Progress 01/15/10 to 01/14/15
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? For each specificeducational objective the major outputs and accomplishments are given below: Objective 4 - Establish capability in dihaploid (doubled haploid) production to enable hands-on instruction in a new industrial technology and develop teaching materials to demonstrate its use as a tool in modern corn breeding. Output 4 - A protocol for doubled haploid production in corn was developed based on a review of the literature involving successful methodologies used in corn and other cereals, and implemented. Process efficiency was enhanced by developing methods for early detection of doubled haploids to eliminate false positives and prevent wasted greenhouse resources (see Plant Breeding J. publication). Teaching materials were created for use in the new course on "Advanced Plant Breeding" (CPSC 553, see also Objective 5), which debuted in Spring 2012. A publication outlining a method to improve efficiency in doubled haploid was published (Choe E., C. Hayot Carbonero, K. Mulvaney, A.L. Rayburn and R.H. Mumm. 2011. Improving in vivo maize doubled haploid production efficiency through early detection of false positives. Plant Breeding 131: 399-401.). In addition, results were presented to an international audience at the Maize Genetics Conference (2011, St. Charles, IL). Objective 5 - Develop 1 new plant breeding course and upgrade 2 current courses to expand and enhance the plant breeding curriculum. Output 5 - A new second-level course in "Advanced Plant Breeding" (CPSC 553) was developed by Dr. Rita Mumm. This course focuses on practical application of plant breeding, genetics, and statistics to devise effective approaches to meet particular breeding goals. Highlighting real-life situations and key decisions facing the plant breeder, the course builds upon knowledge of plant breeding methods and quantitative genetic theory. Four specific functional areas, which somewhat reflect divisions of labor in the seed industry, are addressed: population development, population evaluation, trait integration, and product commercialization and supply. Debuted in Spring 2012, the course received top ratings by the 8 PhD students enrolled. In addition to CPSC 553, we developed the "Plant Breeding Literature" (CPSC 556) course. CPSC 556 is team-taught by all plant breeding related faculty members. The goal of CPSC 556 is to expose the students to a diverse set of plant breeding journal articles and to critically evaluate their usefulness and impact. CPSC 556 started in the Spring semester of 2010 and reached >110 palnt breeding students. In addition, CPSC 466 "Genomics for Plant Improvement", a literature-based survey course in applied plant genomics taught by Dr. Stephen Moose, has been upgraded to a format effective for classroom delivery or across distances. Five self-contained modules were created and made available to enrolled students through the Illinois Compass software system, which included copies of journal articles, Power Point presentations that highlight important concepts and practices for each topic area, self-paced exercises that allow students to gain experience with genomics data analysis, and homework assignments that assess competence with course content. The Illinois Compass system also allows for discussion of course topics, and was used to field questions from students about homework assignments outside of class. The updated course is in its third term of instruction and has benefited >75 students in total so far. To update CSPC 558 "Quantitative Genetics and Plant Breeding" taught by Dr. Martin Bohn, an interactive Mathematica-based notebook was developed to provide students with the opportunity to explore quantitative-genetic concepts and how these apply to the design of plant breeding programs. Eight chapters of the 'notebook' covering topics from Hardy-Weinberg's Law to the use of linear mixed models in phenotypic selection in plant breeding and variety testing are designed to manipulate and visualize mathematical code on which quantitative-genetic concepts rest. All materials provided are interactive and can be controlled by the student to meet his/her's learning style and needs. This class was taught in its new format in the Fall semesters of 2011 to 2014 and reached > 50, mostly PhD level, students in crop and animal sciences. Objective 6 - Develop a new course to provide a background in agriculture to students who received their undergraduate degree in a non-agricultural area to support graduate recruitment from disciplines related to basic biology and mathematics. Output 6 - A new course to provide a background in agriculture to new graduate students who received previous degrees in non-agricultural areas (e.g. Biology, Math, Bioinformatics) was developed and debuted in Fall 2010: Midwest Agricultural Practices (CPSC 419). A 'crash course' in agronomy, the course features 8 lectures on various basics related to farm practices and the agricultural value chain taught by experts in each area. Students receive a high-level introduction to topics key to field testing and cultivar improvement as well as resources to direct further study in these areas. To date (Fall 2014), 73 students have enrolled and several others have audited at least one class/topic. The course has enjoyed top rating by students and has become a model for a continuing education course as well. Objective 7 - Provide summer internships in University of Illinois breeding programs for undergraduates from the University of Puerto Rico in support of graduate recruitment from underrepresented groups. Output 7 - The internship program for undergraduates from the University of Puerto Rico was implemented in the Summer of 2010, 2011, and 2012. Each year, applicants were recruited and pre-screened at the Universidad de Puerto Rico (UPR) by collaborator Dr. Linda Wessel-Beaver, and then interviewed by an Illinois Plant Breeding Center leader in January/February to select students for internship awards. Although the 2010 program offered 10 weeks, the length of the internships was modified to 6 weeks in 2011 to fit the altered academic calendar at UPR. With this change, we were able to accommodate 4 interns in 2011 versus 2 in 2010. Interns rotated through 3-4 different breeding programs involving corn, broccoli, miscanthus, sorghum, and wheat. The interns participated in planting, tissue sampling, pollinating, and harvesting activities in field, lab, and greenhouse. This experience provided exposure to an array of crops, breeding objectives, work settings, and research teams. Interns experienced campus life at UIUC; student housing and bicycles for campus transportation were provided. An exit interview with the interns and written evaluations highlighted strengths and is used to guide program improvements for the following year. In total, 8 UPR students were served. 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?
Nothing Reported
Impacts
What was accomplished under these goals?
All research and educational objectives were accomplished before the project ended on January 15, 2015. We requested a no-cost extension to finalize the complex data analyses for Objective 2. For each specific research objective the major outputs and accomplishments are given below: Objective 1 - Evaluate different combinations of inbreds from various elite heterotic subgroups to identify hybrid combinations that can yield proportionately higher under intense plant densities (≥45K plants per acre). Output 1 - A set of four maize inbred lines from the Stiff-Stalk (SS) heterotic group was crossed with eight inbreds from the diverse non-Stiff-Stalk (NSS) heterotic group to form 32 SS×NSS hybrids. The parental inbred lines represent a broad range of germplasm relevant to the U.S. commercial corn base. All hybrids were grown at five population densities (25K, 32K, 40K, 47K and 54K plants per acre) in 3 environments with varying levels of moisture availability (from summer drought to irrigated) across 2010 and 2011. Traits correlated with yield response were associated with the following five trait categories: (1) source-sink relationship, (2) photosynthetic capacity, (3) plant architecture, (4) hormonal balance, and (5) general stress tolerances. Gene action for grain yield across all densities was mostly additive, but with increasing stress levels associated with increasing plant density the contribution of non-additive gene action to the genotypic variance among hybrids increased significantly. Among our experimental hybrids five hybrids yielded more than 175 bushel per acre (11 tons per hectare) at the highest population densities across environments. Results of Objective 1 were published in Mansfield and Mumm (2014, Survey of plant density tolerance in U.S. maize germplasm. Crop Sci. 54:157-173) and presented at the ASTA Seed Expo (2012, Chicago, IL) and the National Association of Plant Breeders 6th Annual Meeting (2012, Indianapolis, IN). Objective 2 - Identify QTLs in key heterotic subgroups through map-based approaches and/or association mapping and screen candidate genes to investigate factors underlying the characteristic. Output 2 - The inbred parents of the five best performing hybrids at high density (see Output 1) were utilized to create a mapping population to identify chromosomal segments underlying plant density tolerance. A set of 217 recombinant inbred lines (RILs) derived from all possible crosses among the SS inbred lines and from all possible crosses between the NSS lines using single seed decent or doubled haploid methods were increased and crossed to form 320 SS×NSS double cross hybrids, which could be grouped in nine subpopulations. All 217 RILs were DNA-extracted and genotyped-by-sequencing (GBS). The GBS was performed by the Buckler Lab for Maize Genetics and Diversity (USDA-ARS). The 320 test hybrids were evaluated for grain yield and 33 agronomic and morphological traits at high population density in five environments (two locations in 2012; three locations in 2013). QTL mapping within the nine subpopulations revealed 246 QTL and genome wide association study (GWAS) identified 11 single nucleotide polymorphisms (SNPs) with significant trait associations. Based on these findings we identified putative candidate genes involved in agronomic performance under high plant density. Results of this research were presented at the 50th Illinois Corn Breeders' School (2014, Champaign-Urbana, IL), the Corn Breeding Webinar Series (2014, sponsored by DOW-DAS). This webinar series is organized by Dr. Bernardo (University of Minnesota) and reaches an international audience composed of public and private breeders, scientists and graduate students. Manuscripts focusing on QTL and GWAS results are in preparation. Objective 3 - Validate results and devise methods to utilize information in hybrid improvement selection schemes. Output 3 - We used the phenotypic and genotypic information obtained for our test hybrids (see Output 2) to investigate the usefulness of genomic prediction for agronomic performance under high plant density stress. Hybrid performance was predicted by genomic best linear unbiased prediction (G-BLUP) including additive and dominance relationship matrices. We observed in cross validation a prediction accuracy of 0.70 for across family hybrid prediction. Interestingly, modeling dominance did not increase prediction accuracy. The prediction accuracies for within-family hybrid prediction were moderate to high, illustrating the potential of genomic prediction to estimate hybrid performance within a family when the training set consist of hybrids from other related families. Overall, our results suggest that genomic prediction of hybrid performance holds good potential to increase the efficiency of hybrid breeding. As part of this project, we also develop a method for genomic prediction of performance, which allows modeling of epistatic interactions. The method employs a non-parametric approach featuring a combination of supervised principal component analysis and reproducing kernel Hilbert spaces regression to help guide choice of parents in plant breeding. Results of Objective 3 were published in Sun et al. (2012. Nonparametric method for genomics-based prediction of performance of quantitative traits involving epistasis in plant breeding. PLoS ONE 7(11): e50604. doi:10.1371/journal.pone.0050604) and at the Maize Genetics Conference (2015, St. Charles, IL) and the NCC-167 Annual Meeting (2015, St. Charles, IL). Additional publications are in preparation.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2015
Citation:
Kadam D., Potts S.M., Bohn M, and Lorenz A. 2015. Genomic prediction of hybrid performance in maize (Zea mays L.). 57th Annual Maize Genetics Conference, P263, March 12-15, 2015, St Charles, IL.
- Type:
Theses/Dissertations
Status:
Accepted
Year Published:
2014
Citation:
Potts S. 2014. Identification of QTL and candidate genes for plant density tolerance in maize. Ph.D. Dissertation. University of Illinois at Urbana-Champaign. http://hdl.handle.net/2142/49814.
- Type:
Theses/Dissertations
Status:
Accepted
Year Published:
2012
Citation:
Mansfield B. 2012. Survey of plant density tolerance in U.S. maize germplasm. M.S. Thesis. University of Illinois at Urbana-Champaign. http://hdl.handle.net/2142/34539.
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Progress 01/15/13 to 01/14/14
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest? Sarah Potts presented this research to a diverse audience, including, scientists, farmers, university officials and others, at the Crop Science Agronomy Day in 2013, and has given brief presentations on the topic of plant density tolerance research in Dr. Fred Kolb’s class, Principles of Plant Breeding, as well as Crop Sciences 101. Sarah Potts also made research presentations to scientists and managerial professionals at the headquarters of Dow AgroSciences, Monsanto, and DuPont Pioneer. She also presented her research at the Achievement Rewards for Collegiate Scientists awards luncheon in Chicago, furthering understanding of this important area of research to the general public. To scientific audiences, Sarah has presented a webinar in a corn breeding webinar series attended by leading corn breeding professors, industry professionals, and graduate students, and she also presented a poster on her research at the National Association of Plant Breeders annual meeting, held in June of 2013. What do you plan to do during the next reporting period to accomplish the goals? The genotypic analysis and candidate gene identification for high plant density tolerance in maize will be completed and published.
Impacts
What was accomplished under these goals?
The following progress was achieved in 2013/01 to 2014/01: Field trials were conducted over three locations during the 2013 growing season to evaluate trait responses to high plant density towards the goals of dissecting the genetics underlying plant density tolerance. (Planting by field technician Nicole Yana, M.S. students Alex Brohammer and Liz Blissett, and Ph.D. students Carrie Butts and Sarah Potts). A connected population (having six grandparents in common) of 320 testcross hybrids were evaluated at 47,000 plants per acre for a comprehensive set of traits determined to be correlated with plant density tolerance. Undergraduate students (Emily Darby, Jerome Knight, Kim Kotowski, Yucheng Lin, Steve Montez, Gordon Stone and Matt Wasmund), M.S. students (Liz Blissett and Alex Brohammer) and Ph.D. students Carrie Butts and Sarah Potts were trained in phenotypic data collection and the following traits were evaluated in the field: stand count, plant height, ear height, leaf angle, upper stem diameter, barrenness, stalk lodging, and root lodging. Subsamples of ear leaves and tassels were selected for lab phenotyping and ear leaf area, tassel branch number, tassel weight, and central spike length were measured. Subjective measurements, such as canopy closure, days to anthesis, days to silking, and staygreen, were taken by Ph.D. candidate Sarah Potts. For harvest, five ears were sampled from each plot to measure ear width, ear length, fill length, number of rows, number of kernels per row, and grain weight per ear (Harvesting and phenotyping by field technician Nicole Yana, undergraduate students Jerome Knight, Steve Montez, Matt Wasmund and Eric Vermillion, M.S. students Alex Brohammer and Liz Blissett and Ph.D. students Carrie Butts and Sarah Potts). Plots were then machine harvested and yield, test weight and moisture were measured. Data collection is ongoing for kernel length, kernel depth, and kernel width. Summary statistics for all phenotypic data have been calculated and correlations between grain yield and multiple traits have detected important yield-trait relationships. Principle component analysis has also been done on the data and subfamilies segregate as expected. Variance components have been calculated for all traits and broad sense heritability has been calculated. Quantitative genetics analysis and determining narrow sense heritability is the next step of the phenotypic analysis. Least square means were calculated for all traits for all genotypes, by year, for use in analyzing genotype-phenotype correlations. For the initial quantitative trait loci (QTL) analysis we imputed missing data from the genotype-by-sequencing (GBS) and chose only markers which differed for inbred parents for QTL analysis within each of the nine subfamilies. Using single marker mapping and false discovery rate testing, we detected over 240 QTL. Stringent criteria, for selection of which QTL would be chosen for candidate gene analysis, were applied, resulting in six high-confidence QTL to further investigate. For the genome wide association study (GWAS), multiple methods of filtering the GBS data have been implemented to determine the most accurate parameters for detecting QTL. A marker set of 2,673 markers (filtered for 20% missing data and minor allele frequency of >.001) was selected for the final analysis using GAPIT software. Both kinship (K) and structure (Q) matrices were calculated for use in the final model to reduce spurious associations resulting from confounding familial effects. Two highly significant molecular markers have been identified as high-confidence QTL for future candidate gene analysis. Due to the complexity of this trait, this additional QTL will also be pursued for candidate gene analysis.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
B.D. Mansfield and R.H. Mumm. Survey of plant density tolerance in U.S. maize germplasm. Crop Sci. 54:157-173.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2013
Citation:
Potts, S.M., R.H. Mumm and M.O. Bohn. Plant density tolerance: Old premise, new research. Agronomy Day, Urbana, 15 August 2013.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2013
Citation:
Potts, S.M., R.H. Mumm and M.O. Bohn. Dissecting the Genetic Basis of Plant Density Tolerance. Proc. Nat. Assc. Plant Breed 7th Annual Meeting. Tampa, 2-5 June 2013.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2013
Citation:
Potts, S.M., M.O. Bohn and R.H. Mumm. Utilizing GBS to dissect plant density tolerance. Corn Breeding Webinar Series, Citrix Online, 5 April 2013.
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Progress 01/15/12 to 01/14/13
Outputs
OUTPUTS: Toward research objectives, performance data from 32 genetically diverse hybrids which had been grown at 5 population densities (25K, 32K, 40K, 47K and 54K plants per acre) in 3 environments across 2010 and 2011, were analyzed. Five hybrids yielded above 175 bushel per acre at the highest population densities across environments, and were distinguished in performance from the other 27 hybrids. Six inbreds parents were used to create RILs used in testcross hybrid production. In addition, 20 traits were found to be associated with plant density tolerance, paving the way for the QTL mapping and candidate gene objectives. 300+ testcross hybrids were grown at high plant density at 2 locations in Summer 2012 and evaluated for the 20 key traits. In addition, 273 RILs were genotyped (genotype-by-sequence), providing >220K SNPs for QTL mapping. GBS data were produced and delivered by Ed Buckler's lab. In addition, a method was developed for genomics-based prediction of performance, especially for quantitative traits involving epistasis. The method employs a non-parametric approach featuring a combination of supervised principal component analysis and reproducing kernel Hilbert spaces regression to estimate breeding values. Toward education objectives, a protocol for dihaploid production in corn was developed and implemented. Process efficiency was enhanced by developing methods for early detection of doubled haploids to eliminate false positives and prevent wasted greenhouse resources. Teaching materials were created and used in the new course on Advanced Plant Breeding which debuted in Spring 2012 and a publication outlining a method to improve efficiency in DH production in maize was produced. A new second-level course in Advanced Plant Breeding (CPSC 553) was developed and taught by Dr. Rita Mumm. This course focuses on practical application of plant breeding, genetics, and statistics to devise effective approaches to meet particular breeding goals. Highlighting real life situations and key decisions facing the plant breeder, the course builds upon knowledge of plant breeding methods and quantitative genetic theory. Four specific functional areas, which somewhat reflect divisions of labor in the seed industry, are addressed: population development, population evaluation, trait integration, and product commercialization and supply. Debuted in Spring 2012, the course received top ratings by the 8 PhD students enrolled. The newly-developed course, CPSC 419 - Midwest Agricultural Practices, and upgrades courses CPSC 466 - Genomics for Plant Improvement and CSPC 558 - Quantitative Genetics and Plant Breeding, were again taught in 2012, benefitting more students and achieving top rankings by students. The internship program for undergraduates from the University of Puerto Rico served its final cohort in Summer 2012. Applicants were recruited and pre-screened at UPR by collaborator Dr. Linda Wessel-Beaver, and then interviewed by an IPBC lead in February to select students. Interns rotated through 4 different breeding programs and participated in planting, tissue sampling, pollinating, and harvesting activities in field, lab, and greenhouse. PARTICIPANTS: Collaborations include: 1) Dr. Edward Buckler (USDA ARS, Cornell Univ.) and team were involved in genotyping the RIL population created to identify factors underlying plant density tolerance. 2) Dr. Ping Ma, Assoc. Prof., Statistics Department, University of Illinois at Urbana-Champaign, collaborated on the statistical method for predicting performance. 3) Dr. Linda Wessel-Beaver, University of Puerto Rico-Mayaguez, collaborated to facilitate and support undergraduate summer internships in plant breeding. 4) Dow Foundation Aid-To-Education Program, Katherine Armstrong and Jeff Rosichan, liaisons. 5) Dr. Jeffrey Ross-Ibarra, Dept. of Plant Sciences and Genome Center, University of California at Davis is collaborating to share and extend use of genotypic data and phenotypic data collected on the ex-PVP diallel population. TARGET AUDIENCES: Students in the Illinois Plant Breeding Center have benefitted from course additions and upgrades. We look to increase both the number and proficiency of the next generation of plant breeders. Traditionally under-represented groups in plant breeding have been targeted, especially seeking to increase the number of quality-trained plant breeders for the plentiful positions based in Puerto Rico at winter/continuous nursery facilities. PROJECT MODIFICATIONS: Martin O. Bohn is taking over the position as PI for the project in 2013; Rita Mumm will continue as a co-PI.
Impacts
Graduate education in plant breeding is a primary target for long-term impact, by increasing the number and diversity of plant breeding professionals well prepared to lead industrial and academic research programs and make vital contributions to crop improvement. Furthermore, the increased quality of this educational preparation resulting from this project support will have lasting and broad-reaching impact, especially as graduate numbers from the University of Illinois increase. In particular, we look to increase the number of quality-trained plant breeders for the plentiful industrial positions based in Puerto Rico at winter/continuous nursery facilities. Evidence of progress toward these targets is seen by 1) An increase in the number of students in the Illinois Plant Breeding Center, from 21 in 2007 (and earlier) to 67 in 2012, representing a >3-fold increase and achievement of our organizational goal. 2) An increase in the caliber of student applicants to the Illinois Plant Breeding Center; Fall 2012 applicant pool had an average GPA of 3.6. 3) Students graduating from the IPBC are in high demand and have seen excellent opportunities in job placement. 4) Several past UPR interns have taken steps to pursue an educational pathway/career in plant breeding. The internship program structure and success was leveraged to solicit support from Dow Foundation to expand internship opportunities for under-represented groups as well as military veterans (6 internships in total), enhancing our intern sponsorship, outreach, education and recruiting programs for future plant breeders. Moreover, students have the opportunity through research to explore a trait that is essential to doubling yields in the near future, plant density tolerance. The research impact will result from identification of chromosomal regions/genes impacting plant density tolerance and other stress tolerance. Because the germplasm is directly relevant to the current corn commercial base, the markers will be useful for tracking key genetic factors for trait improvement. Furthermore, we anticipate new insights into factors and interactions underlying high yield under intense plant-to-plant competition will come from this work. The research conducted with this project has also had an educational impact. An undergraduate worker, Mallory Plocher, took a job with Bayer CropScience in their cotton breeding program at Memphis, TN after completing her BS in Crop Sciences. Others are investigating graduate opportunities in plant breeding. Brian Mansfield completed his MS degree program and took a position with the University of Illinois as a Research Agronomist at the Agricultural Experiment Station at Monmouth, IL. Xiaochun Sun who contributed to the statistical method work was hired as a Quantitative Geneticist with Dow AgroSciences upon completion of his PhD program.
Publications
- Sun, X., P. Ma and R.H. Mumm. 2012. Nonparametric method for genomics-based prediction of performance of quantitative traits involving epistasis in plant breeding. PLoS ONE 7(11): e50604. doi:10.1371/journal.pone.0050604.
- Choe E., C. Hayot Carbonero, K. Mulvaney, A.L. Rayburn and R.H. Mumm. 2011. Improving in vivo maize doubled haploid production efficiency through early detection of false positives. Plant Breeding 131: 399-401. http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0523.2012.01962.x/p df.
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Progress 01/15/11 to 01/14/12
Outputs
OUTPUTS: Toward our research objectives, 32 genetically diverse hybrids were grown at 5 population densities (25K, 32K, 40K, 47K and 54K plants per acre) in 3 environments across 2010 and 2011. Five hybrids yielded above 175 bushels per acre at the highest population densities across environments. The parents of these hybrids will be the focus of a deep dive to identify QTLs associated with factors underlying the capacity for high yield under high population density. RILs (doubled haploid lines or single-seed descent lines) from all possible crosses of 3 female lines and from all possible crosses of 3 male lines were increased in the greenhouse in Winter 2010 to prepare for testcross hybrid production in Summer 2011. Furthermore, RILs were grown to V3 stage in the greenhouse to collect leaf tissue for genotyping. DNA extraction is being done in a manner to ensure high quality DNA for producing genotype-by-sequence data for each RIL; genotypes of the testcross hybrids will be inferred from parental genotypes. Toward our education objectives, a protocol for dihaploid production in corn was developed and implemented. Process efficiency was enhanced by developing methods for early detection of doubled haploids to eliminate false positives and prevent wasted greenhouse resources. Teaching materials were created for use in the new course on Advanced Plant Breeding to debut in Spring 2012. A new course to provide a background in agriculture to new graduate students who received previous degrees in non-agricultural areas debuted in Fall 2010: CPSC 419 - Midwest Agricultural Practices. A crash course in agronomy, the course features 8 lectures on various basics related to farm practices and the agricultural value chain taught by experts in each area. To date, 22 students have enrolled. In addition, CPSC 466 Genomics for Plant Improvement, a literature-based survey course in applied plant genomics taught by Dr. Stephen Moose, has been upgraded to a format effective for classroom delivery or across distances. The updated course is in its second term of instruction and has benefited 53 students in total so far. To update CSPC 558 Quantitative Genetics and Plant Breeding taught by Dr. Martin Bohn, an interactive MATHEMATICA-based notebook was developed to provide students with the opportunity to explore quantitative-genetic concepts and how these apply to the design of plant breeding programs. This class was taught in its new format in Fall 2011. The internship program for undergraduates from the University of Puerto Rico was implemented in Summers 2010 and 2011. Each year, applicants were recruited and pre-screened at UPR by collaborator Dr. Linda Wessel-Beaver, and then interviewed by an Illinois Plant Breeding Center leader in January/February to select students for internship awards. We hosted 4 interns in 2011 and 2 in 2010. Interns rotated through 3 or 4 different breeding programs involving various crops and participated in planting, tissue sampling, pollinating, and harvesting activities in field, lab, and greenhouse. PARTICIPANTS: The training provided through this project vastly deepens and intensifies its reach and impact: Stephen Phillips - MS-level technical manager assisting in seed and field aspects for all facets of the project and Wendy White - MS-level coordinator for the Illinois Plant Breeding Center, organizing the UPR internships; Eunsoo Choe and Christine Hayot Carbonero - post docs employed on the dihaploid project; Brian Mansfield - MS candidate in the Mumm Lab researching population density effects; Sarah Potts - PhD candidate in the Mumm Lab researching population density effects; Christine Lucas - PhD candidate in the Moose Lab creating course materials. Undergraduate intern, Kelly A. Mulvaney, from Northeastern Illinois University (supported on CREAR (Collaboration and Retention through Environmental and Agricultural Research) Project funded by USDA-NIFA HSI Grant No. ILLE-2010-02093) worked on the dihaploid project. Undergraduate student interns from UPR include Krystel Navarro, Gabriela Nazario Ramos, Virgilio Olivera, Sara Gonzalez, Pedro Cruz, and Veronica Brotons. Undergraduate students involved in the high population density research include Joseph Brines, Sylwia Budzik, Kyle Carpenter, Daniel Hay, Brenda Ha, Kit Heller, Daniel Herriott, Haley Johnson, Danielle Lekas, Adam Massie, Lindsay Martinez, Sondra Monier, Russell Montgomery, Kord Nolte, Mallory Plocher, Emily Roberts, Bianca Rog, and Jeffrey Trost. New and updated plant breeding courses have already been relevant to 79 students so far, providing improved instruction to 59 graduate students and 20 undergraduates. Collaborators include: Dr. Edward Buckler (USDA ARS, Cornell) and team will be involved in genotyping the connected population created to identify factors underlying high yield at high population density. Dr. Nancy Wrinkle, Assoc.Prof. Mathematics, Northeastern Illinois University, Chicago, IL collaborated to facilitate and support undergraduate research internship of Kelly Mulvaney through CREAR (Collaboration and Retention through Environmental and Agricultural Research) Project funded by USDA-NIFA HSI Grant No. ILLE-2010-02093. Dow Foundation Aid-To-Education Program, Katherine Armstrong, liaison. Dr. Jeffrey Ross-Ibarra, Dept. of Plant Sciences and Genome Center, University of California at Davis is collaborating to share and extend use of genotypic data and phenotypic data collected on the ex-PVP diallel population. TARGET AUDIENCES: The research portion of this project has generated phenotypic data relevant to a set of ex-PVP lines for which seed is publicly available through GRIN. Likewise, this project is generating genotypic and phenotypic data relevant to RILs for which seed will be publicly available in the future. All serve as educational resources. Teaching materials relevant to dihaploid production were created to facilitate instruction in this important area gaining momentum in plant breeding. Furthermore, USDA funding has supported the development of the structure and content for extension of plant breeding curricula to be delivered on-line; thus, impacts can reach beyond the UIUC campus. CPSC 466 was recorded with integrated audio and video of power point presentations and lectures archived, so that the course could be taken remotely and self-paced, without the need for any additional, specialized software. Internship opportunities have been established and expanded for UPR undergraduates to experience plant breeding firsthand, to explore professional roles in crop improvement, and to sample the graduate school experience. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Graduate education in plant breeding is a primary target for long-term impact, by increasing the number and diversity of plant breeding professionals well prepared to lead industrial and academic research programs and make vital contributions to crop improvement. Furthermore, increasing the quality of this educational preparation will have lasting and broad-reaching impact, especially as graduate numbers from the University of Illinois increase. In particular, we look to increase the number of quality-trained plant breeders for the plentiful industrial positions based in Puerto Rico at winter/continuous nursery facilities. Evidence of progress toward these targets is seen by 1) an increase in the number of students in the Illinois Plant Breeding Center, from 21 in 2007 (and earlier) to 58 in 2011, a 2.76-fold increase, 2) an increase in the caliber of student applicants to the Illinois Plant Breeding Center; Fall 2011 applicant pool had an average GPA of 3.7, and 3) several past UPR interns have taken steps to pursue an educational pathway/career in plant breeding (V. Olivera has begun an MS program in plant breeding at UPR and K. Navarro interned with Pioneer Hi-Bred International at their Ivesdale, Illinois corn breeding station in Summer 2011). The internship program structure and success was leveraged to solicit support from Dow Foundation to expand internship opportunities for under-represented groups as well as military veterans (6 internships in total), enhancing our intern sponsorship, outreach, education and recruiting programs for future plant breeders. Moreover, students have the opportunity through research to explore a trait that is essential to doubling yields in the near future: high yield under high population density. Having one location under irrigation allows us to see the impact of moisture stress on intense interplant competition. Furthermore, because some inbreds contributed to both high-yielding and low-yielding hybrids, we have the opportunity to explore general and specific combining ability in a high plant density environment. We anticipate new insights into factors and interactions underlying high yield under intense plant-to-plant competition will come from this work. The research conducted with this project has also had an educational impact. An undergraduate worker, Mallory Plocher, took a job with Bayer CropScience in their cotton breeding program at Memphis, TN after completing her BS in Crop Sciences. Others are investigating graduate opportunities in plant breeding.
Publications
- Choe, E., Hayot Carbonero, C., Mulvaney, K., Rayburn, A.L. and Mumm, R.H. 2011. Improving in vivo maize doubled haploid production efficiency through early detection of false positives. Plant Breeding (Accepted).
- Choe, E., Bohn, M.O. and Mumm, R.H. 2011. Establishing in vivo maize doubled haploid production at the University of Illinois for education and research purposes. Abstract and poster at the Maize Genetics Conference,17-20 March 2011. St. Charles, IL.
- Mansfield, B.D. and Mumm, R.H. 2011. Survey of plant density tolerance in U.S. maize germplasm. Poster and abstract at ASTA Seed Expo, Chicago, IL, 7-9 December 2011.
- Potts, S.M. and Mumm, R.H. 2011. Utilizing connected populations for QTL discovery. Poster and abstract in the Proc. Amer. Soc. Hort. Science 108th Annual Meeting, Waikoloa HI, 25-28 September 2011.
- Mulvaney, K.A., Choe, E. and Mumm, R.H. 2011. Improving efficiencies in maize dihaploid production. Poster at the Third Annual Research Symposium. Northeastern Illinois University Student Center for Science Engagement, Northeastern Illinois University, September 16, 2011.
- Potts, S.M., Mansfield, B.D. and Mumm, R.H. 2011. Development of stress-tolerant maize lines under high plant density. Poster at Agronomy Field Day, University of Illinois Farm, Urbana IL, 18 August 2011.
- Potts, S.M. and Mumm, R.H. 2011. Utilizing connected populations for QTL discovery. Poster at NAPB/PBCC 6th Annual Workshop, College Station TX, 23-25 May 2011.
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Progress 01/15/10 to 01/14/11
Outputs
OUTPUTS: Toward the research objective to identify hybrid combinations that can yield proportionately higher under intense plant densities: 32 hybrids representing a broad range of germplasm relevant to U.S. commercial corn hybrids were grown at 5 population densities (25K, 32K, 40K, 47K and 54K plants per acre) at 2 locations in Summer 2010. Data were collected on traits important to source-sink relationship (e.g. yield, yield components, grain fill), photosynthetic capacity (e.g. leaf angle, leaf area), plant architecture (e.g. stem diameter, tassel morphology), hormonal balance (e.g. plant height), and stress tolerances (e.g. barrenness, anthesis-silking interval), among others. There were several hybrids that yielded above 200 bushel per acre at the highest population densities. The parents of these hybrids will be the focus of efforts to identify QTLs associated with factors underlying the capacity for high yield under high population density. Toward the objective to identify QTLs, a design for a connected population for QTL mapping has been developed to maximize mapping resolution, which utilizes 3 of each of the superior female and male parents. RILs from all possible crosses of the female lines and from all possible crosses of the male lines are being increased in the greenhouse this winter to prepare for testcross hybrid production next summer to create the connected population of >250 hybrids. Toward education objectives, progress has been made to establish and implement a protocol for dihaploid production in corn. After review of the literature was conducted to assemble information on successful methodologies used in corn and other cereals, a protocol utilizing colchicine has been developed and successfully implemented. Focus now centers on improving the protocol. A new course to provide a background in agriculture to new graduate students who received previous degrees in non-agricultural areas (e.g. Biology, Math, Bioinformatics) debuted in Fall 2010 as CPSC 499 - Midwest Agricultural Practices. The course featured 8 lectures on various basics related to farm practices and the agricultural value chain taught by experts in each area. In addition, CPSC 466 - Genomics for Plant Improvement has been upgraded to a format effective for classroom delivery or across distances, including 5 self-contained modules. To update CSPC 558 - Quantitative Genetics and Plant Breeding an interactive MATHEMATICA-based notebook was developed to provide students with the opportunity to explore quantitative-genetic concepts and how these apply to the design of plant breeding programs. The internship program for undergraduates from the University of Puerto Rico was instituted in Summer 2010 with assistance by collaborator Dr. Linda Wessel-Beaver. Two interns rotated through 4 different breeding programs involving corn, broccoli, miscanthus, and wheat and participated in planting, tissue sampling, pollinating, and harvesting in activities from field to lab to greenhouse, providing exposure to an array of crops, breeding objectives, work settings, and research teams. PARTICIPANTS: The internship program for undergraduates from the University of Puerto Rico was instituted in Summer 2010 with assistance by collaborator Dr. Linda Wessel-Beaver. The training provided through this project vastly deepens and intensifies its reach and impact: S. Phillips, MS-level technical manager; W. White, MS-level IPBC coordinator; E. Choe, post doc employed on the dihaploid project; B. Mansfield, MS candidate in the Mumm Lab; S. Potts, PhD candidate in the Mumm Lab; C. Lucas, PhD candidate in the Moose Lab; undergraduate students involved in the high population density research: J. Brines, K. Heller, D. Herriott, A. Massie, and M. Plocher. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Graduate education in plant breeding is a primary target for long-term impact, by increasing the number and diversity of plant breeding professionals well prepared to lead industrial and academic research programs and make vital contributions to crop improvement. Furthermore, increasing the quality of this educational preparation will have lasting and broad-reaching impact, especially as the number of graduates increases. In particular, we look to increase the number of quality-trained plant breeders for the plentiful industrial positions based in Puerto Rico at winter/continuous nursery facilities. Furthermore, students have opportunity through research to explore a trait that is essential to doubling yields in the near future: high yield under high population density. Having one location under irrigation allows us to see the impact of moisture stress on intense interplant competition. Furthermore, because some inbreds contributed to both high-yielding and low-yielding hybrids, we have the opportunity to explore general and specific combining ability in a high population density environment. We anticipate new insights into factors and interactions underlying high yield under intense plant-to-plant competition will come from this work. To date, new and improved courses central to plant breeding education, some designed for distance-sharing, have significantly strengthened the overall quality of the plant breeding curriculum offered by the University of Illinois. Educational modules including relevant journal articles, key concepts, and self-guided tutorials that were developed for "Genomics for Plant Improvement", a literature-based survey course in applied plant genomics taught by Dr. Stephen Moose, for each of five topics: 1) In silico gene discovery via DNA sequence databases; 2) Analysis of genetic diversity; 3) Genetic mapping; 4) RNA profiling; and 5) Functional modifications to plant genes via transgenics or mutant analysis. The course is accessible through the University of Illinois via the Compass System and is appropriate for distance-sharing as well as classroom delivery. In addition, 8 interactive MATHEMATICA-based notebook chapters were developed to facilitate "Quantitative Genetics and Plant Breeding" taught by Dr. Martin Bohn. Internship opportunities have been established for UPR undergraduates to experience plant breeding firsthand, to explore professional roles in crop improvement, and to sample the graduate school experience. The training provided through this project vastly deepens and intensifies its reach and impact. New and updated plant breeding courses have already been relevant to 41 students, providing improved instruction for 34 students enrolled in CPSC 466 and 7 students enrolled in CPSC 499 in Fall 2010.
Publications
- No publications reported this period
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