Progress 09/01/23 to 08/31/24
Outputs
Target Audience:The target audience for this work is farmers, ranchers, agricultural professionals, and researchers. Efforts focused specifically on small grain farmers throughout the northern Great Plains and agricultural consultants who focus on small grain crops. Efforts to reach this audience include presentations at field days, training events organized by Extension, and meetings hosted by industry groups. Changes/Problems:The challenging labor market delayed hiring of a post-doc to assist with the Greenhouse drought experiments and transcriptomics work. We were successful in recruiting a post-doc who started April, 2024 and the final experiments for the project were successfully performed. What opportunities for training and professional development has the project provided?One Ph.D. student has recieved training in bioinformatics methods for analyzing microbial community data. Co-PI Jennifer Lachowiec has an undergraduate student who was trained in greenhouse experiment set up, data collection, and analysis. This student is also being trained in microbial DNA and RNA extractions. How have the results been disseminated to communities of interest?Results of this work were presented at the Montana Agribusiness Association annual convention, Great Falls, MT, on January 26, 2024 to a diverse group of stakeholders which included producers, consultants, agribusiness professionals, and members of the public. What do you plan to do during the next reporting period to accomplish the goals?Goals 1, 2, and 3: Completed. Goal 4: In the next reporting period, we will complete DNA and RNA extractions and sequencing. Analysis of the resulting genomic and transcriptomic datasets will be performed and we anticipate writing and submitting at least 2 additional papers.
Impacts
What was accomplished under these goals?
Goals 1 & 2: Project accomplishments this past year addressed Goals 1 & 2 which are to (1) Characterize the rhizosphere microbiome associated with diverse barley lines and perform a GWAS and (2) Assess the contribution of host genotype and environment to the structure of the recruited rhizosphere microbiome. Results from the rhizosphere microbiome analysis were used to peform a genome-wide association study (GWAS) to identify genetic elements contributing to differences in microbial community composition across different environments. Multiple gene loci have been identified and the results of this work have been submitted for publication. Goal 3: Based on yield and home field advantage scores, a subset of 10 barley lines were selected for a greanhouse reciprocal transplant study where sterile soil from the CARC site were inoculated with microorganisms from Bozeman soil and sterile soils from the Bozeman site were inoculated with CARC soil microorganisms. Agronomic data were collected from the barley lines grown under these conditions and rhizosphere microbiome sequencing was performed. Data analysis has been performed and results submitted for publication. Goals 4: A subset of barley lines that were characterized as drough resistant or drought sensitive were selected for greenhouse drought experiments. Greenhouse drought experiments have been completed and agronomic data collected.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Ewing, P. M., M. B. Kantar, E. Killian, J. L. Neyhart, J. D. Sherman, J. L. Williams, J. A. Lachowiec and J. O. Eberly (2023). "Local adaptation and broad performance are synergistic to productivity in modern barley." Crop Science 64(1):192-199.
- Type:
Peer Reviewed Journal Articles
Status:
Submitted
Year Published:
2024
Citation:
Jessica L Williams, Erik Z Killian, Anna Halpin-McCormick, Michael Benjamin Kantar, Jamie D Sherman, Patrick M Ewing, Jed O Eberly, Jennifer Lachowiec. Uncovering genetic linkages in the rhizosphere contributing to adaptation. Nature Plants
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Progress 09/01/22 to 08/31/23
Outputs
Target Audience:The targetaudience for this work isfarmers, ranchers, agricultural professionals, and researchers. Efforts focused specifically onsmall grain farmers throughout the northern Great Plains and agricultural consultants who focus on small grain crops.Efforts to reach this audience include presentations at field days, training events organized by Extension, and meetings hosted by industry groups. Changes/Problems:Supply chain constraints have delayed completion of DNA sequencing for the second year of the study. Results are expected within the next 2-3 months. The challenging labor market has delayed hiring of a post-doc to assist with the transcriptomics work. We have been successful in recruiting a post-doc who will be starting January, 2024. We anticipate this may neccessitate a request for a one-year no-cost extension to complete these experiments. What opportunities for training and professional development has the project provided?Ph.D. student Killian has recieved training in bioinformatics methods for analyzing microbial community data. Co-PI Jennifer Lachowiec's has an undergraduate student who is receiving training in laboratory techniques for research in plants and microbes through this project. Co-PI Patrick Ewing has two undergraduate students he is mentoring and training as part of this project. How have the results been disseminated to communities of interest?Outreach activities included Co-PDLachowiecpresenting the project at the MSU Northern Agricultural Research Center annual Field Day to around 200 regional farmers, ranchers, agricultural professionals, and researchers. Co-PDEwing presented this work to the USDA-ARS Food Systems Research Unit, The Montana State University Department of Plant Sciences and Plant Pathology, and the South Dakota State University Agronomy, horticulture, and Pland Sciences Department. What do you plan to do during the next reporting period to accomplish the goals?Goal 4: Greenhouse drought stress experiments will be performed. Agronomic performance of select barley lines identified in Goal 3 will be determined under a range of simulated drought conditions. Based on the outcome of these experiments, one linewill be selected for subsequent RNA-seq and metatranscriptomics experiments to elucidate key genes that are expressed in the plant and rhizosphere microbiome in response to different levels of drought.
Impacts
What was accomplished under these goals?
Goals 1 & 2: Project accomplishments this past year addressed Goals 1 & 2 which are to (1) Characterize the rhizosphere microbiome associated with diverse barley lines and perform a GWAS and (2) Assess the contribution of host genotype and environment to the structure of the recruited rhizosphere microbiome. To address these goals, analysis was performed on a diverse panel of 281 barley lines that was grown in 3 locations in 2021 and 2022. Rhizosphere microbiome data analysis is under way. Multi-location comparisons of microbial community alpha and beta diversity measurements are underway. Random forest and core microbiome analysis have been performed to identify key microorganisms in each environment. These results are being used to peform GWAS toidentify genetic elements contributing to differences in microbial community composition across different environments. A manuscript has been submitted whichevaluates the local adaptation of these lines in different environments. Goal 3: Based on yield and home field advantage scores, a subset of 10 barley lines were selected for a greanhouse reciprocal transplant study where sterile soil from the CARC site were inoculated with microorganisms from Bozeman soil and sterile soils from the Bozeman site were inoculated with CARC soil microorganisms. Agronomic data were collected from the barley lines grown under these conditions and analysis of the data are under way.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2023
Citation:
Ewing, P, Kantar, MB, Williams, J, Killian, E, Sherman, J, Neyhart, J, Lachowiec, J, Eberly, J. Local adaptation and broad performance are synergistic to productivity in modern barley. Crop Science
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Progress 09/01/21 to 08/31/22
Outputs
Target Audience:Co-PI Lachowiec and Ph.D. student Williams presented at the MSU Post Farms annual Field Day to around 100 regional farmers, ranchers, agricultural professionals ,and researchers. Co-PI Ewing presented this work at the Brookings, SD field day to around 50 participants. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Ph.D. student Killian has recieved training in bioinformatics methods for analyzing microbial community data. Co-PI Jennifer Lachowiec's has an undergraduate student who is receiving training in laboratory techniques for research in plants and microbes through this project. Co-PI Patrick Ewing has two undergraduate students he is mentoring and training as part of this project. How have the results been disseminated to communities of interest?Outreach activities included Co-PI Lachowiec and Ph.D. student Williams presenting the project at the MSU Post Farms annual Field Day to around 100 regional farmers, ranchers, agricultural professionals, and researchers. Co-PI Ewing presented this work at the Brookings, SD field day to around 50 participants. What do you plan to do during the next reporting period to accomplish the goals?Goals 1 & 2 Data analysis will continue. We anticipate completing the microbial community analysis from the field trials and GWAS analysis during the next reporting period. A manuscript is currently in preparation and we anticipate submitting it in the spring. Goal 3 Greenhouse reciprocal transplant and drought stress experiments will be performed. Agronomic performance of select barley lines will be determined under a range of simulated drought conditions. Based on the outcome of these experiments, a subset of lines will be selected for subsequent metatranscriptomics experiments.
Impacts
What was accomplished under these goals?
Goals 1 & 2 Project accomplishments this past year addressed Goals 1 & 2 which are to (1) Characterize the rhizosphere microbiome associated with diverse barley lines and perform a GWAS and (2) Assess the contribution of host genotype and environment to the structure of the recruited rhizosphere microbiome. To address these goals, a diverse panel of 281 barley lines was grown in 3 locations this past growing season. At the MSU Central Ag Research Center (CARC) in Moccasin, MT, the study was planted and managed by PI Jed Eberly with assistance from Ph.D. students Erik Killian and Jessica Williams, along with support staff at the CARC. At the Post Farm in Bozeman, MT The study was planted and managed by Co-PI Jamie Sherman with support from Ph.D. students Erik Killian and Jessica Williams, along with support staff from Post Farm. At the 3rd location at USDA-ARS Integrated Cropping Systems Research Unit in Brookings, SD, co-PI Patrick Ewing was responsible for planting and managing the study. Root samples were collected at early stem elongation and rhizosphere extractions were performed. DNA extractions are underway in preparation for sequencing the rhizosphere microbial community. Agronomic data, including yield, protein, productive tillers, and biomass was collected for each study. Rhizosphere microbiome data analysis is under way. Microbial community alpha and beta diversity measurements have been performed and multi-location comparisons are underway. GWAS is being performed with the microbial community alpha and beta diversity measurements in order to identify genetic elements contributing to differences in microbial community composition. A manuscript has been drafted which compares performance of the barley lines across 3 locations and evaluates the local adaptation of these lines in different environments. Goal 3 Based on yield and home field advantage scores, a subset of 10 barley lines were selected for a greanhouse reciprocal transplant study where sterile soil from the CARC site were inoculated with microorganisms from Bozeman soil and sterile soils from the Bozeman site were inoculated with CARC soil microorganisms. Agronomic data were collected from the barley lines grown under these conditions and rhizosphere DNA sequencing will be performed this winter to compare differences in the rhizosphere microbiomes recruited under these conditions to those in soils containing the native microbial community. Based on these results, a subset of these barley lines will be selected to grow under different levels of drought stress to further evaluate changes in the rhizosphere microbiome.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Killian E, Lachowiec J, Eberly J, Cook J. Developing Open-Source Pipelines to Process Plot-Level UAV Imagery. ASA, CSSA and SSSA Annual Meeting. 6-9 November, Baltimore, MD
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Progress 09/01/20 to 08/31/21
Outputs
Target Audience:PI Jed Eberly along with Ph.D. students Jessica Williams and Erik Killian, presented this project at the MSU Central Ag Research Center annual Field Day on July 13, 2021 to an audience of around 50 regional farmers and ranchers. Ph.D. students Williams and Killian also presented this work at the MSU Post Farms annual Field Day to around 100 regional farmers, ranchers, and researchers. PI Eberly presented this work to the Chouteau County Extension Advisory Board. Graduate studen Erik Killian also presented this work for the PSPP Department Graduate Seminar Series on April 13, 2021 to an audience of around 30 students. Co-PI Patrick Ewing also discussed this project with stakeholders in a meeting with the North American Millers Association on May 18th, 2021. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Co-PI Jennifer Lachowiec's has an undergraduate student who is receiving training in laboratory techniques for research in plants and microbes through this project. Co-PI Patrick Ewing has two undergraduate students he is mentoring and training as part of this project. He also had three additional undergraduate students who were mentored during the summer. 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?To accomplish Goals 1 & 2, DNA sequencing and analysis will be performed during the winter of 2021-2022 on rhizosphere samples collected this past growing season. Microbial community sequncing results along with agronomic data will be used to perform a Genome Wide Association Study (GWAS) to identify QTL that contribute to local adaptation due to microbial recruitment within the barley genome. Reciprocal transplant studies will also be initiated in the greenhouse to assess microbiome recruitmentin locally adapted lines identified in the GWAS. In the secound half of 2022, additional greenhouse studies will be established to address the aim of Goal 3 which is to characterize the sources of variation in crop phenotype and microbiome functions that lead to enhanced performance in drought response. Top performing lines identifed in the field studies will be grown in the greenhouse under five drought stress levels and barley root and rhizosphere microbiome transcriptomics will be performed to identify candidate genes, pathways and networks involved in drought response.
Impacts
What was accomplished under these goals?
Impact Plant breeding contributes approximately 50% of yearly yield increases, but current rates of gain are not sufficient to meet future food demands. Crops have historically been bred for consistent performance across multiple locations, rather than high performance in a few locations. However, recent work has suggested leveraging local adaptation may increase both yields and breeding efficiency. Evidence suggests that much of this local compatibility is a result of synergy between the host crop genotype, local environment, and the local soil microbiome. More research is needed to understand these complex interactions. To gain insight into these interactions between crop genotyp, environment, and the soil microbiome, field studies were performed with a genetically diverse selection of barley lines. These barley lines were planted in 3 different environments and agronomic performance data, including yield, biomass, and protein, was collected. Root samples were also collected to evaluate the root-associated microbial community. Accomplishments Goals 1 & 2 Project accomplishments this past year addressed Goals 1 & 2 which are to (1) Characterize the rhizosphere microbiome associated with diverse barley lines and perform a GWAS and (2) Assess the contribution of host genotype and environment to the structure of the recruited rhizosphere microbiome. To address these goals, a diverse panel of 281 barley lines was grown in 3 locations this past growing season. At the MSU Central Ag Research Center (CARC) in Moccasin, MT, the study was planted and managed by PI Jed Eberly with assistance from Ph.D. students Erik Killian and Jessica Williams, along with support staff at the CARC. At the Post Farm in Bozeman, MT The study was planted and managed by Co-PI Jamie Sherman with support from Ph.D. students Erik Killian and Jessica Williams, along with support staff from Post Farm. At the 3rd location at USDA-ARS Integrated Cropping Systems Research Unit in Brookings, SD, co-PI Patrick Ewing was responsible for planting and managing the study. Root samples were collected at early stem elongation and rhizosphere extractions were performed. DNA extractions are underway in preparation for sequencing the rhizosphere microbial community. Agronomic data, including yield, protein, productive tillers, and biomass was collected for each study. An additional study was planted this fall by PI Jed Eberly and Co-PI Mikey Kantar at the Kunia Research Farm in Oahu, HI. Goal 3 Nothing to report Goal 4 Nothing to report
Publications
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