Progress 01/23/17 to 09/30/18
Outputs
Target Audience:The research presented here will be of interest to potato researchers and potato breeders in academic institutions as well as in industry. The outcome of this proposal will also be beneficial to potato growers and processors in the state. At the same time, the knowledge gained on aneuploidy and chromothripsis will be of interest to cancer researchers who study genomic evolution. In addition, outreach efforts will help STEM-educators, and foster collaborations and better communication between science communicators, industry and scientists with the general public. Changes/Problems:The haploid induction frequency and method appears to be sensitive to temperature and variety that's used. We have not been able to isolate dihaploids from Caribou Russet, using that as a female parent. We will continue our efforts. The cloning of the CENH3 gene from US-W4 has not been successful so far. We will include an genomics approach using RNA-seq for this project as well to increase our likelihood of identifying this gene. What opportunities for training and professional development has the project provided?Through this project, I have been able to present the results of work on potato haploid induction and diploid breeding efforts to a broad scientific community as well as stakeholders in Maine. These opportunities have also led to numerous grant writing efforts with many potato breeders from the US and abroad. We were also able to obtain some funding from the Maine Potato Board to work on the insect resistance aspect of diploid breeding on green peach aphid, an important pest in Maine that spreads diseases including the PVY virus. I'm also a reviewer for the American Journal for Potato Research and the Maine State representative for the Plant Breeding Coordinating Committee. How have the results been disseminated to communities of interest?I've attended conferences and symposia to present our work, and my graduate students have attended Field Days at Aroostok Farms to present our work as well. 6/3/18 - Plant Genome Stability and Change, Gatersleben, Germany 8/7/18 - National Association of Plant Breeders, PBCC/SCC80, Guelph, CA 8/8/19 -- Field Day in Aroostook Farms, Presque Isle, ME (Grad student represented) 9/7/18 -- Plant in New England Meeting, MIT, MA 9/26/18 -- Potato Genomics Workshop, Webcast, McGill University, QC What do you plan to do during the next reporting period to accomplish the goals?We will continue the efforts in dihaploid extraction to also include NY121 and Caribou Russet clones to expand our germplasm collection. Identification of the CENH3 gene in US-W4 will continue as well, and we hope to attempt transformation protocols that will be utilized. Field testing of diploid varieties plots will be undertaken next summer.
Impacts
What was accomplished under these goals?
1. With collaborators from UC Davis, we have identified dihaploid Desiree lines in their population with aneuploid chromosomes from the haploid inducer IVP48. We have currently isolated ~150 dihaploids from the variety Atlantic and these have been confirmed by chloroplast counting. We anticipate trialling these Atlantic dihaploids in the field in 2019.As part of the phenotyping process, we have assayed for resistance of the IVP38 line usinggreen peach aphids as well. 2. We obtained the line US-W4 from the potato gene bank, and this line will be assessed for transformation efficiency via callus induction methods. In order to identify the CENH3 gene, we have attempted to clone this gene from US-W4 but we have not been successful so far. Other methods we have considered include using an RNAseq approach to identify the expressed version of this gene. 3.We will begin working on phu-stn diploid selections from Dr. Kathy Haynes' program. These are wild potato relatives that have desireable traits that could be used in diploid potato breeding.In particular, we hope to transfer the self-compatibility and male fertility traits from the phu-stn to diploids derived from Tuberosum varieties. Disease resistance traits such as resistance to late blight will also be considered.
Publications
- Type:
Book Chapters
Status:
Accepted
Year Published:
2018
Citation:
Detection of Chromothripsis in Plants.
Henry I.M., Comai L., Tan E.H. (2018) In: Pellestor F. (eds) Chromothripsis. Methods in Molecular Biology, Vol 1769, pp 119-132 doi: 10.1007/978-1-4939-7780-2_8
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Progress 01/23/17 to 09/30/17
Outputs
Target Audience:The audience that will be interested in this work includes researchers in potato breeding as well as growers and processors who are the potato industry stakeholders in the state, nationally and internationally. We use a combination genomics and haploid induction techniques to complement conventional potato breeding methods. The topic of plant breeding and advance genetic manipulation is also of interest and can be a source of discussion for science outreach between plant scientists and the general public. Changes/Problems:None encountered so far. What opportunities for training and professional development has the project provided?We have trained six undergraduate researchers with molecular lab techniques, and exposed them to potato breeding techniques such as haploid induction for the duration of this reporting period. A PhD graduate student (co-advised by Dr. Gregory Porter) has also been trained in this lab in haploid induction and large scale genomics work. A PhD graduate student will be joining this lab beginning the Spring of 2018. How have the results been disseminated to communities of interest?Seven scientific presentations and seminars were presented during this perfiod: NCCC, PAA, ICAR, Field days in Aroostook Research Farms, Workshops (4H outreach and Orono Middle School), and through the lab website (www.haploidgenomics.com). See 'other products' section for details. What do you plan to do during the next reporting period to accomplish the goals?Continued efforts to recruit undergraduate and graduate students as well as submitting research proposals for extramural funding.
Impacts
What was accomplished under these goals?
Objective 1: We have utilized whole genome sequencing methods to describe the number of chromosomes (karyotype) as well as the parent of origin on a dihaploid population from the landrace Alca Tarma with collaborators from UC Davis and the International Potato Center. A manuscript has been submitted to a peer-reviewed journal. We will use the same methods to describe the Desiree dihaploid (BB) population and are on track to obtain BB population for agronomic assessments in Summer 2018. Objective 2: RNA isolation, RT-PCR for StCENH3 has been optimized on tetraploid potato cultivars. Cloning of constructs has begun in the lab. We have initiated the request from USDA-ARS for US-W4, but this line is under quality control in their tissue culture labs and they will send us the material when it is ready. A laminar flow tissue culture hood has been delivered to expand tissue culture facilities. Objective 3: NY121 line is no longer available at UMaine but true potato seed populations with NY121 as the parent has been identified. We will be contacting Cornell for NY121 seed stocks. Tissue culture of Caribou Russet has been obtained and is now maintained in our tissue culture collection. Literature search and PCR sequencing has been started to identify target for RenSeq probes.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Wang, J., Blevins, T., Podicheti R., Haag, J.R., Tan, E.H., Wang, F., Pikaard, C.S. (2017) Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes. Genes and Development, 31:1-16 doi: 10.1101/gad.301499.117
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