Progress 10/01/19 to 09/30/20
Outputs
Target Audience:The target audience for this project includes scientists working in plant genomics, plant breeders, and seed industry representatives. Changes/Problems:We were unable to conduct wet lab experiments because of the COVID-19 related university closures and other safety protocols. During the spring and summer of 2020, our lab was mostly closed for wet-lab/greenhouse experiments as part of the university's response to COVID-19 pandemic. In the fall of 2021, we were re-opened for the experiments, but we often had to close labs for weeks again, because of Dillon Nelson having contracted COVID-19, his travel back and forth from the reservation and exposure of other lab members. We had to go through associated isolation and quarantine, each time we thought we were exposed. Therefore, during the reporting period, our lab members were engaged/productive in bioinformatics portions of their research projects. What opportunities for training and professional development has the project provided?Two graduate students (Dillon Nelson and Bijaya Pradhan) were mentored for bioinformatics skills needed for their graduate projects. Dillon received a week-long bioinformatics training at the NIH Headquarters early March 2020. Both students are non-traditional: Nelson is an American Indian student while Pradhan represents an under-represented group. Dillon Nelson was trained for in-silico lab skills using data from this project. Both graduate students also received training on sequence identification, alignment, homology assessment and phylogenetic analyses. As per the journal reviewers' requests, Nepal and Dillon Nelson re-examined the original data (determined by former PhD student Ethan Andersen) and re-analyzed for the presence of integrated domains in wheat R-genes. Dillon and Bijaya were mentored in revising manuscripts addressing concerns or questions from the journal reviewers and writing a good rebuttal. Thus, through virtual mentoring and remote computing, Dillon acquired skills including writing technical reports, and contributed as a co-author in Andersen et al. 2020 (see citation in the product section). Undergraduate student, Carter Hunter (biology senior) was mentored to disseminate the results from his capstone project. All students attended the Virtual Annual Conference of Botanical Society of America. How have the results been disseminated to communities of interest?The research was disseminated through 2 peer reviewed journal articles and 3 conference presentations. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Identification of MAPK and R genes in wheat and sunflower Given that we have returned to more normal operation from the pandemic, current PhD student Dillon Nelson and MS student Bijaya Pradhan will be utilizing available bioinformatics analyses of R genes in wheat and MAPKKK genes of sunflower to validate the results of two undergraduate/graduate students. Both will also be trained in drafting manuscripts for publication. Objective 2: Characterization of MAPK and R genes in wheat and sunflower The graduate students will design and conduct gene expression experiments. PI Nepal will submit proposals for extramural funding to complete the experiment.
Impacts
What was accomplished under these goals?
Goal 1. Identification of MAPK and R genes in wheat and sunflower and their wild relatives (15% accomplished) A new graduate student, Dillon Nelson, resident of Pine Ridge reservation, was recruited for his PhD project on the plants of ethnobotanical values. Undergraduate student Carter Hunter completed his capstone project on in-silico analyses of MAP3K genes of sunflower. Nepal invested time in preparing manuscripts for the unpublished portions of the dissertation work from Ethan Andersen and Surendra Neupane. Nepal revisited the sequence data acquired by former PhD students Surendra Neupane and Ethan Andersen and mentored new graduate students Dillon Nelson and Bijaya Pradhan on managing and curating sequence data in the program Geneious. Their reexamination/analyses of the data reconfirmed the presence of 2,151 NB-ARC-encoding genes in the wheat genome. MS student Bijaya Pradhan identified WRKY transcription factors in Amborella (most basal angiosperms) genome, which is needed for comparative genomic analyses to understand stress regulation in all flowering plants including wheat and sunflower. As part of his research on Ethnobotany of Lokota people, Dillon Nelson reviewed literature on the native legume plants and found that tubers and seeds of Groundnut (Apios americana; reported from Custer, Union, Roberts and Minnehaha Counties) are used by Lakota people. Dillon plans to develop and analyze genomic and transcriptomic data to understand the mechanism of stress regulation in Apios americana. Goal 2. Characterization of MAPK and R genes in wheat and sunflower and their wild relatives (15% accomplished) Just before the pandemic began, with the help of our collaborators (not supported by this grant) in Greece, we were able to show the process of alternate splicing of wheat R genes previously reported in the dissertation work of former PhD student Ethan Andersen. Amino acid sequences and corresponding annotations were uploaded to the program Geneious for sequence alignment, homology assessment, and motif visualization. The integrated domains (IDs) were investigated to assess protein location, potential function, homology to proteins in other species (Aegilops tauschii, Amborella trichopoda, Arabidopsis thaliana, Brachypodium distachyon, Hordeum vulgare, Musa acuminata, Oryza sativa, Setaria italica, Triticum urartu, and Zea mays), and the presence of variant transcripts in wheat. The in-silico inferences on the alternate splicing were validated in Farris Lab in Greece. Together, we showed that some of wheat R genes utilize alternate splicing to defend against rapidly evolving pathogens. The results are now published in Frontiers in Genetics (see Andersen et al 2020 cited in the Product section).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Andersen, E.J., Nelson, D., Mermigka, G., Purintun, J.P., Sarris, P.F., Nepal, M.P. 2020. Wheat Disease Resistance Genes and their Diversification through Integrated Domain Fusions. Frontiers in Genetics 11: 898. (https://doi.org/10.3389/fgene.2020.00898)
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Xue, J., Takken, F.L.W., Nepal, M. P., Maekawa, T., Shao, Z. 2020.Editorial: Evolution and Functional Mechanisms of Plant Disease Resistance. Frontiers in Genetics. 11:593240. (https://doi.org/10.3389/fgene.2020.593240 )
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Nelson, D., Nepal, M.P. 2020. Developing Genetic Resources for Lakota Plants Used in Traditional Medicine. Lightning talk presented at the Annual Conference of Botanical Society of America. July 27-31. Virtual.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Pradhan, B., Hunter, C., Nepal, M.P. 2020. Genome-wide Identification of WRKY Genes in Amborella trichopoda Bail. (Amborellaceae). Annual Conference of Botanical Society of America. July 27-31. Virtual.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Pradhan, B., Nepal M.P. 2020. Evolutionary Trends of WRKY Transcription Factors in Higher Plants. Lightning talk presented at the Annual Conference of Botanical Society of America. July 27-31. Virtual.
|
Progress 10/01/18 to 09/30/19
Outputs
Target Audience:The target audience for this project includes scientists working in plant genomics, plant breeders, and seed industry representatives. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two undergraduate students (Kaluwahandi Shanika and Carter Hunter, both biology majors) were mentored for their capstone research experience. Two undergraduate students (Charles Bush and Candy DuBray, STEM majors) from Oglala Lakota College (supported by FAST-REEU) were also mentored for their research experience. Two PhD graduate students (Ethan Andersen and Surendra Neupane) were mentored for completion of their degrees. One student is now employed as a postdoctoral researcher at the University of Florida (Gainesville, FL) and another started a tenure-track faculty position at Francis Marion University (Florence, SC). How have the results been disseminated to communities of interest?The research was disseminated through 4 peer reviewed journal articles, 3 conference presentations, and 2 Ph.D. dissertations. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Identification of MAPK and R genes in wheat and sunflower Current PhD student Jordan Purintun is conducting bioinformatics analyses of R genes in wheat and MAPKKK genes of sunflower to validate the results of the undergraduate students. Jordan will also draft a manuscript for publication. Objective 2: Characterization of MAPK and R genes in wheat and sunflower Using the preliminary data developed, Jordan Purintun and another PhD student will conduct gene expression experiments, and work with breeders on campus to develop new wheat cultivars. PI Nepal will submit proposals for extramural funding to complete the experiment.
Impacts
What was accomplished under these goals?
Goal 1. Identification of MAPK and R genes in wheat and sunflower and their wild relatives (10% accomplished) Disease resistance genes in sunflower were studied by PhD Student Surendra Neupane and published in the Journal "Genes." Surendra used bioinformatics approaches including Hidden Markov Model (HMM) to profile 52,243 putative protein sequences from sunflower, which resulted in the identification of 352 NBS-encoding R genes. We also identified signal peptides and nuclear localization signals for the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. We also found that Arabidopsisand sunflower shared 87 syntenic blocks with high synteny hits between chromosome 5 ofArabidopsisand chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement. The research article has been highly accessed by the scientific community (in less than a year the article had received 1,937 views, 1,572 downloads, and 2 citations). The results from this project and those from the previous hatch project were included in the PhD dissertation of Surendra Neupane, who is now a post-doc at the University of Florida. SDSU Honors College sophomore Sarah Schweitzer was the first to conduct genome-wide identification of MAPK and MAPKK genes of sunflower (published in the journal "Plants"). Sarah also used bioinformatics approaches including Hidden Markov Model (HMM) to identify and confirm 28 MPKs and 8 MKKs insunflower. Analyses of transcriptomic data showed that at least 19 HaMPK and seven HaMKK genes were induced in response to salicylic acid (SA), sodium chloride (NaCl), and polyethylene glycol (Peg) in leaves and roots. The research article was highly accessed, with 1,702 views and 1,075 downloads as of December 16 2019. Her findings have implications for sunflower crop-improvement for regulating abiotic stresses. Sarah presented her research findings at a national conference last summer. PhD student Ethan Andersen undertook the project to identify and characterize R genes in wheat. Ethan used similar approaches as outlined above to identify R genes in wheat and assess integrated domains (IDs) associated with the immune signaling. He identified 2,151 NLR-like genes, of which 1,298 formed 547 gene clusters; and the NLR clade relationships were similar to those in barley and Aegilops. He also identified wheat 'NLR-ID fusion proteins' as candidates for NLR functional diversification. Homology assessment indicated that these IDs may have originated as functional non-NLR-encoding genes incorporated into the NLR-encoding genes through duplications. This prediction of occurrence of alternate splicing in wheat was tested by researchers in the United Kingdom and have invited us to collaborate on their project. Analysis of wheat RNA-seq data also supported Ethan's prediction of alternative splicing through the inclusion or exclusion of IDs from the NLR proteins. We were the first to reveal that the wheat genome has 802 NLR R genes. We also found that R gene sequences necessary for effector detection were diversified through the fusions of integrated domains (IDs). Hatch projects (current and previous) provided research mentoring opportunities and career preparation for Ethan (first-generation college student), as well as scholarship accomplishments leading him to earn a PhD degree and a subsequent job placement (tenure-track assistant professor position at Francis Marion University in Florence, SC). Goal 2. Characterization of MAPK and R genes in wheat and sunflower and their wild relatives (10% accomplished) We were also the first to conduct greenhouse experiments to assess gene expression when resistant and susceptible wheat cultivars are challenged by the pathogen Pyrenophora tritici-repentis (Ptr). The pathogen Ptr uses wheat R gene Tsn1 as a susceptibility gene to facilitate infection. A greenhouse experiment was conducted to assess wheat-Ptrinteraction. Wheat seedlings were grown for two weeks prior to the experiment under greenhouse conditions and were challenged by the pathogen. Plants were transferred to a humidity chamber and leaf sample were collected at 0, 8, and 16hr after infestation (three biological replicates) for gene expression assessment. After RNA extraction and sequencing, 48 RNA datasets were reported. This data will be useful in understanding how resistant wheat responds toPtrcompared to susceptible wheat. The data were published in BMC Research Notes in June 2019. We were the first to develop RNA-seq data (over 50GB of expression data) and make them available to other scientists and public. The article was accessed by over 500 individuals in less than 6 months (as of December 16, 2019).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Neupane, S., Mathew, F.M., Varenhorst A.J., Nepal, M.P. 2019. Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean. Scientific Data. 6:133 (https://www.nature.com/articles/s41597-019-0140-4; doi:10.1038/s41597-019-0140-4
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Neupane, S., Purintun, J., Mathew, F.M., Varenhorst, A.J., Nepal, M.P. 2019. Molecular basis of soybean resistance to soybean aphid and soybean cyst nematode. Plants. 8(10): 374; doi: 10.3390/plants8100374
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Andersen, E.J., Ali, S., Nepal, M.P. 2019. Transcriptomic changes in wheat during tan spot (Pyrenophora tritici-repentis) disease. BMC Research Notes. 12:471; doi: 10.1186/s13104-019-4517-4.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Neupane, S., Schweitzer, S.E., Neupane, A., Andersen, E.J., Fennell, A., Zhou, R., Nepal. M.P. 2019. Identification and characterization of mitogen-activated protein kinase (MAPK) genes in sunflower (Helianthus annuus L.). Plants. 8(2), 28; doi: 10.3390/plants8020028.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Neupane, S., Schweitzer, S., Kaluwahandi, S., Bush, C., DuBray, C., Nepal, M.P. 2019. Characterization of mitogen-activated protein kinase kinase kinase (MKKK) genes in sunflower (Helianthus annuus L.). Annual Conference of Botanical Society of America. July 27-31. Tucson AZ.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Purintun, J.M., Andersen, E., Neupane, S., Nepal, M.P. 2019. Evolution of resistance genes in wheat (Triticum aestivum L.) and its relatives. Annual Conference of Botanical Society of America. July 27-31. Tucson AZ.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Schweitzer, S., Nepal, M.P. 2019. Identification and characterization of MAP kinase genes in sunflower. Upper Midwest Honors Conference April 4-6. University of Wisconsin-Stout, Menomonie WI.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2019
Citation:
Neupane, S. 2019. Identification and characterization of stress responsive genes in soybean and sunflower. PhD Dissertation. South Dakota State University, Brookings, SD.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2019
Citation:
Andersen, A. 2019. Disease resistance in wheat and its relatives. PhD Dissertation. South Dakota State University, Brookings, SD.
|
Progress 08/01/18 to 09/30/18
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
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?Objective 1: Identification of MAPK and R genes in wheat and sunflower Using approaches in bioinformatics, newly released sunflower and wheat genomes will be scanned in search for both MAPK and R genes. Objective 2: Characterization of MAPK and R genes in wheat and sunflower Using characterized genes from Arabidopsis and other plant species, homologs in wheat, sunflower and corresponding wild relatives will be determined. Further characterization requires greenhouse experiments challenging the plants to biotic and abiotic stresses. Therefore, using the preliminary data from this project, an extramural funding opportunity will be sought out.
Impacts
What was accomplished under these goals?
Nothing to report at this time due to the short time period of this report
Publications
|
|