, an Andean common bean variety. As we have to use non-inoculated controls in our rust inoculation experiments, we are in the process of working on Objective 2-biotic stressed methylomes and at that time will also collect leaf samples for our reference methylome and transcriptome work. This will save time and efforts and has allowed us in the first year to develop robust methods of analyses of the methylomes while using the released common bean genome as a valuable reference. Obj 3-We have initiated discussions with the bean and legume genomics community representatives for hosting our data (Legume Federation). As we generate more epigenomic and transcriptomics data, we plan to share these resources, protocols, and data with these collaborators to enable use by the broader bean and legume/plant biology communities.