Progress 04/15/18 to 04/14/20
Outputs
Target Audience:Peanut researchers and breeders. Changes/Problems:We were unable to combine data from the older Arachis_axion SNP array (used earlier to genotype the U.S. mini-core collection) with data from the Arachis_axion2 array used in this study. This would have enabled additional testing for mixed/heterogeneous accessions within the US peanut mini-core collection. What opportunities for training and professional development has the project provided?The data produced by this project has been used in research by two Ph.D. students, Roshan Kulkarni and Paul Otyama, both students at Iowa State University, with separate funding (not funded by this grant). How have the results been disseminated to communities of interest? Results were presented in a poster session at the 2019 National Association of Plant Breeders meeting in Pine Mountain, GA. The paper, 'Genotypic characterization of the U.S. peanut core collection', has been submitted and is under review. A preprint is available at bioRxiv (https://doi.org/10.1101/2020.04.17.047019). What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The intent of this project was to collect genetic data for each accession (variety) in the US peanut core collection (Holbrook et al., 1993), which contains 812 accessions. Of these, 787 accessions were available for this project. The data produced by this project, combined with trait observations for each accession, can be used to look for genetic markers that are associated with agronomically important traits, enabling peanut breeders to more quickly develop new varieties of peanut. Another objective of the project was to assess the genetic diversity of the US peanut core collection, that is, to address the question: does it include all (or most) of the genetic variation across all varieties of peanut. The project also sought to assess the genetic "purity" or homogeneity within accessions, for example, to determine whether any accessions contained mixtures of genetically distinct seeds, or represented recent crosses with other accessions. Knowledge about genetic homogeneity is important for determining breeding strategies. To check for this, 247 accessions were selected to test for purity. The final objective was to carry out preliminary genotype - trait analyses to look for genetic markers for 18 key agronomic traits. This data, and the preliminary analyses, will benefit both peanut breeding work and basic research on peanut, with the goal of producing new varieties of peanuts with improved nutrition, agronomic characteristics, and increased resilience to environmental and disease and pest challenges. Goal I: generate public genotype data for each accession in the USDA core peanut collection. Twenty seeds from each accession were acquired from Dr. Greg MacDonald (University of Florida) for DNA sampling. The remaining seeds for each accession were transferred to Dr. Shyam Tallury at the USDA Plant Genetic Resources Conservation Unit in Griffin, GA. The accessions for DNA sampling were divided between Dr. Peggy Ozias-Akins' lab at the University of Georgia in Tifton, GA and Dr. Kelly Chamberlain's lab, USDA, Stillwater, OK where they were sampled, then grown to maturity and seed collected. Leaf samples were sent to Iowa State University from the Graham and Chamberlain labs and DNA was extracted by Dr. Michelle Graham's lab, and shipped to ThermoFisher/Affymetrix for processing on the Arachis_axiom2 SNP array. The ThermoFisher/Affymetrix analysis on the raw data were used in the core collection genetic assessment. The resulting genotype data is available at PeanutBase (https://peanutbase.org) as a bulk download: https:/peanutbase.org/data/public/Arachis_hypogaea/minicore.trt.JWYM/, and can be browsed using Gigwa: https://peanutbase.org/gigwa. The data are also available at the National Agricultural Library's Ag Data Commons: https://doi.org/10.15482/USDA.ADC/1518508 Diversity analysis using this data showed that the collection is genetically very diverse and likely spans most or all of the genetic diversity found in peanut worldwide. Analysis of genetic diversity and geographical location of the accessions determines that most genetic diversity in peanut had arisen in South America, before global distribution during colonial trade. Goal II: test a subset of accessions for heterogeneity A set of ~400 replicates from 247 accessions were grown to seedling stage at Iowa State University by the project team, sampled, and genotyped. Of these, 44% were found to be genetically impure accessions, meaning that the accessions in the core collection cannot be assumed, in general, to be homogeneous within each accession. This has important implications for breeding work. Goal III: test uniqueness of the USDA core peanut collection The project determined that 120 (15%) accessions in the core collection were nearly-identical, although it is possible that minor genetic differences still result in distinct phenotypes, so these may still be justified as distinct accessions. Goal IV: collect and consolidate all available phenotype data for the US core peanut collection. Phenotype data was collected from all available sources - the Germplasm Resource Information Network (GRIN), publications (Anderson et al., 1993, Anderson et al., 1996, Holbrook et al., 1983, Simpson et al., 1992), and from a phenotype study carried out by Dr. Greg MacDonald at the University of Florida in collaboration with Dr. Noelle Anglin, then curator of the USDA peanut collection in 2013-2015. The GRIN data varied in collection method, so only the latter two phenotype data sets were considered in analyses. While studies looking for genetic predictors of traits are still ongoing, data from the 2013-2015 has been made publicly available, but only for the US Mini Core (Holbrook and Dong, 2005). (https:/peanutbase.org/data/public/Arachis_hypogaea/minicore.trt.JWYM/) The entire data set will be publicly available when the phenotype paper has been submitted. This paper is in preparation. Goal V: provide a set of marker-trait associations for 18 important agronomic traits. This goal has not yet been met, but the paper describing the work and results is in preparation. References: W. F. Anderson, C. C. Holbrook, T. B. Brenneman. Resistance to Cercosporulium Personatum Within Peanut Cermplasm. Peanut Science (1993) 20:53-57. W. F. Anderson, C. C. Holbrook, A. K. Culbreath. Screening the Peanut Core Collection for Resistance to Tomato Spotted Wilt Virus. Peanut Science (1996) 23:57-61 C. Corley Holbrook and William F. Anderson. Evaluation of a Core Collection to Identify Resistance to Late Leafspot in Peanut. Crop Sci. 35:1700-1702(1995). Holbrook CC, Anderson WF, Pittman RN (1993) Selection of a core collection from the U.S. germplasm collection of peanut. Crop Sci 33:859-861 Holbrook CC, Dong W (2005) Development and evaluation of a mini core collection for the U.S. peanut germplasm collection. Crop Sci 45:1540-1544 C.C. Holbrook, DA Knauft, DW Dickson. A Technique for Screening Peanut for Resistance to Meloidogyne arenaria. Plant Disease Vol. 67 No. 9(1983) Simpson, C.E., Higgins, D.L., Thomas, G.D., Howard, E.R. Catalog of passport data and minimum descriptors of Arachis hypogaea L. germplasm collected in South America 1977-1986 College Station, TX. : Texas Agricultural Experiment Station, Texas A & M University System, [1992]
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2020
Citation:
Genotypic characterization of the U.S. peanut core collection. Paul I. Otyama, Roshan Kulkarni, Kelly Chamberlin, Peggy Ozias-Akins, Ye Chu, Lori M. Lincoln, Gregory E. MacDonald, Noelle L. Anglin, Sudhansu Dash, David J. Bertioli, David Fern�ndez-Baca, Michelle A. Graham, Steven B. Cannon, Ethalinda K.S. Cannon.
|
Progress 04/15/18 to 04/14/19
Outputs
Target Audience:Multiple meetings were held with the peanut breeding community to insure the data would provide the expected benefits. Changes/Problems:Discussions with representatives from the peanut breeding community raised the concern that the data would be of limited use unless paired with single-seed descent of the sampled plants. As this could not be managed within the scope of the funded project, two researchers - Dr Peggy Ozias-Akins at University of Georgia, and Dr. Kelly Chamberlain, USDA, Stillwater, OK - each agreed to grow half of the collection to maturity and collect seed. Neither researcher received funds from this grant. This project was originally planned to be a single year project, but numerous and significant delays have pushed it into a second year: Initially, there was a 5 month delay in receiving the seeds: we hoped to plant in April, 2018, but didn't receive the seed until late September, 2018. Given the lateness of the season and cold Iowa fall/winter weather, and in spite of multiple approaches to increasing the warmth and light quality, the seedlings intended for biological replicate sampling were slow to germinate and showed very poor germination (<50%). Replanting of the failed accessions was delayed by the government shutdown. In the second attempt the failed accessions were grown in a grown chamber, which improved the germination rate. What opportunities for training and professional development has the project provided?The project has thus far provided opportunities for learning greenhouse and growth chamber skills, and for developing skills in use of seed imaging equipment and automated image analysis. 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?The DNA samples will haven been sent to Affymetix/ThermoFisher by the time this report is received. When the data has been returned, we will complete the remainder of the goals in roughly this order: filter raw data for clear SNP signals investigate population structure of the core collection identify heterogenous accessions with in the core combine genotype and phenotype data to look for marker-trait associations prepare publication provide all data through PeanutBase
Impacts
What was accomplished under these goals?
Goal 1: provide public genotype data for each accession in the USDA core peanut collection Up to 25 seeds for each accession for the USDA core peanut collection was received from Greg MacDonald, along with an agreement from Dr. MacDonald to send the remaining seed stocks for the collection to Dr. Shyam Tallury at the Plant Genetic Resources Conservation Unit in Griffin, GA. the accessions were divided between two unfunded, collaborator labs which grew the plants to maturity and collected progeny seed. Leaf tissue was sampled at 2-4 weeks after germination. Samples have been collected and DNA extracted. Goal 2: test a subset of accessions for heterogeneity 400 biological replicates were selected to test for heterogeneous accessions. Leaf samples were taken from these plants at 2-4 wks after germination. DNA has been extracted from the samples. Goal 3: test uniqueness of the USDA core peanut collection This goal partially overlaps with Goal 2. No data is yet availalble to carry out the planned analysis of heterogeneous accessions within the US peanut mini core. Goal 4: collect and consolidate all available phenotype data for the US core peanut collection All available phenotype data for the US peanut core collection has been merged with GRIN data and consolidated into PeanutBase. Additional phenotype data was collected through image analysis of the seeds before they were planted. Correlating trait terms used by GRIN and the multiple phenotype studies is in progress. Goal 5: provide a set of marker-trait associations for 18 important agronomic traits No data is yet availalble so this goal has not been addressed.
Publications
|