Progress 09/01/15 to 08/31/20
Outputs
Target Audience:High school and undergraduate students were exposed to the work that is being carried out in this NIFA Capacity building grant. Graduate students in the research group (not funded by this grant) were also exposed to the details of this grant. Research scientists were also exposed to this work, especially the bioinformatics analysis. Changes/Problems:As reported earlier, wewere 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?We have consistently trained high school, undergraduate, and graduate students (whether funded by the project or not) with information on this project and its goals. Given the importance of plant biotic stresses and the importance of common bean as the number one source of vegetarian protein in the world, it is important that we disseminate this information to our students and get them interested in plant genetics and breeding. How have the results been disseminated to communities of interest?Yes, we have presented this work to undergraduate and graduate students as well as research scientists. We have also included information about this project in discussions with visitors to the research group. We are working on a publication (s) to report on this work. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
1. We met the project goal Object 1. through methylome development between rust resistant and susceptible genotypes. We developed methylomes references for several genotypes of rust resistant and susceptible bean associated with the proposed research. 2. We met Objective 2. in regard to methylome development for resistant and susceptible genotypes challenged with fungal rust. We have methylome sequence data for rust-inoculated susceptible and resistant genotypes of common bean. 3. Through developing reference methylomes and rust challenged methylomes, we were able to add genomics resources to the research community, completing Objective 3. Through the proposed work, we have been successful in developing resources towards the understanding of sodium bisulfite sequencing in common bean and the impact of methylation across the genome. Due to limited funds, and the need for extensive sampling during the inolulation phase of the work, we have been able to use the transcriptomes that we have developed through prior funding for this project. This has actually helped us to develop a very comprehensive view of this project. Impacts Under the proposed work, we have been able to identify differential methylation sites between common bean genotypes as well as between non inoculated and inoculated sequence samples. We also have data that has added towards current projects, including subsequent capacity building grants.
Publications
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Progress 09/01/18 to 08/31/19
Outputs
Target Audience:High school and undergraduate students were exposed to the work that is being carried out in this NIFA Capacity building grant. Graduate students in the research group (not funded by this grant) were also exposed to the details of this grant. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?We have consistently trained high school, undergraduate, and graduate students (whether funded by the project or not) with information on this project and its goals. Given the importance of plant biotic stresses and the importance of common bean as the number one source of vegeterian protein in the world, it is important that we disseminate this information to our students and get them interested in plant genetics and breeding. 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 are requesting a final no-cost extension so that we can complete the bioinformatic analysis of the methylome and transcriptome data. This is needed because of delays in our ability to do the initial inoculation at DSU because of environmental conditions. We then had to request our USDA-ARS collaborators in Beltsville for help with the inoculations. These inoculations of the bean material were extremely successful, and we were able to process our methylome samples for sequencing. In this final year, we plan to complete the bioinformatic analysis of the methylome and transcriptome data, identify methods to integrate the methylome and transcriptome data (something that has not been done in the bean-bean rust interaction in Mesoamerican Phaseolus), and traina graduate student who is starting with the research group on this work.
Impacts
What was accomplished under these goals?
Objective 1: The reference leaf methylomes have been sequenced, and the research group has developed several reference transcriptomes ofcommon bean, which is being used for analysis. Analysis is progressing at this time. Objective 2: The rust stressed leaf methylomes have been sequenced, and the rust stressed leaf transcriptomes that are available with the research group are being used for analysis. Both objective 1 and objective 2 are going to be very useful in helping our understanding of the resistance of common bean to bean rust, especially with the two target rust resistance genes, Ur-3 and Crg. Since the material that we have used are deletion mutants at these two loci, and are hence susceptible, comparison of the methylome data from the inoculatedsusceptible mutants to that from the inoculated parental genotype Sierra would be very valuable. Objective 3: The research group has been in discussion with the bean/broader legume community on how best to integrate and share the knowledge and resources with the community bioinformatics resources. There is not much information available in the common bean/legume community about methylation in beans, especially with rust stressed leaf material.
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Progress 09/01/17 to 08/31/18
Outputs
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.
Impacts
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.
Publications
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Progress 09/01/16 to 08/31/17
Outputs
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.
Impacts
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.
Publications
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Progress 09/01/15 to 08/31/16
Outputs
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.
Impacts
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.
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