Progress 05/15/19 to 05/14/21
Outputs
Target Audience:The target audiences for this project included bioenergy researchers and producers (optimal protocols for chromosome doubling of Miscanthus hybrids), Miscanthus growers (Chromosome doubling of high-yielding hybrids), plant breeders interested in genetics of high-yielding interspecific hybrids and biology, and students (R programming course, plant science summer course). Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Laboratory experience with polyploid generation via colchicine application, tissue culture, QTL mapping strategies, and GBS library preparation were provided by the project. Completed Software Carpentry Instructor Training (Spring 2019) at UIUC. Professional development experience with course development, instructional methods, and mentoring graduate students was obtained. How have the results been disseminated to communities of interest?A pair of manuscripts is in preparation for the results of the QTL analysis refinement work. Course materials for the R course were shared for subsequent instructors of the course to use. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Genomics of Allopolyploid Hybrids In fall 2019, several putative allopolyploids of Miscanthus sacchariflorus ssp. lutarioriparius and interspecific hybrids were generated with colchicine treatment of rooted node cuttings. The transformed plants had low vigor and the yield of this method was low. Subsequently, an experiment was conducted using the same colchicine treatment on sorghum seedlings and higher yields of polyploids were obtained, indicating that the Miscanthus plant material was more recalcitrant to this method for obtaining polyploid plants. After an interruption in lab work due to the COVID-19 pandemic, a tissue culture strategy was used to grow plantlets of Miscanthus F1 and F2 interspecific hybrids from a Miscanthus sinensis x lutarioriparius cross. This method generated more suitable plant material but the experiment was not completed due to Dr. LaBonte leaving the University of Illinois to take a Geneticist position with the U.S. Forest Service in fall 2020. Genetics of High-Yielding Miscanthus Hybrids During spring and summer 2020, Miscanthus QTL mapping methods for GBS SNP datasets were optimized using existing biomass yield Miscanthus datasets and new data from the Miscanthus sinensis x lutarioriparius F1 and F2 populations. Genetic mapping in Miscanthus is complicated by its allopolyploidy and its obligate outcrossing nature. We determined that, due to the high genetic diversity of open-pollinated F1 and F2 Miscanthus populations, using half-sib or full-sib family membership as a covariate improved power to identify QTL in complex F2 populations. We also identified depth filtering parameters that improved the precision of QTL position estimates in Miscanthus F1 and F2 interspecific hybrid mapping populations. These insights, which are also applicable to other obligately outcrossing polyploidy crops, will improve the efficiency of breeding these crops and thus benefit agricultural producers and consumers. Co-Teaching and Professional Development Dr. Clark, who was planned to co-teach a bioinformatics course with Dr. LaBonte, left the Sacks lab for another position in 2019 and had to abandon plans for co-teaching. However, Dr. LaBonte was able to teach an R programming course for crop sciences graduate students in fall 2019, with course materials and mentorship provided by Dr. Clark, to accomplish this goal of the fellowship. Dr. LaBonte also participated in teaching a summer 2019 field course for high school and college students underrepresented in STEM fields, with cooperators at Hudson-Alpha in Huntsville, Alabama and at Alabama A&M University. Dr. Labonte also mentored graduate students in the Sacks lab, including instructing multiple graduate students in GBS library preparation and data analysis.
Publications
- Type:
Journal Articles
Status:
Other
Year Published:
2022
Citation:
LaBonte, N., S, Liu, L. Xiao, L.V. Clark and E.J. Sacks. 2022. Accuracy and precision of genetic mapping in heterozygous populations using genotyping-by-sequencing data is improved by optimizing depth to control the genome-wide error rate for genotype-calling.
- Type:
Journal Articles
Status:
Other
Year Published:
2022
Citation:
LaBonte, N., L. Xiao, X. Zheng, L.V. Clark and E.J. Sacks. 2022. Ability to detect quantitative trait loci in an F2 population derived from multiple segregating F1s of the obligately-outcrossing crop Miscanthus is improved by accounting for kinship.
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Progress 05/15/19 to 05/14/20
Outputs
Target Audience:The target audiences for this project that were served during the reporting period include bioenergy researchers and producers (optimal protocols for chromosome doubling of Miscanthus hybrids), Miscanthus growers (Chromosome doubling of high-yielding hybrids), and biology and bioinformatics students (R programming course, plant science summer course). Changes/Problems:Problem 1. An extreme cold event in early 2019 completely killed the observation plots and replicated field trial at Urbana, Illinoisthat we had initially planned on using to make selections of F1s and F2s. This set back the timeline for making selections and obtaining plant material from these genotypes. Ultimately, a separate observation planting in Alabama was used to make selections of F1s and a combination of plugs from cold storage at UIUC and stem cuttings from the Alabama observation planting were used to propagate plant material for chromosome doubling. For the F2 population, first-year measurements from a new replicated field trial at Urbana were used to make selections. Resulting Changes: The timeline for planting a field trial of doubled plants has been moved to spring 2021 and will probably be planted with collaborators in Mississippi- survival of F2s was poor in Illinois even with a mild winter in 2019-2020. Problem 2. The colchicine application protocol for chromosome doubling-applying colchicine to young leaf whorls had some success with the Miscanthus sacchariflorus ssp. lutarioriparius parent of the population and with some F1s. However, many of the F1s have long, densely wrapped leaves surrounding the apical meristem and the colchicine solution was unable to penetrate the leaf whorl. This resulted in chimeric plants with some doubled leaves, or leaves killed by colchicine, but no meristematic doubling. Resulting Change: We have moved most of the F1 selections into tissue culture (this process is ongoing) to double in vitro shoots on colchicine containing growth media. This has the advantage of being more efficient (in terms of tetraploids per treated shoot) and safer (less handling of colchicine solutions). The novel coronavirus pandemic delayed this work between March and June 2020 but I have resumed working in the lab following University of Illinois safety guidelines for on-campus research work. Problem 3. I originally planned to co-instruct an R for Bioinformatics course with Dr. Lindsay Clark. Dr. Clark departed the Crop Sciences department in summer 2019 for a new position and was unable to go through with this plan. Instead I was the primary instructor for an Introduction to R Programming course, fulfilling that aspect of the professional development plan. Resulting Change: I developed a separate course on my own with input and guidance from Dr. Clark before she departed the Sacks lab. This met the instructional experience objectives of the project. What opportunities for training and professional development has the project provided?Completed Software Carpentry Instructor Training (Spring 2019) at UIUC. 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?Successful tetraploid induction via colchicine treatment was low using the original protocol (treatment of young shoots growing in soil in growth chambers). We have developed in vitro shoot proliferation cultures of most of the F1 selections to conduct chromosome doubling more efficiently (Objectives 1,2, and 3). Once doubled plants are obtained, RNA sequencing can proceed in pursuit of Objectives 1 and 2. I plan to attend an RNA sequencing workshop to develop skills necessary for Objectives 1 and 2 in pursuit of the project's career development goals.
Impacts
What was accomplished under these goals?
Research Project Goals: Made selections of Miscanthus F1 and F2 interspecific hybrids with high and low biomass yield potential relative to the mean yield potential of the cross (Summer 2019) (Objective 3). Treated 24 high-yielding and 24 low-yielding F1 selections, along with parents, with colchicine to induce chromosome doubling, testing different aqueous concentrations (Fall 2019) (Objective 3). Began tissue culture of 24 high-yielding and 24 low-yielding F1 selections, along with parents, to obtain doubled plants with greater efficacy (Spring 2020) (Objective 3). Professional Development Goals: Developed and instructed Introduction to R Programming course for graduate students in the Crop Sciences department, with guidance from Dr. Clark (Fall semester 2019) (Objective 4). Helped Dr. Sacks produce a summer program for STEM students in Huntsville, Alabamain cooperation with Alabama A&M University and Hudson-Alpha Biosciences, including travel to Huntsville for in-person instruction (July 2019) (Objective 4).
Publications
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