Source: TEXAS A&M UNIVERSITY submitted to
QUANTITATIVE GENETICS AND MAIZE BREEDING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
1005472
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Dec 8, 2014
Project End Date
Nov 13, 2019
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
Soil & Crop Sciences
Non Technical Summary
Safe, secure, healthy, inexpensive and increasingly productive agricultural commodities are a cornerstone of increasing American prosperity. Maize (corn) is the most productive crop and farmers plant it because there is high end-user demand, it is easy to grow and often profitable. Plant breeding and agronomy have increased corn yields eight-fold over the last 100 years, a trend that began through research and development in the public sector. While the private sector now excels in corn improvement in the Midwest, the Southern US receives little investment and productivity is lagging. Major problems facing Southern US corn farmers include losses due to drought and aflatoxin (a carcinogen produced in the grain by a fungus); these problems are expected to increase in the Midwest under a changing climate. Corn losses can be most efficiently reduced through scientific plant breeding and genetic improvement. New and improved plant breeding techniques leveraging the latest in scientific technologies need to be developed to meet current and future crop production challenges. Additionally, highly trained students are needed who understand problems in agriculture and can respond with appropriate solutions. In this project we will improve the yield, adaptation, healthfulness and sustainability of corn production through plant breeding; assisted by genomics and computer modeling. We will increase the genetic diversity of corn and incorporate drought tolerance, aflatoxin resistance, higher yield, blue grain and improved antioxidants, reduced fertilizer requirements, and increased ecosystem services (such as provided by perennial corn). We will develop new knowledge and techniques that will help all crops be able to be improved to meet societal needs faster (such as increasing genetic recombination). We will also train the graduate students and undergraduate students to use modern science to meet farmers and society's needs in the future.
Animal Health Component
40%
Research Effort Categories
Basic
35%
Applied
40%
Developmental
25%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011510108020%
2011510209010%
2021510108110%
2021510209010%
2031510108110%
2041510108110%
2061510108110%
2121510108110%
7121510108110%
Goals / Objectives
The three major goals of this project are to 1) develop and apply methodologies to improve plant improvement; 2) improve maize through breeding for South Central states, and 3) to educate and train future generations of plant breeders and quantitative geneticists.Objectives Molecular Quantitative Genetics G1: Identify genetic relationships among grain maize lines and use various genetic mapping techniques to identify loci of importance for relevant phenotypic traits. G2: Develop and investigate populations to understand the genetic basis of yield, agronomic and specialty traits in maize. G3: Develop and investigate populations to understand the genetic basis of tillering ability, perennial growth habit and photoperiod sensitivity in the C4 grasses: maize, sorghum and sugarcane. G4: Use computer simulations to increase knowledge for protocols of genetic investigation and plant breeding methodology.Maize Breeding for South Central States B1: Introgress exotic maize alleles to increase the genetic diversity of US maize germplasm. B2: Improve yield, resistance to biotic (mycotoxins- especially aflatoxin) stress and tolerance to abiotic stresses (salinity, drought and heat) through breeding in addition to genetics. B3: Develop maize inbred lines and populations processing improved quality attributes and properties for foods, feeds, and industrial products while enhancing agronomic characteristics for Texas growing regions. B4: Use molecular techniques such as marker-assisted selection (MAS) and genomic-assisted selection, where feasible, to facilitate the selection of economically and agronomically important traits.Education E1: Involve graduate students on various projects for training and experience. E2: Jointly develop projects initiated by graduate students to deliver scientifically well-rounded, self-motivated and confident leaders of breeding and genetics for the future.Techniques: To accomplish these objectives in an effective manner, techniques must first be developed for the program that will reduce burdens in cost, labor and time. T1: Develop/select appropriate genetic marker screening platform. T2: Develop data handling pipelines to track and link germplasm with phenotypic and genotypic information. T3: Develop methods of rapid phenotypic analysis, such as near infrared spectroscopy (NIRS) and automated field and laboratory based machines. T4: Develop technologies that increase the speed of a reproductive and breeding cycle (CoGiV). T5: Develop methods to evaluate and increase safety in the handling of aflatoxin contaminated material.
Project Methods
Exotic (tropical, subtropical, and wild perennial - e.g. Zea diploperennis, Sorghum propinquum) germplasm and some temperate germplasm will be used to generate segregating populations with adapted material. Molecular markers, mostly single nucleotide polymorphic (SNPs) will be employed on these populations for various types of QTL mapping (linkage mapping, association mapping, and selection mapping) and genomic selection where appropriate (Poland and Rife 2012). Inbred lines will also be developed from these populations through pedigree breeding and MAS. Selected inbred lines will be crossed to appropriate testers, including commercial transgenic testers in cooperation with industry breeding programs as specific opportunities are developed. A Fall/Winter nursery in Weslaco, TX will be used to rapidly advance material while development of CoGiV technology (Murray et al. 2013) will also be pursued. Test hybrid evaluations will be conducted in 2 to 20 diverse Texas environments for adaptation, maturity, grain yield, tolerance to drought and heat stress, resistance to mycotoxins, composition, and kernel quality for determining inbred superiority. In addition, inbred lines and hybrids will be evaluated under stressed conditions including limiting irrigation, limiting fertilization, late planting, increased salinity and inoculation with A. flavus. Near infrared spectroscopy (NIRS) calibrations will be developed and used to more rapidly phenotype material including that resistant to A. flavus colonization and those with improved kernel quality (Fernández-Ibañeza et al. 2008). Specific kernel quality traits of interest will include improved QPM, red and blue colors, increased endosperm hardness, and superior micronutrient profiles. Molecular fingerprinting data will be used to classify inbred lines and to choose parental lines for breeding populations. Computer simulations of population development and selection will be performed to refine genetics and breeding methodology. High-throughput, automated field phenotyping technologies will also be developed in cooperation with agricultural engineers and physicists. Graduate students will be involved in all of these processes. Major outputs will include improved germplasm for Texas, well-trained graduate students, professional presentations, and journal publications.

Progress 12/08/14 to 11/13/19

Outputs
Target Audience:Scientists and colleagues, graduate and undergraduate students, farmers/ producers, industry (seed companies primarily) and the public. Changes/Problems:The approved replacement project: TEX0-2-9348 "Field Phenomicsand Quantitative Genetics in Applied Maize Breeding" will replace this one. Additional progress of work begun here will be reported under TEX0-2-9348. What opportunities for training and professional development has the project provided?Nearly all employed personnel were pursuing a degree (graduate students and technical support were pursuing MS or PhD, undergraduates were pursuing BS) and took classes; on PhD level technical support staff excepted. Personnel were given an opportunity to lead one or more research projects. Personnel were introduced to outside visitors and encouraged to meet one on one. All personnel attended multiple professional and research seminarsthroughout the year and some presented their work at regional or national conferences including the ASA/CSSA/SSA meeting, National Association of Plant Breeders, Phenome and other regional or localmeetings. Multiple students won awards and graduated over the five years of this project. How have the results been disseminated to communities of interest?Scientists and colleagues were reached through presentations, publications, and collaborative research activities. Graduate and undergraduate students were reached through formal classroom instructions and in assisting and leading independent research projects. Farmers/ producers were reached through presentations, publications, field days and on-farm research. Industry was reached through personal communication (in person, phone, email) and evaluated our inbred lines and hybrids. The public was reached through popular press presentations, publications and social media. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Over the last five years, significant and substantial accomplishments were made towards thethree major goals of the project: 1) Newmethodologies to improve plant improvement were developed and applied; 2) Maize was improvedthrough breeding for South Central states, and 3) future generations of plant breeders and quantitative geneticists were educated and trained. However, within a five year project, these remain far from solved problems and substantial work, including new tools and technologies are needed to makeprogress overfuture years. Objectives Molecular Quantitative Genetics G1: Genetic relationships among grain maize lines were identified as were loci from using arious genetic mapping techniques for relevant phenotypic traits.G2: The genetic basis of yield, agronomic and specialty traits in maize wasinvestigated in newly developed populations. G3: The genetic basis of tillering ability, perennial growth habit and photoperiod sensitivity in the C4 grasses: maize, sorghum were better understood through newly developed populations ( given the timeline, these publications will be reported in future projects).G4:Computer simulations to increase knowledge for protocols of genetic investigation and plant breeding methodology (to be published next year) Maize Breeding for South Central States B1:Exotic maize alleles were introgressed into elite germplasm to increase the genetic diversity of US maize germplasm.B2:Yield, resistance to biotic (mycotoxins- especially aflatoxin) stress and tolerance to abiotic stresses (salinity, drought and heat) were improved through breeding in addition to charecterizations using genetics.B3:Maize inbred lines and populations processing improved quality attributes and properties for foods, feeds, and industrial products were produced, while enhancing agronomic characteristics for Texas growing regions.B4:Molecular techniques such as marker-assisted selection (MAS) were used to facilitate the selection of photoperiodism, an economically and agronomically important trait. Education E1:Fraduate students were involved on various projects for training and experience.E2:Projects were jointly developed and initiated by graduate students to deliver scientifically well-rounded, self-motivated and confident leaders of breeding and genetics for the future. Techniques:To accomplish these objectives in an effective manner, techniques were first developed for the program that reduced burdens in cost, labor and time.T1: Appropriate genetic marker screening platforms were selected.T2: Data handling pipelines to track and link germplasm with phenotypic and genotypic information were developed and used.T3: Methods of rapid phenotypic analysis, such as near infrared spectroscopy (NIRS) and automated field and laboratory based machines were developed.T4:Technologies that increasedthe speed of a reproductive and breeding cycle (CoGiV) were attempted, but deemed to be too difficult given program resources. T5:Improved methods to evaluate and increase safety in the handling of aflatoxin contaminated material were developed and evaluated.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: de Oliveira, G.H.F., S. C. Murray, L.C.C. J�nior, K.M.G. de Lima, C.D.L.M. de Morais, G.H. de Almeida Teixeira, and G.V. M�ro. 2020. Estimation and classification of popping expansion capacity in popcorn breeding programs using NIR spectroscopy. Journal of Cereal Science, 91, 102861.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: Foster, Tyler L., Heather D. Baldi, Xiaoqing Shen, Byron L. Burson, Robert R. Klein, Seth C. Murray, Russell Jessup (In Press). Development of novel perennial Sorghum bicolor x S. propinquum Hybrids. Crop Science. doi: 10.2135/cropsci2019.08.0546


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Scientists and colleagues, graduate and undergraduate students, farmers/ producers, industry (seed companies primarily) and the public. Changes/Problems:There are only a few more months on this project before the approved replacement project:TEX0-2-9348 "Field Phenomics and Quantitative Genetics in Applied Maize Breeding" will replacethis one. Additional progress will be reported under TEX0-2-9348. What opportunities for training and professional development has the project provided?Nearly all employed personnel were pursuing a degree (graduate students and technical support were pursuing MS or PhD, undergraduates were pursuing BS) and took classes; on PhD level technical support staff excepted. Personnel were given an opportunity to lead one or more research projects. Personnelwere introduced to outside visitors and encouraged to meet one on one.All personnel attended multiple professional and research seminarsthroughout the year and some presented their work at regional or national conferences including the ASA/CSSA/SSAmeeting, Phenomeand other regional or local meetings.PhD student Mr. Alper Adak won first place for his poster on "Identifying Loci for Photoperiod Associated Flowering: A Critical Need for Improving Maize (Zea mays L.). The program hosted Dr. Sofija Bo~inovi?, Maize Breeders and Research Associate from theMaize Research Institute Zemun Polje (Serbia) for 6 months; she greatly contributed to the program. How have the results been disseminated to communities of interest?Scientists and colleagues were reached through presentations, publications, and collaborative research activities. Graduate and undergraduate students were reached through formal classroom instructions and in assisting and leading independent research projects. Farmers/ producers were reached through presentations, publications, field days and on-farm research. Industry was reached through personal communication (in person, phone, email) and evaluated our inbred lines and hybrids. The public was reached through popular press presentations, publications and social media. What do you plan to do during the next reporting period to accomplish the goals?There are only a few more months on this project before the approved replacement project:TEX0-2-9348 "Field Phenomics and Quantitative Genetics in Applied Maize Breeding" will replacethis one. Additional progress will be reported under TEX0-2-9348.

Impacts
What was accomplished under these goals? Activities in all proposed objectives were accomplished as evidenced by publications as well as presentations and students trained. Multi-disciplinary approaches in high throughput field-based phenotyping (HTFP) for maize breeding using unoccupied aerial vehicles / systems (UAV / UAS / i.e. drones) remained a major research focus. Students and colleagues worked on improving UAS measures as well as to conduct new measurements with this data. New approaches to data analysis and reanalysis were attempted to make better decisions in the program. Maize populations, inbred lines and hybrids were advanced for improving aflatoxin, yield, and/or other traits for Texas and southern US farmers. Elitelines were increased and both crossing blocks and isolation blocks were employed to create hybrids for future testing. Experimental hybrids were tested in replicated multi-location trials. The three SNP markers validated previously to increase yield in testcrosses were tested as heterogeneous inbred families (HIFs) and found to work in multiple biparental population backgrounds.NIRS calibrations were used, improved and applied to other genetic mapping and breeding germplasm. Additional progress was made on understanding GxE through the southeast regional aflatoxin trials (SERAT), genomes to fields projects, and a photoperiod sensitivity project supported by the Texas Corn Producers Board. A paper on the collaborativemaize ATLAS project was published. Perennial sorghum, perennial maize and colored (red, blue, purple) maize populations and germplasm were all advanced.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Steven L. Anderson II, Seth C. Murray*, Lonesome Malambo, Colby Ratcliff, Sorin Popescu, Dale Cope, Anjin Chang, Jinha Jung, and Alex Thomasson. 2019. Prediction of maize grain yield before maturity using improved temporal height estimates of unmanned aerial systems. The Plant Phenome Journal. 2:1 doi: 10.2135/tppj2019.02.0004
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Pekar, Jacob J., Seth C. Murray*, Thomas S. Isakeit, Brian T. Scully, Baozhu Guo, Joseph E. Knoll, Xinzhi Ni, Hamed K. Abbas, Paul Williams, Wenwei Xu. (In Press). Evaluation of Elite Maize Inbred Lines for Reduced Aspergillus flavus Infection, Aflatoxin Accumulation, and Agronomic Traits. Crop Science 59:2562-2571.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Arnold, Robert J., Alejandra Ochoa, Chris R. Kerth, Rhonda K. Miller, Seth C. Murray. (2019) Assessing the impact of corn variety and Texas terroir on flavor and alcohol yield in new-make bourbon whiskey. PLoS ONE 14: e0220787
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Zhang, M, Y. Cui, Y.-H. Liu, W. Xu, S.-H. Sze, S.C Murray, S. Xu, H.B. Zhang (2019) Accurate prediction of maize grain yield using its contributing genes for gene-based breeding. Genomics (in press) https://doi.org/10.1016/j.ygeno.2019.02.001
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Pruter, Luke, Michael Brewer, Mark Weaver, Seth C. Murray, Thomas Isakeit, Julio Bernal (accepted with revisions) Association of Insect-Derived Ear Injury with Yield and Aflatoxin of Maize Hybrids Varying in Bt Transgenes. Journal of Environmental Entomology. 48: 1401-1411. pii: nvz112. doi: 10.1093/ee/nvz112
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Falcon, Celeste M., Shawn M. Kaeppler, Edgar P. Spalding, Nathan D. Miller, Naser AlKhalifah, Martin Bohn, Edward S. Buckler, Ignacio Ciampitti, Jode Edwards, David Ertl, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice N. Hirsch, James B. Holland, Diego Jarqu�n, Joseph Knoll, Nick Lauter, Elizabeth C. Lee, Carolyn J. Lawrence-Dill, Aaron Lorenz, Jonathan P. Lynch, Seth C. Murray, Rebecca Nelson, Torbert Rocheford, Patrick S. Schnable, Margaret Smith, Nathan Springer, Mitch Tuinstra, Renee Walton, Randall J. Wisser, Wenwei Xu and Natalia de Leon* (In Press) Relative Utility of Agronomic, Phenological, and Morphological Traits to Assess Genotype by Environment Interaction in Maize Inbreds. Crop Science doi: 10.2135/cropsci2019.05.0294
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Wisser, Randall J., Zhou Fang, James Holland, Juliana Teixeira, John Dougherty, Teclemariam Weldekidan, Natalia de Leon, Sherry Flint-Garcia, Nick Lauter, Seth C. Murray, Wenwei Xu, and Arnel Hallauer. 2019. The genetic basis for rapid evolution of environmental adaptation in maize. Genetics 213:1479-1494.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Shakoor, N., D. Northrup, S.C. Murray, T.C. Mockler. 2019. Big Data Driven Agriculture: Big Data Analytics in Plant Breeding, Genomics, and the Use of Remote Sensing Technologies to Advance Crop Productivity. The Plant Phenome Journal 2:180009
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Chu, T., M.J. Starek, M.J. Brewer, S.C. Murray, L.S. Pruter. 2018. Characterizing canopy height with UAS structure-from-motion photogrammetryresults analysis of a maize field trial with respect to multiple factors. Remote sensing letters 9:753-762


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Scientists and colleagues, graduate and undergraduate students, farmers/ producers, industry (seed companies primarily) and the public. Changes/Problems:Accomplished technicians are transitioning,Jacob Pekar is leaving to start his own company and David Rooney is going to reduced time. This will leave a substantial hole in field and seed handling capacity in the short term. What opportunities for training and professional development has the project provided?Nearly all employed personnel were pursuing a degree (graduate students and technical support were pursuing MS or PhD, undergraduates were pursuing BS) and took classes; on PhD level technical support staff excepted. Personnel were given an opportunity to lead one or more research projects. All personnel attended multiple professional and research seminars throughout the year and some presented their work at regional or national conferences includingthe ASA/CSSA/SSA meeting, the National Association of Plant Breeders meeting, two NIFA FACT meetings, and other local meetings. Personnel were introduced to outside visitors and encouraged to meet one on one. David Rooney, program staff, was awarded the Department of Soil and Crop Sciences Laboratory Support Staff award for his excellent work for the Department and in the seed lab. How have the results been disseminated to communities of interest?Scientists and colleagues were reached through presentations, publications, and collaborative research activities. Graduate and undergraduate students were reached through formal classroom instructions and in assisting and leading independent research projects. Farmers/ producers were reached through presentations, publications, field days and on-farm research. Industry was reached through personal communication (in person, phone, email) and evaluated our inbred lines and hybrids. The public was reached through popular press presentations, publications and social media. What do you plan to do during the next reporting period to accomplish the goals?Many of the same projects will continue in the next reporting period so that additional data can be collected and breeding material advanced. Emphasis in developing and usinghigh-throughput field phenotyping (HTFP) will focus increasingly on unmanned aerial vehicles and systems (i.e. UAVs, UASs, drones) and the analysis and use of the large datasets that result. Not much emphasis onnovel ground vehicles will be undertaken.Breeding program and genetic mapping activities will continue as proposed. Emphasis on graduate student training and undergraduate experiances will continue. Emphasis will continue to be placed on data management, data analys and data analytics of existing data (primarily phenotypic) as well as improving data science abilities and automation in both research and teaching.

Impacts
What was accomplished under these goals? Multi-disciplinary approaches in high throughput field-based phenotyping (HTFP) for maize breeding using unmanned aerial vehicles / systems (UAV / UAS / i.e. drones) remained a major research focus. Aninbred genetic mapping population wasevaluated with standard agronomic measurements but also subjected to weekly UAS flights by both fixed wing and rotary wing aircraft. Data are still being analyzed but we found and published some relatedwork on UAS.The ground vehicle was operated very infrequently due to mud and lack of an operator with availible time. Students and colleagues worked on improving these measures as well as to conduct new measurements with this data. New approaches to data analysis and reanalysis were attempted to make better decisions in the program. The UAS approach was furthered by USDA NIFA-AFRI project funding to expand these HTFP approaches to three different management plantings of the genomes to fields (G2F) project. HTFP technologies remain verypromising but will require a large investment and multi-disciplinary collaborations to make the data collected useful to plant breeders. Different populations were advanced for improving aflatoxin, yield, and/or other traits for Texas and southern US farmers. Elite lines were increased and both crossing blocks and isolation blocks were employed to create hybrids for future testing. Experimental hybrids were tested in replicated multi-location trials. The threeSNP markers validated previously to increase yield in testcrosses, continued to be backcrossed by an undergraduateinto different backgrounds to create near isogenic lines as a research project. NIRS calibrations were used, improved and applied to other genetic mapping and breeding germplasm. Additional progress was made on understanding GxE through the southeast regional aflatoxin trials (SERAT), G2F, and the maize ATLAS project. Perennial sorghum, perennial maize and colored (red, blue, purple) maize populations and germplasm were all advanced.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gage, J., D. Jarquin, C. Romay, A. Lorenz, E. Buckler, S. Kaeppler, N. Alkhalifah, M. Bohn, D. Campbell, J. Edwards, D. Ertl, S. Flint-Garcia, J. Gardiner, B. Good, M. Gore, C. Hirsch, J. Holland, D. Hooker, J. Knoll, J. Kolkman, G. Kruger, N. Lauter, C. Lawrence-Dill, E. Lee, J. Lynch, S.C. Murray, R. Nelson, J. Petzoldt, T. Rocheford, J. Schnable, P. Schnable, B. Scully, M. Smith, N. Springer, S. Srinivasan, R. Walton, T. Weldekidan, R. Wisser, W. Xu, J. Yu, and N. deLeon*. 2018. The effect of artificial selection on phenotypic plasticity in maize. Nature Communications, 8:1348 ; doi:10.1038/s41467-017-01450-2
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Warburton, M.L.*, E.D. Womack, J.D. Tang, A. Thrash, J.S. Smith, W. Xu, S.C. Murray, and W.P. Williams. 2017. Genome-Wide Association and Metabolic Pathway Analysis of Corn Earworm Resistance in Maize. The Plant Genome 11:170069. doi:10.3835/plantgenome2017.08.0069
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mahan, A.L., S.C. Murray*, and P.E. Klein. 2018. Four parent maize population (FPM): development and phenotypic characterization. Crop Science. doi: 10.2135/cropsci2017.07.0450
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Murray, S.C.*, K. Mayfield, J. Pekar, P. Brown, A. Lorenz, T. Isakeit, G. Odvody, W. Xu, and J. Betran. (2019). Tx741, Tx775, Tx777, Tx779, Tx780 and Tx782 inbred maize lines for yield and southern US stress adaptation. Journal of Plant Registrations. 13:258-269. doi:10.3198/jpr2017.07.0044crp
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Anderson, S.L., A.L. Mahan, S.C. Murray*, and P.E. Klein. (2018) Quantification of agronomic traits characterized in the four-parent maize magic population. The Plant Genome. doi: 10.3835/plantgenome2017.11.0102
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Al Khalifah, N., D.A. Campbell, C.M. Falcon, J.M. Gardiner, N.D. Miller, M.C. Romay, R. Walls, R. Walton, C.-T. Yeh, M. Bohn, J. Bubert, E.S. Buckler, I. Ciampitti, S. Flint-Garcia, M.A. Gore, C. Graham, C. Hirsch, J.B. Holland, D. Hooker, S. Kaeppler, J. Knoll, Nick Lauter, E.C. Lee, A. Lorenz, J.P. Lynch, S.P. Moose, S.C. Murray, R. Nelson, T. Rocheford, O. Rodriguez, J.C. Schnable, B. Scully, M. Smith, N. Springer, P. Thomison, M. Tuinstra, R.J. Wisser, W. Xu, D. Ertl, P.S. Schnable, N. De Leon, E.P. Spalding, J. Edwards, C.J. Lawrence-Dill. 2018. Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. BMC Research Notes 11: 452.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Scientists and colleagues,graduate and undergraduate students, farmers/ producers, industry (seed companies primarily) and the public. Changes/Problems:No major changes are needed but will remphasize a shift in focus from data collection to data analysis and from genetics and genomics to field phenotyping. What opportunities for training and professional development has the project provided?All employed personnel were pursuing a degree (graduate students and technical support were pursuing MS or PhD, undergraduates were pursuing BS) and took classes. All personnel were given an opportunity to lead one or more research projects. All personnel attended multiple professional and research seminars throughout the year and some presented their work at regional or national conferences includingthe National Association of Plant Breeders annual meeting, the ASA/CSSA/SSA meeting, among others. Personnel were introduced to outside visitors and encouraged to meet one on one. How have the results been disseminated to communities of interest?Scientists and colleagues were reached through presentations, publications, and collaborative research activities. Graduate and undergraduate students were reached through formal classroom instructions and in assisting and leading independent research projects. Farmers/ producers were reached through presentations, publications, field days and on-farm research. Industry was reached through personal communication (in person, phone, email) and evaluated our inbred lines and hybrids. The public was reached through popular press presentations, publications and social media. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period many of the same projects will be continued so that additional data can be collectedand breeding material advanced. There will continue to be an increasing emphasis in developing and usinghigh-throughput field phenotyping (HTFP), including novel ground vehicles and unmanned aerial vehicles and systems (i.e. UAVs, UASs, drones), and analysis and use of the large datasets that result. Breeding program and genetic mapping activities will continue as proposed.Substantially more emphasiswill be placed on data management, data analys and data analytics of existing data (primarily phenotypic) as well as improving data science abilities and automation in both research and teaching.

Impacts
What was accomplished under these goals? Greater emphasis continued to be made developing and applying multi-disciplinary approaches in high throughput field-based phenotyping (HTFP) for maize breeding using ground vehicles and unmanned aerial vehicles / systems (UAV / UAS / i.e. drones). For the second year an approximately 30 entry hybrid test and an inbred genetic mapping population were evaluated with standard agronomic measurements but also subjected to weekly UAS flights by both fixed wing and rotary wing aircraft; the ground vehicle was operated very infrequently due to mud. Data are still being analyzed but we found and published that UAV plant height had good repeatability and good correlations with manual measurements. Students and colleagues are working on improving these measures as well as to conduct new measurements with this data. New approaches to data analysis and reanalysis were attempted to make better decisions in the program. The UAS approach was furthered by USDA NIFA-AFRI project funding to expand these HTFP approaches to three different management plantings of the genomes to fields (G2F) project. HTFP technologies are very promising but will require a large investment and multi-disciplinary collaborations to make the data collected useful to plant breeders. Many different populations were advanced for improving aflatoxin, yield, and/or other traits for Texas and southern US farmers. Additionally elite lines were increased and both crossing blocks and isolation blocks were employed to create hybrids for future testing. Many experimental hybrids were tested in replicated multi-location trials. We confirmed three SNP markers increase yield significantly in testcrosses, and in inbred lines per se; an undergraduate has been backcrossing these into different backgrounds to create near isogenic lines as a research project. NIRS calibrations were used, improved and applied to other genetic mapping and breeding germplasm. Additional progress was made on understanding GxE through the southeast regional aflatoxin trials (SERAT), G2F, and the maize ATLAS project. Perennial sorghum, perennial maize and colored (red, blue, purple) maize populations and germplasm were not advanced this year but will be next year.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Jessup, R.W., R.R. Klein, B.L. Burson, S.C. Murray, J.D. Washburn, J.J. Heitholt and J.L Foster. 2017. Registration of Perennial� Line PSH12TX09. Journal of Plant Registrations 11: 76-79.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Chu, T., M.J. Starek, M.J. Brewer, S.C. Murray, L.S. Pruter. 2017. Assessing Lodging Severity over an Experimental Maize (Zea mays L.) Field Using UAS Images.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Malambo, L., S.C. Popescu, S.C. Murray, E. Putman, N.A. Pugh, D.W. Horne, M. Vidrine. 2018. Multitemporal field-based plant height estimation using 3D point clouds generated from small unmanned aerial systems high-resolution imagery. International Journal of Applied Earth Observation and Geoinformation, 64, 31-42.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Echeverria-Beirute, F., S.C. Murray, P. Klein, C. Kerth, R. Miller, B. Bertrand. 2017. Rust and Thinning Management Effect on Cup Quality and Plant Performance for Two Cultivars of Coffea arabica L. Journal of Agricultural and Food Chemistry DOI: 10.1021/acs.jafc.7b03180
  • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: Pugh, N.A.; D.W. Horne; S.C. Murray, G. Carvalho Jr, L. Malambo, J. Jung, A. Chang, M. Maeda, S. Popescu, G. Richardson, T. Chu, M.J. Starek, M.J. Brewer, and W.L. Rooney* (in press) Temporal estimates of crop growth in sorghum and maize breeding enabled by unmanned aerial systems. The Plant Phenome.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Scientists and colleagues were reached through presentations, publications, and collaborative research activities.Graduate and undergraduate students were reached through formal classroom instructions and in assisting and leading independent research projects. Farmers/ producers were reached through presentations, publications, field days and on-farm research. The public was reached through popular press presentations, publications and social media. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?All employed personnel were pursuing a degree (graduate students and technical support were pursuing MS or PhD, undergraduates were pursuing BS) and took classes; visiting scholars sat in on classes. All personnel were given an opportunity to lead one or more research projects. All personnel attended multiple professional and research seminars throughout the year and some presented their work at regional or national conferences including the American Seed Trade Association CSS conference, the National Association of Plant Breeders annual meeting, the Genetics of Maize Microbe Interactions Workshop, and the Maize Genetics Conference(among others). Personnel were introduced to outside visitors and encouraged to meet one on one. How have the results been disseminated to communities of interest?Results were disseminated through: peer reviewed publications, oral/ poster presentations at regional or national meetings, one on one meetings, webpages, social media,graduates with jobs, and other informal interactions. What do you plan to do during the next reporting period to accomplish the goals?There will continue to be an increasingemphasis in developing and usinghigh-throughput field-based phenotyping (HTFBP), including novel ground vehicles and UAVs, and analysis and use of the large datasets that result.The breeding program and genetic mapping activities will continue as proposed. There will be continued focus oncommercializing successful material and participating in larger cooperative projects: southeast regional aflatoxin trials (SERAT), the genotypes to fields initiative (G2F), the maize ATLAS project, etc.

Impacts
What was accomplished under these goals? A greater emphasis than past years was made on developing and applying multi-disciplinary approaches in high throughput field-based phenotyping (HTFP) for maize breeding using ground vehicles and unmanned aerial vehicles (UAVs / drones). A fourreplicate20 to30 entry hybrid test was planted and subjected to HTFP and conventional yield and agronomicphenotyping throughout the growing season in four environments across Texas; an inbred genetic mapping population was also subjected to the same approaches. Data are still being analyzed but plant height had good repeatability and good correlations with manual measurements. These technologies are very promising but will require a large investment and multi-disciplinary collaborations to make the data collected useful in plant breeding. Many different populations were advanced for improving aflatoxin, yield, and/or other traits for Texas and southern US farmers. Additionally elite lines were increased and both crossing blocks and isolation blocks were employed to create hybrids for future testing. Many experimental hybrids were tested in replicated multi-location trial. Additional progress was made on confirming three SNP markers that increase yield significantly in testcrosses, it was discovered that these SNPs also have an effect in inbred lines per se.NIRS calibrations were improved and applied to other genetic mapping and breeding germplasm. Additional progress was made on understanding GxE through the southeast regional aflatoxin trials (SERAT), the genotypes to fields initiative (G2F), and the maize ATLAS project. Perennial sorghum and perennial maize populations and germplasm were further advanced.?

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Shi, Y., S.C. Murray, W.L. Rooney, J. Valasek, J. Olsenholler, N.A. Pugh, J. Henrickson, E. Bowden, D. Zhang, and J.A. Thomasson. (2016). Corn and sorghum phenotyping using a fixed-wing UAV-based remote sensing system. SPIE 9866-11
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Thomasson, J.A., Y. Shi, J. Olsenholler, J. Valasek, S.C. Murray, and M.P. Bishop. (2016). Comprehensive UAV agricultural remote-sensing research at Texas A&M University. SPIE 9866-28
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Murray, S.C., L. Knox, B. Hartley, M.A. M�ndez-Dorado, G. Richardson, J.A. Thomasson, Y. Shi, N. Rajan, H. Neely, M. Bagavathiannan, X. Dong, and W.L. Rooney. (2016). High clearance phenotyping systems for season-long measurement of corn, sorghum and other row crops to complement unmanned aerial vehicle systems. SPIE 9866-4
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Shi, Y., J.A. Thomasson?, S.C. Murray, N.A. Pugh, W.L. Rooney, S. Shafian, N. Rajan, G. Rouze, C.L.S. Morgan, H.L. Neely, A. Rana, M.V. Bagavathiannan, J. Henrickson, E. Bowden, J. Valasek, J. Olsenholler, M.P., Bishop, R., Sheridan, E.B. Putman, S. Popescu, T. Burks, D. Cope, A. Ibrahim, B.F. McCutchen, D. Baltensperger, R.V. Avant, M. Vidrine, and C. Yang. 2016. Unmanned aerial vehicles for high-throughput phenotyping and agronomic research. PLoS ONE 11: e0159781. doi:10.1371/journal.pone.0159781
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Smith, S.D., S.C. Murray, and E. Heffner. 2015. Molecular analysis of genetic diversity in a Texas maize (Zea mays L.) breeding program. Maydica 60.2 - M 20.
  • Type: Websites Status: Published Year Published: 2016 Citation: The genetics of maize-microbe interactions workshop website https://gmdw.tamu.edu/


Progress 12/08/14 to 09/30/15

Outputs
Target Audience:Undergraduate and graduate students were reached through both formal classroom instruction and in assiting and leading independent research projects. Other scientists were reached through presentations, publications and collaborative research activities. Farmers/ producers were reached through presentations, publications, field days and on-farm research. The public was reached through presentations, publications. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?All employed personnel were pursuing a degree (graduate students and technical support were pursuing MS or PhD, undergraduates were pursuing BS) and took classes; visiting scholars sat in on classes. All personnel attended multiple professional seminars throughout the year and some presented their work at regional or national conferences. Personnel were introduced to outside visitors and encouraged to meet one on one. How have the results been disseminated to communities of interest?Results were disseminated through: peer reviewed publications, oral/ poster presentations at regional or national meetings, one on one meetings, webpages, graduates with jobs, and other informal interactions. What do you plan to do during the next reporting period to accomplish the goals?The breeding program and genetic mapping activities will continue as proposed. Additional focus will be made on commercializing successful material and participating in larger cooperative projects: southeast regional aflatoxin trials (SERAT), the genotypes to fields initiative (G2F), the maize ATLAS project, etc. Additionally, there will be a much stronger focus on high-throughput field-based phenotyping (HTFBP) and analysis and use of the large datasets that result.

Impacts
What was accomplished under these goals? Many different populations were created and advanced for improving aflatoxin, yield, and/or other traits for Texas and southern US farmers. Progress was made on confirming three SNP markers that increase yield significantly in testcrosses. A large genetic mapping population detected multiple new loci (QTL)for traits such as height, flowering time and leaf rolling. NIRS calibrations were improved and applied to bother genetic mapping and breeding germplasm. Progress was made on understanding GxE through thesoutheast regional aflatoxin trials (SERAT), the genotypes to fields initiative (G2F), and the maize ATLAS project. A large multi-disciplinary project on unmanned arial vehicles/systems (UAV/UAS) was pursued to better phenotyping the germplasm in the field.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Teixeira, Juliana E. C., Teclemariam Weldekidan, Natalia de Leon, Sherry Flint-Garcia, James B. Holland, Nick Lauter, Seth C. Murray, Wenwei Xu, David A. Hessel, Adrienne E. Kleintop, James A. Hawk, Arnel Hallauer, and Randall J. Wisser.2015. Hallauers Tus�n: a Decade of Selection for Tropical-to-Temperate Phenological Adaptation in Maize. Heredity 114:229240. doi: 10.1038/hdy.2014.90
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Barerro, I.D.F., Gerald De La Fuente, Seth C. Murray, Thomas Isakeit, Pei-Cheng Huang, Marilyn Warburton, Paul Williams, Gary L. Windham, Mike Kolomiets. 2015. Genome Wide Association Study for Drought, Aflatoxin Resistance, and Important Agronomic Traits of Maize Hybrids in the Sub-Tropics. PLoS ONE 10: e0117737.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Meng, Qingchang, Seth C Murray, Adam Mahan, Amy Collison, Liyi Yang, Joseph Awika. 2015. Rapid estimation of phenolic content in colored maize by near-infrared reflectance spectroscopy and its use in a breeding program. Crop Science. 55:2234-2243. doi:10.2135/cropsci2014.11.0767
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Warburton, Marilyn, Juliet Tang, Gary Windham, Leigh Hawkins, Seth Murray, Wenwei Xu, Debbie Boykin, Andy Perkins, W. Paul Williams. 2015. Genome-wide association mapping of Aspergillus flavus and aflatoxin accumulation resistance in maize. Crop Science. 55:1857-1867. doi:10.2135/cropsci2014.06.0424
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Collison, Amy, Liyi Yang, Linda Dykes, Seth C. Murray, Joseph Awika. 2015. Influence of genetic background on anthocyanin composition and behavior during thermo-alkaline processing of maize. Journal of Agricultural and Food Chemistry. 63:5528-5538. DOI: 10.1021/acs.jafc.5b00798