Progress 02/15/17 to 02/14/21
Outputs Target Audience:The maize genetics community and breeders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Wang and Hu (with other colleagues) co-organized and presented in two summer workshops on Operations Research in Plant Breeding. The workshop was offered in 2017 at ISU and in 2019 at Cornell University. Wang designed and organized class competitions on genomic selection to engineering students in one undergraduate and two graduate level courses: IE 312 (Optimization) -- 2017 IE 534 (Linear Optimization) -- 2017 IE 634 (Linear Optimization) -- 2017 and 2019 Some of the journal and conference publications resulted from these competitions. How have the results been disseminated to communities of interest?The results were disseminated to the communities via conference presentations and publications, please refer to the product section. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts What was accomplished under these goals?
Overall impact statement: We have designed and developed several improved GS algorithms and proposed an integrated framework. We designed several computer simulation programs to evaluate these GS algorithms. A web-based simulation tool is available for educational purpose. We also developed early flowering populations that can be used for validation experiment in future projects. These tools can facilitate the rapid design, development, evaluation, and modeling of new crop cultivars under genetic and environmental uncertainty. Due to population growth and changing consumer preferences, maintenance of global food security requires more than maintaining current rates of genetic gain, particularly in the context of the diminishing returns of R&D investments in breeding major crops. The data-driven approaches we describe and their integration into decision-support tools have the potential to revolutionize twenty-first century plant breeding by enabling breeders to rapidly and cost-effectively design and develop appropriate cultivars for these future environments. Project Goal 1: Design of Improved Genomic Selection Strategies:We will apply operations research methodology to design and optimize four distinct GS strategies to address various research needs. We have published several new GS algorithms: · The optimal population value (OPV) approach that selects breeding parents with complementary favorable alleles was developed. · Three GS algorithms proposed by engineering students were found to be comparable with state-of-the-art algorithms in the literature. · Look ahead selection (LAS) that selects breeding parents based on the performance of their progeny in a future generation rather than the current generation was developed. · The complementarity-based selection algorithm to identify the most beneficial and complementary breeding parents was developed. · An extension of the look ahead selection algorithm suitable for use with multiple traits was developed. · The look ahead trace back algorithm was proposed to address imperfect prediction of allele effects. · An opaque simulator was developed for GS, which is more realistic than most simulators used in the literature. We also proposed and published a vision for a framework that integrates crop growth models, high-throughput genotyping, high-throughput phenotyping, and environmental sensing and modeling with new advances in statistical modeling, machine learning, and operations research in flexible and efficient decision-support tools. These tools will facilitate the rapid design, development, evaluation, and modeling of new crop cultivars under genetic and environmental uncertainty, such as future climates. Project Goal 2: Develop an Exploratory Simulation Platform to Evaluate Novel GS Strategies:An exploratory simulation platform will be developed in Matlab to evaluate the GS strategies developed in Specific Aim 1. We have designed several computer programs for GS simulation, which were used for the evaluation of GS algorithms. Forexample, one simulation toolcan producea diagram which shows the distributions of genomic estimated breeding values (GEBV) over 10 generations. It will also showthe loss of upper and lower potentials, respectively, of GEBV as a result of selection. Project Goal 3: Evaluate Novel GS Strategies using the Simulation Platform. All new GS algorithms were rigorously evaluated using the simulation programs. Project Goal 4: Create populations that could be used for empirical validation experiments as part of another project sometime in the future. Flowering time is an important agronomic trait for maize, as it allows the plant to adapt to a certain local environment to optimize the growing period. A selection project focusing on flowering time could help us understand not only the genetic architecture but also the causal relationship of flowering time with other traits. We created an early flowering population from 327 maize inbred lines from a diversity panel. In the summer 2020, we planted 1,400 seeds from populations from the initial cycle year and the final cycle year in a single plot and collected trait data. The collected traits included days to anthesis (DTA), days to silking (DTA), leaf appearance rate (LAR), total leaf number (TLN), plant height (PHT), number of tillers, brace root numbers, and number of nodes with brace roots. The secondary trait anthesis silking interval (ASI) was calculated by subtracting DTS from DTA. We collected tissue samples for each individual around stage V3-V4, extracted DNA, and conducted tGBS and SNP calling. We obtained 970,514 SNPs and 743,834 SNPs in the two populations, respectively. The significant response to selection (R) for DTA is -3.2 days. The indirect responses include reduced DTS (-3.6 days), TLN (-1.8 leaves), brace-root number (-2.5 roots), nodes number with brace-root (-0.26 nodes), and increased ASI (0.56 days). We identified 462 candidate genes for which there is evidence of selection, among which are previously identified flowering time and related genes. Within each of the two populations, we conducted GWAS and identified 7 SNPs significantly associated with DTA, 11 SNPs for DTS, 14 SNPs for ASI, 46 SNPs for TLN, 35 SNPs for brace-root number, and 35 SNPs for number of nodes with brace roots. Considering the nearest genes to these candidate SNPs, 138 candidate genes were identified and 4 of these overlapped with the candidate selection response genes. These populations could be used for empirical validation experiments in future research projects. Project Goal 5: Develop a user-friendly interface for our GS simulation platform:A graphical user interface will be designed and implemented to allow breeders to explore alternative GS strategies using the simulation platform developed in Project Goal2. We have designed several computer programs for GS simulation, which were used for evaluate the GS algorithms developed during the project. We also made a web-based tool for illustration and educational purposes, which allows users to select breeding parents and simulate the results. The tool is available at https://lzwang2017.github.io/MATI/.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Amini, F., Franco, F.R., Hu, G., and Wang, L., The look ahead trace back optimizer for genomic selection under transpar-ent and opaque simulators. Sci Rep 11, 4124 (2021). https://doi.org/10.1038/s41598-021-83567-5
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Moeinizade, S., Han, Y., Pham, H., Hu, G., and Wang, L., A look-ahead Monte Carlo simulation method for improving parental selection in trait introgression. Sci Rep 11, 3918 (2021). https://doi.org/10.1038/s41598-021-83634-x
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Moeinizade, S. Kusmec, A., Hu,G., Wang, L., and Schnable, P., Multi-trait Genomic Selection Methods for Crop Improvement. Genetics 215, 931-945 (2020) 10.1534/genetics.120.303305, 2020.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Kusmec, A., Zheng, Z ., Archontoulis, S.V., Ganapathysubramanian, B., Hu, G., Wang, L., Yu, J., Schnable, P.S., Interdisciplinary strategies to enable data-driven plant breeding in a changing climate. One Earth, 4, 372-383 (2021). doi:10.1016/j.oneear.2021.02.005
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Fatemeh Amini, Felipe Restrepo Franco, Guiping Hu, and Lizhi Wang, Trace-back Approach In Genomic Selection, INFORMS Annual Meeting, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Saba Moeinizade, Aaron Kusmec, Guiping Hu, Lizhi Wang, and Patrick Schnable, "A Simulation-based Optimization Approach For Improving Response In Multi-trait Genomic Selection", INFORMS Annual Meeting, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Guiping Hu, Saba Moeinizade, and Lizhi Wang,"Reinforcement Learning Based Resource Allocation for Genomic Selection", INFORMS Annual Meeting, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Saba Moeinizade, Han Ye, Hieu Trung Pham, Guiping Hu, and Lizhi Wang, "Optimizing Parental Selection In Trait Introgression Process'', INFORMS Annual Meeting, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Lizhi Wang, Descriptive, predictive, and prescriptive models for plant genomics, Invited Symposium, ASA-CSSA-
SSSA Annual Meeting, 2020.
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Progress 02/15/19 to 02/14/20
Outputs Target Audience:The plant genetics community and breeders. 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?The results were disseminatedto the communities via conference presentations and publications, please refer to the product section. What do you plan to do during the next reporting period to accomplish the goals?• Attend and present our work at INFORMS 2020 • We are working on another GS strategy based on active learning, which we plan to submit for journal publication during the next reporting period. • We are working on a genomic selection simulation program for educational purposes. We will compare different options, including online version (using Java Script) or off line version (using Matlab or R), and choose the most appropriate format.
Impacts What was accomplished under these goals?
Overall impact statement: We made improvement to our Matlab-based GS simulation platform and now users can evaluate different GS strategies on the platform. We shared this result with the community through our publications and presentations at major conferences. Project Goal 1: Design of Improved Genomic Selection Strategies:We will apply operations research methodology to design and optimize four distinct GS strategies to address various research needs. Nothing to report. Project Goal 2: Develop an Exploratory Simulation Platform to Evaluate Novel GS Strategies:An exploratory simulation platform will be developed in Matlab to evaluate the GS strategies developed in Specific Aim 1. Nothing to report. Project Goal 3: Evaluate Novel GS Strategies using the Simulation Platform. Nothing to report. Project Goal 4: We will create populations that could be used for empirical validation experiments as part of another project sometime in the future. Nothing to report. Project Goal 5: Develop a user-friendly interface for our GS simulation platform:A graphical user interface will be designed and implemented to allow breeders to explore alternative GS strategies using the simulation platform developed in Project Goal2. • The Look-ahead selection method has been published in G3: Genes Genomes Genetics. • A manuscript on Multi-trait genomic selection has been submitted to Genetics. This study is an extension from the Look-ahead selection to multi-trait scenarios. • A paper on Complementarity-Based Selection Strategy for Genomic Selection has been published in Crop Science. • Five conference presentations have been made in 2019 at INFORMS annual meeting, PAG Asia meeting. • We continue to improve a Matlab-based GS simulation platform, which allows users to test and evaluate different GS strategies. This platform was used in the above mentioned journal and conference publications to compare the new GS strategies with previous ones.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Saba Moeinizade, Guiping Hu, Lizhi Wang, and Patrick Schnable, Optimizing Selection and Mating in Genomic Selection with a Look-ahead Approach: An Operations Research Framework, G3: Genes|Genomes|Genetics
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Moeinizade, Saba, Megan Wellner, Guiping Hu,
and Lizhi Wang. "Complementarity?based selection strategy for genomic selection." Crop Science 60, no.
1 (2020): 149-156
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Saba Moeinizade, Lizhi Wang, Guiping Hu, and Patrick Schnable, Multi-trait Selection Strategy for Genomic Selection, PAG Aisa, 2019
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Saba Moeinizade, Megan Wellner, Guiping Hu, and Lizhi Wang, Complementarity-Based Selection Strategy for Genomic Selection, PAG Aisa, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Saba Moeinizade, Aaron Kusmec, Guiping Hu, Lizhi Wang, and Patrick Schnable Multi-trait Genomic Selection Methods For Crop Improvement, INFORMS Annual Meeting, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Fatemeh Amini and Guiping Hu, Prediction of the Performance of Maize Hybrids Via Machine Learning Methods Using DNA Markers and Seedling Transcriptome Profiles of Parents and Offspring, INFORMS Annual Meeting, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Saba Moeinizade, Guiping Hu, and Lizhi Wang Operations Research Methods For Enhancing Efficiency In Plant Breeding, INFORMS Annual Meeting, 2019.
|
Progress 02/15/18 to 02/14/19
Outputs Target Audience:The maize genetics community and breeders. 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?Wang and Hu attended and presented GS related research in the Institute for Operations Research and the Management Sciences (INFORMS) 2018 annual meeting. Luning Bi and Guiping Hu, "A Genetic Algorithm Based Deep Learning Approach to Understand Genotype-Environment Interaction (G x E)," INFORMS Data Mining workshop, 2018. Saba Moeinizade, Guiping Hu, Lizhi Wang, and Patrick Schnable, "Look-ahead Selection Strategy for Genomic Selection: Optimizing selection and Pairing Strategies with a Time-dependent Approach," INFORMS Annual Meeting, 2018. Megan Wellner, Saba Moeinizade, Guiping Hu, and Lizhi Wang, "Gender-based Selection Strategy for Genomic Selection," INFORMS Annual Meeting, 2018. What do you plan to do during the next reporting period to accomplish the goals? Attend and present our work at PAG Asia 2019 Attend and present our work at INFORMS 2019 We are working on another GS strategy, which we plan to submit for journal publication during the next reporting period.
Impacts What was accomplished under these goals?
Project Goal 1: Design of Improved Genomic Selection Strategies:We will apply operations research methodology to design and optimize four distinct GS strategies to address various research needs. Nothing to report. Project Goal 2: Develop an Exploratory Simulation Platform to Evaluate Novel GS Strategies:An exploratory simulation platform will be developed in Matlab to evaluate the GS strategies developed in Specific Aim 1. Nothing to report. Project Goal 3: Evaluate Novel GS Strategies using the Simulation Platform. Nothing to report. Project Goal 4: We will create populations that could be used for empirical validation experiments as part of another project sometime in the future. Nothing to report. Project Goal 5: Develop a user-friendly interface for our GS simulation platform:A graphical user interface will be designed and implemented to allow breeders to explore alternative GS strategies using the simulation platform developed in Project Goal2. We designed a new GS strategy, called Look-ahead selection. We presented this GS strategy in a journal paper, which has been accepted for publication in G3 subject to minor revisions. We have developed a Matlab-based GS simulation platform, which allows users to test and evaluate different GS strategies. This platform was used in the above mentioned journal and conference publications to compare the new GS strategies with previous ones.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Lizhi Wang, Guodong Zhu, Will Johnson, and Mriga Kher, "Three new approaches to genomic selection", Plant Breeding, vol. 137(5), p. 673-681, 2018.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2019
Citation:
Saba Moeinizade, Guiping Hu, Lizhi Wang, and Patrick Schnable, Optimizing Selection and Mating in Genomic Selection with a Look-ahead Approach: An Operations Research Framework, under review, G3
|
Progress 02/15/17 to 02/14/18
Outputs Target Audience:The maize genetics community and breeders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The graduate student working on this project is receving training in conducting research and collaborating with colleagues in a different research area. How have the results been disseminated to communities of interest?Journal publications and conference proceedings (see Products) Conference presentations The Institute for Operations Research and the Management Sciences meeting, 2017 Institute of Industrial and Systems Engineers annual meeting, 2017 Plant and Animal Genome, 2017 What do you plan to do during the next reporting period to accomplish the goals? Design new and more efficient algorithms. Develop more comprehensive simulation experiments to test algorithms. Disseminate results with more journal and conference publications and conference presentations.
Impacts What was accomplished under these goals?
IMPACT STATEMENT: As a consequence of growing populations, changing diets, and the challenges of climate change agricultural systems must produce more with less.Breeding is a key tool for making agriculture systems more productive, sustainable and resilient.Genomic selection (GS) has the potential to increase the rate of genetic gain in breeding programs and is therefore transforming breeding programs.GS includes three steps: genomic prediction, selection and mating. Most research on GS has focused on improving the first step, genomic prediction. Our preliminary simulation studies have, however, shown that the success of GS is sensitive to both the selection and mating steps. Hence, this project uses the framework of operations research to optimize selection and mating parameters for specific types of breeding programs. Our research is increasing knowledge of how to enhance the efficiency of breeding programs by introducing engineering processes.In addition, this project is training graduate students at the intersection of operations research and plant breeding, helping to develop "next generation plant breeders." Goal1: Design of Improved Genomic Selection Strategies. We designed three versions of genomic selection algorithms. The first one is the OPV (optimal population value) approach, which was published in Genetics in 2017. The second one is the gender-based algorithm, which was published in a conference proceeding. The first author of this conference paper is an undergraduate student, and she has been invited to present in the Institute of Industrial and Systems Engineers annual meeting as one of three finalists of an undergraduate research competition, which will take place in May 2018. The third algorithm is the look-ahead selection, which was published in a conference proceeding and will be extended as a journal paper. Goal 2: Develop an Exploratory Simulation Platform to Evaluate Novel GS Strategies. The look-ahead selection algorithm mentioned above also applies to this specific goal. Goal 3: Evaluate Novel GS Strategies using the Simulation Platform. Nothing to report this period. Goal 4: Create populations that could be used for empirical validation experiments. Nothing to report this period. Goal 5: Develop a user-friendly interface for our GS simulation platform. Nothing to report this period.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Matt Goiffon, Aaron Kusmec, Lizhi Wang, Guiping Hu, and Patrick Schnable, "Improving Response in Genomic Selection with Optimal Population Value Selection: a Population-Based Selection Strategy," vol. 206 no. 3, 1675-1682, Genetics, 2017.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2018
Citation:
Megan Wellner, Saba Moeinizade, Yulu Chen, Guiping Hu, and Lizhi Wang, Gender-based Selection Strategy for Genomic Selection, Proceedings of IISE 2018.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2018
Citation:
Saba Moeinizade, Lizhi Wang, and Guiping Hu, Improving Response in Genomic Selection with a look-ahead approach, Proceedings of IISE 2018.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2018
Citation:
Lizhi Wang, Guodong Zhu, Will Jonson, Mriga Kher, Three new algorithms for genomic selection,
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