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United States Department of Agriculture

Agricultural Research Service

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ALARC Highlights - Winter/Spring 2012

Featured Recent Accomplishment

Field-based phenomics for plant genetics research. Perhaps the greatest challenge for crop improvement research in the 21st century is how to integrate information from genetics, physiology, climatology and other research fields to improve the predictability of crop yields. Advances in “next generation” DNA sequencing have greatly reduced the cost of obtaining genetic data. Methods for characterization of plant traits (“phenotypes”), however, have evolved little over the past 30 years. As a result, this limits our ability to rapidly measure plant traits on a large number of plants, especially needed for traits related to economic yield and stress tolerance, thus weakening predictability accuracies.

Researchers at ALARC in collaboration with scientists at the Maricopa Agricultural Center (Univ. Arizona) are embarking on a major initiative to develop new approaches for rapid, accurate measurement of plant traits. This research considers novel experimental approaches, equipment and data analysis tools required for measuring plant traits at an unprecedented large scale. The main focus is on simultaneous measurement of multiple traits related to plant color (reflectance), temperature and architecture. The proposed “field-based phenotyping” (FBP) system uses a vehicle to move replicated sets of sensors over four or more individual plots at once and has the potential to record data throughout the life history of a crop. For traits such as drought or heat tolerance, plots should be assessed several times during a single day in a narrow time interval, which is now possible with our vehicle.

Many of the underlying methods and instruments exist and are used in precision crop management. Innovations are required in integrating the multiple sets of instruments and ensuring efficient, robust analysis of the large volumes of data that are anticipated. Further development of sensors and imaging systems will continue to improve our ability to phenotype large experiments or crop breeding nurseries, but the core FBP abilities appear to be achievable through a strong interdisciplinary effort drawing largely on assembling existing technologies in novel ways. Developing FBP capabilities is key to attaining a better understanding of how genetics influences crop yields and thus breeding new varieties that ultimately benefit farmers and consumers in numerous ways such as improved heat tolerance and ability to yield under reduced water availability.

Initial work at ALARC has focused mainly on drought and heat stress in cotton. Exploratory efforts in wheat and camelina also show promise and allow us to test equipment year around, taking advantage of Maricopa’s clear skies and mild winters. A recent paper in the research journal Field Crops Research (vol. 133, p 101-112) provides further technical information.


Contacts:       Jeff White (

 Mike Gore (


The Maricopa Agricultural Center’s high-clearance tractor in operation over young cotton plants at Maricopa, AZ. Replicated sets of sensors allow simultaneous measurement of plant height, foliage temperature, and foliage color (spectral reflectance). GPS provides positional accuracy under 2 cm. ALARC’s instrument testing vehicle being operated over a field of camelina, a promising biofuels crop. As configured, the vehicle records two images for each plot and foliage temperature from three viewing angles.

 Photograph (left) and forward looking infrared (FLIR) image (right) of a water-limited Monseratt Sea Island cotton plant. Both images were collected in the early afternoon, 3 DAW, on week 15 after planting. The color scale to the right shows the variation in leaf temperature produced by leaf wilting and subsequent shading.  From Carmo-Silva, E. A. et al. 2012 [abstract]


Other Recent Accomplishments

Release of sterile insects suppresses resistance to Bt in transgenic Bt cotton. In this multi-agency cooperative project, ARS scientists in Maricopa, AZ, and Parlier, CA, and scientists from the University of Arizona showed that the release of sterile insects can be used to effectively substitute for the required refuge to suppress pest resistance in pink bollworm to Bt cotton over a very large area. This information benefits government, academic, and industry researchers as well as regulators and administrators of insect control and resistance monitoring programs and provides new information regarding possible benefits of large-scale sterile insect release.

Pollinator movement between conventional and genetically modified (GM) crops. One concern in deploying transgenic plants in the environment is the spread of transgenes to other related crops in the region through pollen flow. ARS scientists in Maricopa, AZ, and researchers at the University of California, Davis showed that bees dispersed a minimum of 45 m and a maximum of 5,983 m from their apiary of origin and that gene flow averaged 1.7% at 50 m, 0.2% at 1600 m. The results are valuable to producers and regulators in for understanding the required distances for isolating biotech and conventional seed alfalfa production.

Characterization of proteins that regulate photosynthesis. Two important enzymes involved in the process of photosynthesis are regulated by a small protein called CP12. ARS scientists in Maricopa, AZ purified a complex containing CP12 from tobacco and the model plant, Arabidopsis. Chemical analysis showed that the purified complex contained only CP12 and the two photosynthetic enzymes indicating that CP12 plays a specific role in controlling the two photosynthetic enzymes in response to light. This information could be used to optimize the photosynthetic performance of plants to maximize yield and profits in hot and arid environments.

Rapid method for determining guayule ploidy levels developed. ARS scientists in Maricopa, AZ and researchers at Kansas State University adapted flow cytometry to examine the ploidy of guayule accessions available from the National Plant Germplasm System, a transgenic breeding population, and a traditional breeding population. The data revealed a series ranging from diploid to pentaploid, with tetratploid being predominant. The frequency and range of ploidy variation observed will help future breeding efforts as well as linkage analysis and genome-wide association studies benefiting the guayule breeders, geneticists, and curators as well as the guayule industry.

Disruption of gene in plants results in increased in oil content. All plants produce small amounts of oil in their leaves, but the mechanisms regulating this process are not understood. ARS scientists in Maricopa, AZ and researchers at the University of Guelph, University of North Texas, and University of Texas Southwestern Medical Center have identified an alpha-beta hydrolase-type gene in Arabidopsis that, when mutated, results in a 10-fold increase in the amount of oil present in plant leaves, with no changes in amount of oil present in the seeds. This opens new avenues of research for producing high amounts of energy-dense oils in the vegetative tissues of crop plants. Results will be useful to researchers increasing the oil content of plants for use in bio-fuels.

Improved irrigation canal management. ARS researchers in Maricopa, AZ developed improved procedures for predicting the discharge through radial gates for irrigation canals. This technology improves the ability of irrigation districts to measure and distribute water to users accurately. The new procedures were incorporated into Wingate, a computer program developed by cooperating scientists at the U.S. Bureau of Reclamation, who will make the software available to interested irrigation districts.

Antibiotics and bacterial resistance in treated municipal water. The development of increased antibiotic resistance in naturally occurring soil microorganisms due to the application of treated municipal waste water containing low concentrations of antibiotics applied to soil is a concern. Scientists in Maricopa, AZ measured the antibiotic content and resistance from soil cores at a recharge site in Gilbert, Arizona that has been used to recharge groundwater with treated municipal wastewater for 20 years. They found that the maximum soil concentration of lincomycin was negligible with no increase in antibiotic resistance in the native gram positive soil microbial community. The town of Gilbert will provide this information to State regulators as evidence of the recharge facilities sustainability.



Recent Journal Publications


Bautista, E, Strelkoff, T., Clemmens, A. 2012. Improved surface volume estimates for surface irrigation balance calculations. Journal of Irrigation and Drainage Engineering (in press) [abstract]

Bautista, E, Strelkoff, T., Clemmens, A. 2012. Errors in infiltration volume calculations in volume balance models. Journal of Irrigation and Drainage Engineering (in press) [abstract]

Brent, C. 2012. Classification of diapause status by color phenotype in Lygus hesperus. Journal of Insect Science (in press) [abstract]

Chapman, K.D., Dyer, J.M., Mullen, R.T., 2012. Biogenesis and functions of lipid droplets in plants. Journal of Lipid Research 53:215-226. [abstract]

Do Carmo Silva, A., Gore, M., Andrade-Sanchez, P, French, A, Hunsaker, D., Salvucci, M. 2012. Decreased CO2 availability and inactivation of Rubisco limit photosynthesis in cotton plants under heat and drought stress in the field. Environmental and Experimental Botany (in press) [PDF]

Gutierrez, M., Norton, R., Thorp, K.R., Wang, G. 2012. Association of spectral reflectance indices with plant growth and lint yield in upland cotton (Gossypium hirsutum L.). Crop Science 52:849-857. [abstract]

Hoffman, E., Castle, S. 2012. Imidacloprid in melon guttation fluid: A mode of exposure for pest and beneficial organisms. Journal of Economic Entomology 105: 67-71. (PDF)

Irvin, N.A., Hagler, J.R., Hoddle, M.S. 2011. Laboratory investigation of triple marking the parasitoid Gonatocerus ashmeadi (Hymenoptera: Mymaridae) with a fluorescent dye and two animal proteins. Entomologia Experimentalis et Applicata 143:1-12. [abstract]

McClain, J., Carlson, M., Lohse, K., McIntosh, J. 2012. Impacts of urbanization on groundwater quality and recharge in a semi-arid alluvial basin.  Journal of Hydrology (in press) [abstract]

Naranjo, S.E., Stefanek, M.A. 2012. Feeding behavior of a potential insect pest, Lygus hesperus, on four new industrial crops for the arid southwestern USA. Industrial Crops and Products 37:358-361. (PDF)

Scafaro, A., Yamon, W., Do Carmo Silva, A., Salvucci, M., Von Caemmerer, S., Atwell, B. 2012. Rubisco activity is associated with photosynthetic thermo-tolerance in the wild rice Oryza meridionalis Physiologia Plantarum (in press) [abstract]

Slosky, L., Hoffman, E., Hagler, J. 2012. A comparative study of the retention and lethality of the first and second generation arthropod protein markers. Entomologia Experimentalis et Applicata (in press) [abstract]

Thorp, K.R., White, J.W., Porter, C.H., Hoogenboom, G., Nearing, G.S., French, A.N. 2012. Methodology to evaluate the performance of simulation models for alternative compiler and operating system configurations. Computers and Electronics in Agriculture 81: 62-71. (PDF)

White, J., Andrade-Sanchez, P, Gore, M., Bronson, K., Coffelt, T., Conley, M., Feldman, K., French, A., Heun, J., Hunsaker, D., Jenks, M., Kimball, B., Roth, R., Strand, R., Thorp, K., Wall, G., Wang, G. 2012. Field-based phenomics for plant genetics field crops research.  Field Crops Research 133: 101–112. (PDF)



Recent Grant Awards


Bridging Genomics and Plant Breeding with a Cotton Nested Association Mapping Population, Cotton Incorporated (PI Mike Gore Co-PIs V. Kuraparthy, North Carolina State and T. Campbell, USDA-ARS Florence) 2012 [abstract]

Ecological and Agricultural Productivity Forecasting Using Root-Zone Soil Moisture Products Derived from the Nasa Smap Mission, NASA (Co-PI Kelly Thorp with W. Crow, USDA-ARS Beltsville [PI]; S. Moran, USDA-ARS Tucson; G. Nearing, University of Arizona; R. Reichle NASA) 2010-2013 [abstract]

Genetic Analysis of Physiological Traits Conferring Heat and Drought Tolerance in Cotton, Cotton Incorporated (PI Mike Gore) 2010-2012 [abstract]

Genetic Dissection of Heterotic Effects in Upland Cotton-Phenotypic Evaluation in Arizona, Cotton Incorporated (PI Mike Gore) 2012

High-Throughput Phenotyping for Time-Related Qtl Mapping of Traits under Supra-Optimal Temperatures and Water-Limited Conditions, Cotton Incorporated (PI Mike Gore with Co-PI P. Andrade-Sanchez, University of Arizona) 2012 [abstract]

High-Throughput Phenotyping Using Portable LIDAR, Cotton Incorporated (PI Andy French with Co-PIs M. Gore and P. Andrade-Sanchez, University of Arizona) 2012

Identification of factors mediating temperature acclimation in Lygus hesperus, Cotton Incorporated (PI Colin Brent; Co-PIs Jeff Fabrick, Joe Hull) 2012

Impact of Bioenergy Crops on Pests, Natural Enemies and Pollinators in Agricultural and Non-Crop Landscapes, USDA-NIFA-AFRI (Co-PI James Hagler with T. Kring and R. Weidenman, University of Arkansas; B. McCornack, Kansas State University; K. Giles, Oklahoma State University) 2011-2016 [abstract]

Improving Nitrogen Fertilizer Management and Fate of Nitrogen in Surface Irrigated Cotton, Cotton Incorporated (PI Kevin Bronson) 2011-2012 [abstract]

Investigation into Effects of Soil Moisture Depletion on Vegetable Crop Uptake of Microcontaminants under Recycled Water Irrigation, USDA-NIFA-AFRI (PI Clinton Williams with C. Ray, Univeresity of Hawaii) 2011-2013 [abstract]

Integrating Biological Control Into Management Decisions: Advancing The IPM Continuum Through Research and Implementation, USDA-NIFA-WRIPM (PI Steve Naranjo with Co-PIs P. Ellsworth, A. Fournier, L. Brown, T. Vandervoet, University of Arizona) 2012-2014

Monitoring Arid Land Cover Change with Simulated Hyspiri Data, NASA (PI Andrew French with Co-PIs Kelly Thorp; T. Schmugge, USDA-ARS; J. Sanchez, University of Castilla-La Mancha; C. Coll, University of Valencia; E. Valor, University of Valencia) 2010-2012 [abstract]

Optimizing Rubisco Regulation for Increased Photosynthetic Performance under Climate Change, DOE (PI Mike Salvucci) 2010-2013 [abstract]


Recent Professional Awards


Andy French received the 2012 Best Paper Award from the EWRI-ASCE Journal of Irrigation and Drainage Engineering.  The paper was entitled “Combining remotely Sensed Data and Ground-based Radiometers to Estimate Crop cover and Surface Temperatures at Daily Time Steps” and his co-authors were Doug Hunsaker, Tom Clarke, Glenn Fitzgerald, P. Jim Pinter, Jr. Andy and his co-authors will be presented the award during the World Environmental & Water Resources Congress 2012, May 20 - 24, in Albuquerque, NM.


Bert Clemmens received 2012 Best Paper Award from the EWRI-ASCE Journal of Irrigation and Drainage Engineering.  The paper was entitled “Routing Demand Changes to Users on the WM Lateral Canal with SacMan” and his co-authors were Robert Strand and Eduardo Bautista. Bert and his co-authors will be presented the award during the World Environmental & Water Resources Congress 2012, May 20 - 24, in Albuquerque, NM.


Steven E. Naranjo was presented with the C.W. Woodworth Award, an annual award given by Pacific Branch of the Entomological Society of America. He gave a plenary lecture on his research at the group’s annual meeting in Portland, OR in March. The C.W. Woodworth Award is PBESA’s highest honor, and recognizes achievement in entomology in the Pacific region of the United States during the past 10 years.


Recent Events and Outreach


In November 2011, about 60 irrigation engineering students and faculty from the University of Chapingo, Mexico. Center scientists discussed ongoing research in irrigation modeling, irrigation management, and remote sensing in irrigated agriculture. The visit was coordinated by the Agricultural and Biosystems Engineering Department of the University of Arizona.

In November 2011, representatives from the Maricopa Community College District visited and toured ALARC to learn about our research programs and the potential for developing partnership/collaboration with community colleges throughout Arizona.

In November 2011, ALARC hosted its annual Focus Group meeting. The group is composed of industry, university and grower representative from the local, regional and national level. This stakeholder group was briefed on recent research by ALARC scientist and is actively supporting several initiatives to enhance research opportunities at ALARC.

In November, 2011, ALARC hosted a visit from the Economic Development Director for the City of Maricopa and representatives of the Canadian Consulate. The city is interested in attracting Canadian investment and business growth in biotech and cleantech-related fields and wanted to showcase potential industry/USDA research partnerships with ALARC.

In January 2012, about 30 students and faculty from Estrella Mountain Community College visited ALARC where they visited individual scientist’s laboratories and learned about on-going research in agricultural biotechnology. After the lab tours, the students and scientists met for a question/answer session.

In January 2012, ALARC hosted grant collaborators and Ph.D. students from the University of Arkansas, Oklahoma State University and Kansas State University to discuss research priorities for a USDA-NIFA-AFRI Biofuel Grant.

In February 2012, the Agriculture Air Quality Task Force visited local businesses in Arizona to learn more about air quality and agriculture. The Task Force toured our Center to learn about the research being conducted here. The Task Force is made up of members that are both agricultural and atmospheric in nature concentrating on pollution, dust, pesticide chemical drift, and carbon sequestration.

In February 2012, the EEO Committee observed Black History month by showing the PBS video, FREEDOM RIDERS.

In February 2012, ALARC hosted the 2012 Cotton Price Risk Management Seminar sponsored by Cotton Incorporated and Calcot, Ltd.

In May 2012, ALARC hosted a visit from about 70 biology and biotechnology students and teachers from Desert Vista High School in Phoenix, AZ.  Visitors toured the laboratory and learned from scientists about the wide range of on-going research in entomology, plant science and agricultural engineering. After the lab tours, the students and scientists met for a question/answer session and enjoyed some refreshments.


Last Modified: 5/17/2012
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