Source: VIRGINIA POLYTECHNIC INSTITUTE submitted to NRP
ENGAGING THE NEW BIOLOGY: INTEGRATING QUANTITATIVE GENETICS AND GENOMICS IN ANIMAL BREEDING GRADUATE LEARNING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
0225951
Grant No.
2011-38411-30551
Cumulative Award Amt.
$700,142.00
Proposal No.
2011-01827
Multistate No.
(N/A)
Project Start Date
Sep 1, 2011
Project End Date
Aug 31, 2015
Grant Year
2011
Program Code
[ER]- Higher Ed Challenge
Recipient Organization
VIRGINIA POLYTECHNIC INSTITUTE
(N/A)
BLACKSBURG,VA 24061
Performing Department
Department of Animal and Poultry Sciences
Non Technical Summary
As noted in the "Blueprint for the USDA efforts in Agricultural Animal Genomics 2008-2017" the efficiency of meat, milk and egg production has increased substantially through innovations in quantitative genetics. Yet, to address Global Food Security and Hunger, production efficiency must improve further. Melding state-of-the-art technologies in animal genomics with quantitative genetics approaches will more accurately identify high merit animals, thereby accelerating rates of genetic improvement. It will also allow for incorporation of novel traits, such as feed efficiency, animal well-being and disease susceptibility, into genetic improvement programs. Over the past 25 years in land-grant institutions, focus on quantitative areas of genetics, particularly animal breeding, has reduced sharply as programs focused new hires in molecular genetics. Many faculty members with expertise in quantitative genetics are in the later stages of their careers. Thus, at a time when integrating genomic information with quantitative genetics is imperative, our capacity to train professionals with such expertise is at risk. The aim of this project is to redress that shortfall by training graduates with the necessary skills to integrate advances in animal genomics with the agricultural systems emerging from our "New Biology for the 21st Century". The Audience is Master-degree level students in quantitative genetics, with focus on its integration with the genome-enabling technologies. The Products to be developed are seven online, instructional modules and three summer short courses in specialized topics that can be taken for graduate credit by students across the nation. There will be two levels of Outcomes/Impacts: (i) demonstrated student performance in meeting targeted learning objectives, positive student attitudes regarding the distance-delivered coursework, and seamless distance delivery of the newly created programming; and, (ii) the ability for inter-institutional sharing of the resulting distance education programming. These outcomes directly support the goal of increasing the number of graduates with higher-level degrees in food and agricultural sciences, thereby attracting and retaining talented students in agricultural careers, both in industry and academia.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
90360993020100%
Goals / Objectives
The goal of this project is to train graduates with the necessary skills to integrate advances in animal genomics with the agricultural systems emerging from our "New Biology for the 21st Century". Such integration is vital for the competitiveness, and sustainability, of agricultural animal production. The genomic revolution offers tremendous opportunity to address Global Food Security and Health. The increasing availability and use of high density genomic-arrays is generating tremendous amounts of data on individual animals, allowing clearer delineation of heritable differences in production efficiencies and product quality. Yet, such volumes of data pose technical challenges, and only through placing them in a quantitative framework can they usefully and seamlessly be incorporated into farming and food systems. The audience is Masters degree-level students, with the objective to offer a stimulating and relevant curriculum that integrates quantitative and molecular genetics. Seven universities will collaborate to develop and instruct courses, and to establish a sustainable infrastructure for its continuation following USDA-NIFA funding. With shrinking numbers of faculty, sharing resources and capacities is essential. With this partnership, faculty members will provide instruction in their area of expertise to a wider audience. The curriculum will consider five areas: prerequisite knowledge, applications, quantitative genetics, statistical methods, and interface with molecular genetics. Educational backgrounds among the students enrolled will inevitably differ. Thus the curriculum will be comprehensive, offering both breadth and depth of coverage, and combine theory with application to solve real-world problems. This curriculum will be offered using innovative programmatic tools in distance-delivery complemented by on-site summer short courses. This approach fits the needs of increasingly technological sophisticated and non-traditional students, allowing engagement of a broader and more diverse audience. An established instructional design model will be used to define educational needs and set measurable learning objectives for each course. Course development and implementation will be iterative, with student and peer review and feedback instrumental in the course revision process. The Impact will be measurable. First and foremost, the project will increase the number of advanced quantitative and molecular genetics courses available to students at the seven participating institutions. Additionally, because of the planned infrastructure development, the courses will be accessible to students at additional institutions through the AG*IDEA consortium, enhancing the curriculum at those universities and preparing students with advanced skills and knowledge directly applicable to the agricultural workplace.
Project Methods
This project will address two objectives. Objective 1 will embrace using an established instructional design model to further develop and implement a distance-learning curriculum that integrates quantitative genetics and genomics in animal breeding. Seven new asynchronous online modules, and three on-site summer short courses, will be produced, which will add to eight modules already existing. To accomplish this objective the project team will engage in the systematic process of instructional design (ID), utilizing a common model for the ID process to guide each stage of module development. The stages of the ADDIE model include Analyze, Design, Develop, Implement, and Evaluate. In the Analyze stage, a task analysis will be conducted for each module to identify specific knowledge and skills that learners must possess in order to be successful, so that an appropriate beginning point may be determined for each set of instruction. The Design stage will center on the instructional planning aspects of ID, with a focus on identifying specific learning outcomes for each module, and on creating corresponding assessment instruments to explicitly measure those outcomes. In the Development stage, subject matter experts will work with information technologists to create the planned modules using distance-delivery technologies. During the Implementation stage, modules will undergo two rounds of pilot testing with graduate students from various institutions across the nation. Approximately 40-50 students will be recruited. Evaluation will be conducted throughout the earlier stages of the ID process. Formative evaluation will occur during the development and implementation of the modules. Instructional, technological, socio-psychological, and logistical issues will be assessed to determine the most effective design for the final curriculum. Courses will be revised based on the formative feedback from both students and content experts, and then implemented once again for summative evaluation. The aim of Objective 2 is to develop the necessary organizational infrastructure to continue this program when the USDA-NIFA funding ends. This will be addressed through collaboration with AG*IDEA, an affiliate of the Great Plains IDEA. The Great Plains IDEA is a collaborative project supporting internet-based programs. Academic programs are the core of the Alliance. Each member institution awards academic credit and degrees for programs in which they participate. Curricula are developed by inter-institutional faculty teams and institutions choose the programs with which to affiliate. All courses and curricula receive full institutional review prior to implementation and meet institutional academic standards. Students seek admission to the institution of their choice and institutional admissions standards and processes prevail. Assessment of instructional program quality and student learning outcomes are coordinated centrally by the Alliance. Using this structure, the aim is offer a separate program in quantitative genetics, and its integration with animal genomics, within the AG*IDEA portfolio.

Progress 09/01/12 to 08/31/13

Outputs
Target Audience: The primary target audience was MS-level graduate students pursuing advanced training in quantitative genetics and genomics with particular application to agricultural species. However, students pursuing PhD-level degrees, and industry professionals, also participated. The curriculum continued to be offered using innovative programmatic tools in distance-delivery. This approach fitted the needs of increasingly technological sophisticated and non-traditional students, allowing engagement of a broader and more diverse audience. In total 64 individuals from 22 U.S. institutions and 5 foreign countries completed as many as 8 of the courses offered. Three of the students were enrolled in a Historically Black University. Many participants mentioned such coursework would otherwise be unavailable to them without this curriculum. Beyond formal instruction, CyberSheep, a web-based genetic simulation game, was used in 7 undergraduate classes at 6 land-grant universities in animal breeding during the reporting period. It provided an important educational experience to 424 students otherwise not possible within a typical university degree. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The project provided 199 credit hours of instruction to 60 graduate students, and 4 industry and academic professionals, in diverse topics that integrate concepts in quantitative genetics and genomics to address challenges in Global Food Security and Health. Beyond the faculty members instructing the course, 2 research assistants gained valuable instructional and interpersonal skills by assisting with the preparation and delivery of the online materials. Beyond the training opportunities offered through the online curriculum, 424 students in 7 undergraduate courses at 6 Universities (Virginia Tech; North Carolina State, Ohio State and Michigan State Universities; Universities of Kentucky and Wyoming) participated in the launch of a new version of CyberSheep. CyberSheep is a web-based, genetic simulation game designed to allow students experience applying principles in quantitative genetics to a virtual sheep breeding cooperative. The game considers both genetic and economic principles. Students learned to collaborate with team members, and with outside teams, to make mutually beneficial selection and mating decisions within a large-scale collaborative breeding program. They saw the results of their decision-making within short timeframes, and used that information to make better selection and mating choices. Feedback from students and their course instructors indicated that this web-based game provided an important educational experience otherwise not possible within a typical university degree. Among the 150 students who completed an anonymous course evaluation, 93% indicated that their play of CyberSheep enhanced their understanding of concepts in animal breeding and genetics introduced in the classroom. Those experiences with the processes encountered in real-life animal breeding programs not only enhanced these student learning but increased their preparedness for professional positions once completing their degrees. How have the results been disseminated to communities of interest? Project results were disseminated through two theatre presentations at the 59th NACTA conference held in Blacksburg, VA (June, 2013) in a session focused on distance learning. In addition two project members participated as panelist in a session organized by USDA-NIFA entitled “Cutting Edge Instructional Methods” at the start of that conference. The project also was featured in an article on the USDA blog (August 20, 2013; http://blogs.usda.gov/2013/08/20/virginia-tech-animal-breeding-graduate-program-makes-strides-in-online-learning/). In addition to describing the impact of the online curriculum, the article mentioned that the CyberSheep development team had received Virginia Tech’s 2013 XCaliber Award for Excellence for their work in contributing to technology-enriched learning. The web interface (http://enbgeo.iddl.vt.edu/index.php) was updated with information on the new courses and instructors. The website also provided a conduit for student online registration. As part of the fall 2012 and spring 2013 course registration, the curriculum was advertised through a targeted list-serv of approximately 130 animal breeding and genetics faculty member nation-wide. Those vehicles for disseminating information about the project appear to have been effective given the large enrollment in the courses offered. What do you plan to do during the next reporting period to accomplish the goals? As part of objective (i), 3 new online courses will be developed and offered during the next reporting period. These are “Applied Variance Components Estimation in Livestock Genetics”, “From Markers to Gene Function: Functional Change” and “An Introduction to R Programming”. In addition, the existing 12 online courses, and 2 summer short courses, will be taught. Expert peer content and instructional design review will be carried out on several additional courses. In addition, student formative and summative feedback will be collected on the individual courses, and on the entirety of the curriculum. The course “An Introduction to R Programming” was originally scheduled to be offered as a face-to-face short course in summer 2013. However, due to unforeseen conflicts in scheduling, the instructor was unable to offer the course at that time. Based on discussions within the project team, and with the instructor, the course will instead be offered as an online course starting spring term 2014. In many ways that change is a positive development. As an online course integrated into the main curriculum, the materials will become available to a wider audience on a regular basis. A priority for the next reporting period will be taking the initial steps to shift the administration of the curriculum to the AG*IDEA consortium (objective (ii)). This will entail further discussion and endorsement of the project business plan by the AG*IDEA executive board, formalizing an AG*IDEA program assessment plan, initiating governance processes for course reviews at AG*IDEA member institutions, and networking with AG*IDEA campus coordinators to integrate the course offerings into class timetables on their campuses.

Impacts
What was accomplished under these goals? The goal of this project is to train graduates with the necessary skills to integrate advances in animal genomics with the agricultural systems emerging from our "New Biology for the 21st Century". Two main objectives are therefore being addressed: (i) further development and implementation of a distance-learning curriculum that integrates quantitative genetics and genomics in animal breeding; and, (ii) development of the organizational infrastructure to continue this program following the period of USDA-NIFA funding. With regards to objective (i), advanced graduate-level coursework encompassing quantitative and genomic aspects of genetics was made accessible nationally through this collaborative, distance-education curriculum. Beyond preparing and offering 2 new online courses – “MCMC Methods in Animal Breeding: A Primer” and “Introduction to Marker Association Analysis and QTL Detection” - 10 existing online courses were revised and taught between fall 2012 and spring 2013. As part of objective (i) anonymous student evaluations were conducted on each course offering. In addition, expert reviews were completed on 2 of the courses by project faculty, as well as external reviewers with expertise in the course content. An instructional design reviews was conducted on 1 course to gain additional external feedback on its pedagogical effectiveness. Since course development and implementation is intended to be iterative, such student and peer review and feedback is instrumental in the course revision process, and for ensuring the quality of the curriculum. As part of objective (ii), a business plan was prepared to establish the infrastructure and program assessment for integrating the curriculum into AG*IDEA, a national consortium of land grant universities. The plan included a critique of potential program revenues based on enrollment figures. Even based on the enrollments from previous years, which were smaller than those enjoyed currently, the program was deemed financially viable. The business plan was discussed (December, 2012), amended and then approved (August, 2013) by the project team as part of its twice-yearly project meeting (teleconference). As the next step, the finalized business plan will be vetted by the Executive committee of AG*IDEA. A key outcome is that the process for establishing a self-sustaining graduate curriculum in quantitative genetics and genomics is now in place. The project’s impact was confirmed by the growing enrollment in the curriculum nationally, and even internationally. During the year, 64 individuals from 22 U.S. academic institutions and 5 foreign countries completed as many as 8 of the courses offered; 12 of these students completed the entirety of the curriculum. Three of the students were enrolled in a Historically Black University. Four of the participants were in industry or professional positions. In total, 199 credit hours of instruction were completed, which was twice that of the previous year. Between 6 and 24 students completed the individual courses offered. Those counts are between 2- and 6-fold that of graduate student numbers in this discipline at a majority of individual universities. Anonymous student feedback on the content and structure of the courses remained overwhelmingly positive. As a key outcome, this curriculum provided a high quality, customized program to fulfill academic and industry needs for individuals with professional skills in quantitative genetics and genomics.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Lewis, R. M., O. Hestnes, E. Gilmore, J. A. Meese, T. Ogle, and B.B. Lockee. 2013. Experiential Learning in Quantitative Genetics Online: CyberSheep. Proc. North Amer. College Teacher Agric. 57(Suppl. 1):54 (Abstr.).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Lewis, R. M., G. C. M�rquez*, and B. B. Lockee. 2013. Integrating quantitative genetics and genomics in online graduate education. Proc. North Amer. College Teacher Agric. 57(Suppl. 1):92 (Abstr.).


Progress 09/01/11 to 08/31/12

Outputs
OUTPUTS: Three new graduate courses were developed and implemented: "Economic Breeding Programs" (spring 2012), "Programming in Animal Breeding" (summer 2012), and "Genomic Selection in Livestock" (summer 2012). Economic Breeding Programs was taught as a 5-week asynchronous online course. The summer short-courses were taught face-to-face. Programming in Animal Breeding was taught over a 3-week period at the University of Georgia, Athens, while Economic Breeding Programs was taught over a 1-week period prior to the 2012 ADSA-AMPA-ASAS-CSAS-WSASAS Joint Annual Meetings in Phoenix, AZ. A new version of the Cybersheep genetic simulation game was developed and tested. Modifications included a complete redesign of the database, which allows several instances of the game to be played simultaneously. Internet access and security were enhanced to allow individual rather than team-based usernames and passwords to be provided to students. The web interface was completely revised to enhance the experience of the end user. A website devoted to the project - Engaging the New Biology, Graduate Education Online (http://enbgeo.iddl.vt.edu/index.php) - was updated with information on the new courses, instructors and partner institutions. The website also provided a conduit for student online registration. Working with Dr. Dale Van Vleck, a digital version of his renown graduate-level course notes in animal genetics (the Green Book) was prepared and released for download from the website. Project activities were disseminated in two theater presentations in the "Teaching/Undergraduate and Graduate Education Symposium: Online Education for a Hands-On Career" at the 2012 ADSA-AMPA-ASAS-CSAS-WSASAS Joint Annual Meetings. In an invited presentation - "Engaging the new biology: integrating quantitative genetics and genomics in animal breeding graduate learning" - the background, expansion and challenges of establishing a sustainable, multi-institutional and national graduate level distance-delivery program were discussed. In a graduate presentation - "Student learning in undergraduate animal breeding courses is improved through play of an online genetic simulation game" - the utility of CyberSheep as an experiential tool to support undergraduate learning in animal genetics was described. PARTICIPANTS: Over the reporting period, 7 collaborators located at 6 partner institutions (Colorado State, Iowa State, Kansas State and North Carolina State Universities, and Universities of Nebraska-Lincoln and Georgia) worked with the project director at Virginia Tech to implement the curriculum (8 online and 2 summer short-courses). The summer short-courses were offered with organizational assistance of the University of Georgia and the American Society of Animal Science. The construct of a new online course - "Economic Breeding Programs" - engaged input of an instructional design specialist in the School of Education at Virginia Tech. Four staff members in the Systems Development, Integration and Technology group at the Institute for Distance and Distributed Learning at Virginia Tech were involved in revising the project website, including course registration. In addition, they invested tremendous and successful effort in the revision of the CyberSheep game web interface and database. The development of guidelines for integrating the curriculum into AG*IDEA was led by a 6-member team at Kansas State University, including hosting a project meeting in Manhattan. In terms of graduate training, a PhD student at Virginia Tech was intimately involved in the development and delivery of online course materials; she gained skills in preparing audio-presentations and interacting with students in a virtual learning environment. Through a non-formal collaboration with the University of Wyoming, an MS student developed an evaluation form for CyberSheep, which was employed at 2 universities (University of Wyoming and North Carolina State University) to measure undergraduate student learning through use of this experiential tool. She analyzed and presented her results at a national meeting. TARGET AUDIENCES: The primary target audience was MS-level graduate students pursuing advanced training in quantitative genetics and genomics with particular application to animal breeding. The curriculum was offered using innovative programmatic tools in distance-delivery, complemented by on-site summer short courses. This approach fitted the needs of increasingly technological sophisticated and non-traditional students, allowing engagement of a broader and more diverse audience. Nearly 100 individuals from 24 states and 13 countries participated in the series of courses offered. The curriculum was advertised through a targeted list-serv, a project website and presentations at a national meeting. Those vehicles appear effective given the broad audience attracted. Beyond formal instruction, CyberSheep, a web-based game, was used as a virtual lab in 1 graduate (10 students) and in 4 undergraduate (nearly 200 students) classes in animal breeding during the reporting period. It provided an important educational experience to those students otherwise not possible within a typical university degree. They learned to collaborate with team members, and with outside teams, to make mutually beneficial selection and mating decisions within a large-scale collaborative breeding program. They saw the results of their decision-making within short timeframes, and used that information to make better selection and mating choices. Such experience with the processes encountered in "real-life" animal breeding programs not only enhances student learning but increases their preparedness for professional positions once completing their coursework. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project addresses two main objectives: (i) to further develop and implement a distance-learning curriculum that integrates quantitative genetics and genomics in animal breeding; and, (ii) to develop the organizational infrastructure to continue this program following the period of USDA-NIFA funding. With regards to objective (i), advanced graduate-level coursework encompassing quantitative and genomic aspects of genetics was made accessible nationally through this collaborative, distance-education curriculum. Beyond one new online course, 8 existing online courses were revised and taught between fall 2011 and spring 2012. Academic programs at 17 universities, including an 1890 land-grant university, benefitted from their students participation in these courses. Thirty-three graduate students and 3 industry participants successfully completed 93 credit hours of online coursework. Between 6 and 19 students completed the individual courses offered. Those counts are between 2- and 6-fold that of graduate student numbers in this discipline at a majority of individual universities. Anonymous student feedback on the content and structure of the courses was overwhelmingly positive, with useful suggestions for improvements. In addition, 43 graduate students, and 10 industry and 17 academic individuals, participated in two carefully targeted summer short-courses. As a key outcome, this curriculum provided a high quality, customized program to fulfill academic and industry needs for individuals with professional skills in animal breeding. As part of objective (ii), guidelines were established for integrating the curriculum into AG*IDEA, a national consortium of land grant universities. Those discussions began at a project meeting held at Kansas State University (November, 2011), followed-up with a teleconference (March, 2012). The guidelines consider agreements for student admissions standards and processing, institutional review of courses and academic standards, a negotiated common price per credit hour, and the opportunity for awarding a graduate certificate in animal genetics. The mechanics for offering courses, including combining current 1-credit courses into 3-credit bundles, also was considered.

Publications

  • Kessler, K. L., R. M. Lewis, J. P. Cassady, and K. M. Cammack. 2012. Student learning in undergraduate animal breeding courses is improved through play of an online genetic simulation game. Vol. 90 (Suppl. 3):742 (Abstr.).
  • Lewis, R. M., and B. B. Lockee. 2012. Engaging the new biology: Integrating quantitative genetics and genomics in animal breeding graduate learning. J. Anim. Sci. Vol. 90 (Suppl. 3):741 (Abstr.).