Progress 11/30/15 to 09/30/20
Outputs
Target Audience:Everyone: Potatoes are the most widely grown vegetable crop in the world and as consumers move toward a plant based diet in response to environmental pressures, potatoes stand to play an even more significant role in world cuisines. Potatoes are a good source of potassium, fiber, and vitamin C. They produce more food per unit water than any other plant and are a cost-effective protein source. Furthermore they are one of the most "satiating" vegetables. Countries around the world including China and India are turning toward potato production as a crucial component of their strategy for feeding a growing populace, and the US produces potatoes for these export markets. Potato Growers and Industry in Minnesota and beyond: Growers and industry report numerous challenges to potato production including: changes in biotic and abiotic stress regimes, evolving consumer preferences, and constraints on growing techniques due to the demands of sustainability. In other words growers are being asked to do more with less. New potato varieties are one potential tool which will allow growers to meet these challenges. Potato Breeders: Potatoes have complex highly heterozygous autopolyploid genomes and reproduce clonally. These are all impediments to potato breeding and have limited genetic gain in potatoes and hampered the adoption of new clones. At this moment, potato breeding is changing drastically, with breeders collaborating to experiment with new approaches featuring genomics and ploidy reduction. Our lab is at the center of many of these national and international collaborations, due to our unique set of expertise in population genetics and evolutionary genomics. Evolutionary Biologists: Polyploidy is a fundamental part of plant evolution. All seed plants have undergone at least one genome duplication. Ploidy changes can result from hybridization (allopolyploids) or genome duplication (autopolyploids). In flowering plants, 15% of speciation events involve polyploidization and 47 to 70% of species are polyploid. Polyploidy in general and autopolyploidy in particular presents numerous technical and theoretical challenges for genomic work. Autopolyploidy violates the assumptions of the models we use to study genetics and evolution. Without tools to study autopolyploid genomes, it is difficult to investigate how evolutionary forces interact with this common phenomenon. Domestication is a model for evolution. Short, recent artificial selection is relatively easy to detect and crop species benefit from a wealth of tools and resources. Potato provides an ideal model for autopolyploid genomics and evolution. In addition to the advantages of crops in general, potato is an attractive model because it ranges from diploid to pentaploid including both auto and allopolyploids. Changes/Problems:Due to covid most of our field days and conferences were cancled or modified What opportunities for training and professional development has the project provided?Heather Tuttle is a PhD student in the Bioinformatics and Computational Biology Program. Tuttle has taken a series of graduate courses including bioinformatics courses and population genetics. She has presented her work at the Potato Association of America Meetings in Winnipeg and The Potato Breeding and Genetics Technical Committee Meeting in Chicago, IL in addition to in several on campus venues. In addition to her thesis work she has used her GBS expertise to contribute to the potato pan genome project, to Dr. Tom Michaels bean breeding project, and to Dr. Jenny Kimball's wild rice breeding project. 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?Finish up the diversity analysis and improve the ploidy calling algorithm and write up the results
Impacts
What was accomplished under these goals?
Heather Tuttle, a PhD student in the lab, has been working with a set of GBS genotyped individuals from the genebank from a range of species and ploidys. Her goal is to develop core-sets which can be used for screening traits more quickly and to do a comparative diversity analysis of diploids and tetraploids. She has called SNPs at the diploid and tetraploid level and compared multiple ways to develop core-subsets. It seems that the ploidy of some of the samples is mislabled so she is developing an algorithm to determine ploidy from GBS data. She is currently working in the diversity analysis
Publications
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:Everyone: Potatoes are the most widely grown vegetable crop in the world and as consumers move toward a plant based diet in response to environmental pressures, potatoes stand to play an even more significant role in world cuisines. Potatoes are a good source of potassium, fiber, and vitamin C. They produce more food per unit water than any other plant and are a cost-effective protein source. Furthermore they are one of the most "satiating" vegetables. Countries around the world including China and India are turning toward potato production as a crucial component of their strategy for feeding a growing populace, and the US produces potatoes for these export markets. Potato Growers and Industry in Minnesota and beyond: Growers and industry report numerous challenges to potato production including: changes in biotic and abiotic stress regimes, evolving consumer preferences, and constraints on growing techniques due to the demands of sustainability. In other words growers are being asked to do more with less. New potato varieties are one potential tool which will allow growers to meet these challenges. Potato Breeders: Potatoes have complex highly heterozygous autopolyploid genomes and reproduce clonally. These are all impediments to potato breeding and have limited genetic gain in potatoes and hampered the adoption of new clones. At this moment, potato breeding is changing drastically, with breeders collaborating to experiment with new approaches featuring genomics and ploidy reduction. Our lab is at the center of many of these national and international collaborations, due to our unique set of expertise in population genetics and evolutionary genomics. Evolutionary Biologists: Polyploidy is a fundamental part of plant evolution. All seed plants have undergone at least one genome duplication. Ploidy changes can result from hybridization (allopolyploids) or genome duplication (autopolyploids). In flowering plants, 15% of speciation events involve polyploidization and 47 to 70% of species are polyploid. Polyploidy in general and autopolyploidy in particular presents numerous technical and theoretical challenges for genomic work. Autopolyploidy violates the assumptions of the models we use to study genetics and evolution. Without tools to study autopolyploid genomes, it is difficult to investigate how evolutionary forces interact with this common phenomenon. Domestication is a model for evolution. Short, recent artificial selection is relatively easy to detect and crop species benefit from a wealth of tools and resources. Potato provides an ideal model for autopolyploid genomics and evolution. In addition to the advantages of crops in general, potato is an attractive model because it ranges from diploid to pentaploid including both auto and allopolyploids. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Heather Tuttle is a master's student in the Bioinformatics and Computational Biology Program. Tuttle has taken a series of graduate courses over the year including bioinformatics courses and quantitative genetics. She has presented her work at the Potato Association of America Meetings in Winnipeg and The Potato Breeding and Genetics Technical Committee Meeting in Chicago, IL. In addition to her thesis work she has used her GBS expertise to contribute to the potato pan genome project, to Dr. Tom Michaels bean breeding project, and to Dr. Jenny Kimball's wild rice breeding project. How have the results been disseminated to communities of interest?Grower/Industry Dissemination August 2019 - "Update on year 2 of the Minnesota Potato Breeding Program" (Presentation - Shannon, Tuttle, and Agha), NPPGA Field Day, Inkster, Hoople and Larimore, ND July 2019 - "Breeding Program Update" (Presentation - Shannon, Tuttle, and Agha), Sand Plains Research Farm Field Day, Becker, MN Academic Dissemination December 2019 - "Core Subsets of the USDA Potato Genebank Collection in Sturgeon Bay WI" (Presentation - Tuttle), Potato Breeding and Technical Committee Meeting, Chicago, IL July 2019 - "Characterization and assembly of a core set for the US potato genebank using genotyping-by-sequencing and GATK" (Presentation - Tuttle), Potato Association of America Meeting, Winnipeg, CA What do you plan to do during the next reporting period to accomplish the goals?We will finish the comparative (diploid, teteraploid) diversity analysis and finalize the core subset.
Impacts
What was accomplished under these goals?
Heather Tuttle, a masters student in my lab, has been working with a set of GBS genotyped individuals from the US potato genebank. Her goal is to develop core-sets which can be used for screening traits more quickly and to do a comparative diversity analysis of diploids and tetraploids. She has called SNPs at the diploid and tetraploid level and compared multiple ways to develop core-subsets.
Publications
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:The two target audiences for this project are potato growers in Minnesota including Minnesota Area II and Northern Plains, and institutional plant breeders with whom this project collaborates. These breeders include Dr. Laura Shannon (Assistant Professor, University of MInnesota), Dr. Shelley Janskey (Research Geneticist, USDA-ARS Madison, WI), Dr. Dave Douches, (Professor, Michigan State University), Dr. John Bamberg (USDA-ARS Potato Genebank Sturgeon Bay, WI), Dr. Jeffrey Endelman (Assistant Professor, University of Wisconsin - Madison), Dr. Asunta (Susie) L. Thompson (Associate Professor, North Dakota State University), Dr. David Holm (Professor, Colorado State University) and Dr. Walter De Jong (Associate Professor, Cornell University). Changes/Problems:In late 2018 or early 2019 leadership for this project will be transferred to Dr. Laura Shannon who is now the faculty member responsible for the potato breeding and genetics program at the University of MInnesota. What opportunities for training and professional development has the project provided?The Shannon lab is training one undergraduate student in genomics techniques, two undergraduates in applied potato breeding and two graduate students in potato genetics. How have the results been disseminated to communities of interest?Results from the genomic studies, crossing blocks and field trialswere shared with attendees of the NCCC215 meeting in Chicago, December 2017. A description of projects and preliminary results for the potato breeding program were shared with Minnesota Area II Potato Growers in July 2018 and with Northern Plains Potato Growers in August 2018.. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period: Additional germplasm will be obtained from NRSP6, evaluated, and if warranted, included in future crossing blocks to generate additional new F1 potato poplulations from which the program can selectimproved cultivars for Minnesota production. The UofM potato breeding and genetics programwill continue genomic studies on potato populations that include NRSP6 germplasm in the pedigree. The potato breeding and genetics program will continue selection and trials of breeding lines that are candidates for cutlivar release. The program will also continue to communicate their progress in cultivar improvement to quad state (MN, ND, SD, MI) growers.
Impacts
What was accomplished under these goals?
Dr. Laura Shannon's breeding and genetics program at the University of Minnesota obtained the following germplasm from NRSP6 and used this germplasm in 2018 crossing blocks to generate new F1 potato poplulations from which the program can select improved cultivars for Minnesota production:Chipeta, Denali, Pungo, Sebago, Eden, Pentland Javelin,BR03, BR05, BR85, DTO-2, DTO-28. Dr. Shannon's project collaborated withthe USDA genebank and PepsiCo on genomic studies. They conducted genotype by sequencing analysis of 730 genebank accessions ranging from diploid to pentaploid. Heather Tuttle, an undergraduate in the Shannon Lab, has developed a bioinformatics pipeline for calling SNPs in this data. The pipeline uses GATK and Samtools. In the 45 diploids 97,991 SNPs have been called. Variants have been identified in the 577 tetraploids, but genotypes for those variants have not been called. Due to low read depth (~8x), it is likely that the heterozygous classes will be collapsed for the purpose of genotype calling. The purpose of this analysis is two-fold. First it will allow us to compare diversity in diploid and tetraploid potato species. Second, these genotyped individuals are being maintained clonally in the genebank. We will identify a core set of these individuals which represent the total diversity of the genebank collection and can be distributed to research programs for phenotyping. Our genotyping data can then be used in conjunction with that phenotyping data for mapping studies.
Publications
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:The two target audiences for this project are Minnesota Area II potato growers and institutional plant breeders with whom this project collaborates. These breeders includeDr. Shelley Janskey (Research Geneticist, USDA-ARS Madison, WI), Dr. Dave Douches, (Professor, Michigan State University), Dr. John Bamberg (USDA-ARS Potato Genebank Sturgeon Bay, WI),Dr. Jeffrey Endelman (Assistant Professor, University of Wisconsin - Madison),Dr. Asunta (Susie) L. Thompson (Associate Professor, North Dakota State University), Dr. David Holm (Professor, Colorado State University) and Dr. Walter De Jong (Associate Professor, Cornell University). Changes/Problems:The University of Minnesota potato breeding program is now in the hands of a new faculty member in the Horticultural Science Department, Dr. Laura Shannon. She will ultimately become responsible for this project since Dr. Michaels is returning to his other vegetable breeding and production responsibilities. What opportunities for training and professional development has the project provided?A graduate student, Colin Jones, who is pursuing a MS degree in Applied Plant Science at the University of MInnesota, is using an indoor hydroponic production system for determining potato root response to standard and half-standard nitrate levels in nutrient solutions. How have the results been disseminated to communities of interest?Preliminary results from the hydropnics trialswere shared with attendees of the NCCC215 meeting in Chicago, December 2016. What do you plan to do during the next reporting period to accomplish the goals?The system is being modified and improved by Colin Jones for use in his MS research project.
Impacts
What was accomplished under these goals?
We are working toward a fresh market potato production system for sandy soils in minnesota with reduced nitrogen application and less potential for nitrate loss to groundwater. A hydroponic method for growing potato germplasm was developed and evaluated. The method is based on static, noncirulating hydroponic approaches described in Kratky, B.A. 2009. Three non-circulating hydroponic methods for growing lettuce.Proceedings of the International Symposium on Soilless Culture and Hydroponics. Acta.Hort. 843:65-72. Trials using the red flesh, red skin variety "Raspberry" (Michigan State University) resulted in successful tuber production although yield per plant was roughly half of what might be expected from field grown plants. Additional experimentation with nutrient and temperature would likely result in identification of a static system with improved tuber yield. The purpose of pursuing this system is to allow rapid screening of a large quantity of potato germplasm for productivity under reduced nitrogen regimes prior to field trials.
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Progress 11/30/15 to 09/30/16
Outputs
Target Audience:This project is coordinated by Dr. Tom Michaels at the University of Minnesota in collaboration with Dr. Shelley Janskey (Research Geneticist, USDA-ARS Madison, WI), Dr. Dave Douches, (Professor, Michigan State University) and Dr. John Bamberg (USDA-ARS Potato Genebank Sturgeon Bay, WI). Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Discussion and presentation of progress on the diploid potato project took place at the 2016NCCC215 Potato Breeding and Technical Committee meeting in Chicago. 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 University of Minnesota project will continue its diploid development in 2017. Seedlings produced from self pollination of existing tetraploid cultivars will be self pollinated to create F2 families. F2 seedlings will be produced and pollinated with S. phureja pollen obtained from the USDA potato genebank. Haploids obtained from this cross will be grown and stable, robust selections evaluated for market potential. Diverse USDA potato genebank materials will be obtained for evaluationwith an emphasis on fresh market types, specialty types, and materials with high nitrogen use efficiency and water use efficiency.
Impacts
What was accomplished under these goals?
A diploid potato breeding project is under development in which tetraploid potatoes will be pollinated with S. phureja pollen to produce diploid progeny. Inbreeding followed by hybrid crossing will result in new diploid potatoes for testing as cultivars. This is along term project that will result in information about inheritance of key attributes in commercial potato.
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