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ARS Home » Pacific West Area » Maricopa, Arizona » U.S. Arid Land Agricultural Research Center » Plant Physiology and Genetics Research » Research » Research Project #424770

Research Project: Genetic Improvement and Phenotyping of Cotton, Bioenergy and Other Industrial Crops

Location: Plant Physiology and Genetics Research

2017 Annual Report

1. Develop genotyping-by-sequencing methods for diverse cotton, oilseed, and industrial crop germplasm, and map genetic markers for economically and agronomically important traits in these crops. 1.1 Genotyping-by-sequencing of cotton. 1.2 Genotyping-by-sequencing of oilseed rape. 1.3 Genetic and phenotypic characterization of new guayule germplasm. 2. Develop novel phenotyping approaches for quantitative genetic analysis of drought and heat tolerance traits in cotton and oilseed crops. 2.1 High-throughput phenotyping of traits related to drought and heat tolerance in cotton. 2.2 High-throughput phenotyping of traits related to drought and heat tolerance in oilseed rape. 3. Identify molecular markers associated with stress tolerance traits in cotton and oilseed crops. 3.1 Genome-wide association studies and marker-trait validation in cotton. 3.2 Genome-wide association studies and marker-trait validation in oilseed rape.

The three objectives of the plan will be carried out using various field-based instrumentation and modern approaches in plant breeding and genetics, and will be focused on the three important crops; cotton, oilseed rape, and guayule. These approaches are targeted toward the creation of genotyping-by-sequencing marker maps, development of novel phenotyping tools for quantitative genetic analysis of heat and drought tolerance traits, and identification of molecular markers associated with stress tolerance, quality, and yield related traits. The experiments will apply translational genomics approaches, leveraging statistical genetics and genomics for dissection of quantitative traits and the utilization of rapid, high-throughput phenotyping.

Progress Report
The overall goal of our research project is to improve the heat and drought tolerance of cotton, oilseeds, and guayule, and identify the genes associated with these traits. In support of Objective 1, which focuses on the identification of genes for crop improvement, we characterized the genome copy (ploidy level) in guayule plants to better understand the genetic variation present in the guayule USDA germplasm collection. Leaf tissue samples were collected then DNA content was analyzed to determine the ploidy level, which describes the total amount of DNA present in each plant line. The guayule accessions showed wide variations in DNA amounts. These results will assist future guayule breeding efforts by allowing scientists to correlate agronomic traits with DNA ploidy level, thus enhancing our understanding of the effects of DNA amount on guayule performance and productivity. To increase our knowledge of the genes in oilseed crops, DNA was extracted from a diverse collection of rapeseed plants, consisting of 520 lines, then samples were sent to the ARS genomics lab in Stoneville, Mississippi, for sequencing. Analysis of the DNA sequences should reveal distinct differences between the plant lines, which is useful for future breeding efforts that correlate these differences to differences observed for crop performance in the field. Objective 2 focuses on the development of field-based, high-throughput phenotyping (FB-HTP) methods that can be used to study cotton, guayule, and other crops under heat and drought conditions. FB-HTP involves the use of tractors, drones, or carts to deliver various sensors in the field which measure important properties of the crops such as plant height, leaf temperature, and plant biomass. These parameters are important for determining crop yields, and by developing these semi-automated FB-HTP methods, scientists can rapidly collect large amounts of “big data” on crop performance. Last season, work was initiated with scientists in the ARS Water Management Research Unit in Maricopa, Arizona, as well as the University of Arizona, to validate FB-HTP measurements collected with a tractor and compared with conventional hand measurements assessed in a Regional Breeders Testing Network (RBTN) with 35 cotton lines. As a result of these studies, a FB-HTP protocol was established, data management tools were developed, and the tractor-based measurements were validated. This season we have worked to further improve the FB-HTP process by developing a database system and various data processing programs that both utilize open source software. ARS scientists in Maricopa, Arizona, are working with the CyVerse consortium, University of Arizona, Tucson, to distribute these software tools to the broader scientific community. Procedures are being developed for the use of regular cameras to measure crop growth and performance in the field. Early efforts have focused on characterizing plant stand counts and cotton flowering. To ensure that the development of this new technology did not disrupt our regular tractor-based data collections, a motorized cart was developed and employed to compare different camera lenses, shading, and camera positions on the ability to generate useful images of the plants. With these comparisons, a protocol was established that can now be added to the overall FB-HTP program. Both FB-HTP and conventional phenotyping methods were used to characterize the variation in heat and drought stress traits in a population of cotton lines provided by collaborators from Arkansas, South Carolina, and the USDA Cotton Germplasm repository in Texas. The trial included two planting dates and four water treatments with three replicates per water treatment. Plant growth was monitored weekly by hand measurements and included soil moisture, growth stage, leaf chlorophyll content, flowering date, photosynthesis, and pollen sterility. Complementary data on plant height, canopy temperature, and biomass were recorded weekly using the FB-HTP tractor. At harvest, the plots will be assessed for yield and fiber quality in response to planting and irrigation treatments. The planting dates will help identify traits heavily influenced by heat stress as opposed to traits influenced by water stress. Understanding these differences will allow us to identify better targets for genetic mapping and plant breeding. FB-HTP and conventional phenotyping was used to characterize the performance of oilseed crops cultivated under drought and heat stress conditions. Crop varieties tested included Brassica napus, B. carianta, B. juncea, B. rapa, Sinapis alba, and Camelina sativa. FB-HTP data were collected on a weekly basis throughout the growing season. Conventional phenotypes were also collected, including flowering time, plant height and chlorophyll content. Once the plants were fully mature, plots were harvested and seed yields determined. A preliminary assessment of the data revealed significant correlations among conventional and FB-HTP-collected data. To develop and release cotton germplasm adapted for growth in multiple environments, populations arising from selected superior lines cultivated under drought and heat stress conditions are being developed. A cotton population developed by ARS collaborators in Texas and South Carolina was received in 2016 and assessed for yield and fiber quality traits in an un-replicated, multi-location trial. The 2016 data were used to select 20 lines from each location with superior performance. This year, 60 selected lines were planted in replicated field trials in each of three locations. In Maricopa, Arizona, the lines were assessed for heat tolerance using weekly high-throughput phenotyping techniques and complementary hand-held measurements described above. After harvest, yield and fiber quality will be assessed. These lines will continue to be evaluated at locations in Arizona, Texas. Objective 3 focuses on the identification of specific genes or genetic “markers” that are associated with stress tolerance traits in cotton and oilseed crops. In collaboration with ARS scientists in Peoria, Illinois, Morris, Minnesota, Sidney, Montana, Mandan, North Dakota, Temple, Texas, Ames, Iowa, Akron, Colorado, Pendleton, Oregon, Idaho State University, and Cornell University, a diverse collection of 782 oilseed rape (B. napus) lines was cultivated in replicated field trials at Akron, Colorado, Ames, Iowa and Genesse, Idaho, over two years. A variety of yield-related traits were measured, including seed oil content and composition. The DNA sequences of each plant line were also determined, revealing subtle differences in the DNA sequences. By comparing these differences to the differences in yield-related traits, specific genes were identified that were strongly correlated with oil content and composition. These genes included fatty acid desaturase 3 and 3-ketoacyl-CoA synthase 18, both of which are known to be important for the formation of oil in plants. This work will ultimately lead to the identification of additional genes and genetic “markers” that will be useful to plant breeders for further increasing yields of B. napus crops.

1. Characterization of leaf waxes in the oilseed crop Camelina sativa. The leaf cuticle contains a waxy protective layer that has low permeability to water, which directly affects the rate of leaf water loss and thus the susceptibility of plants to drought conditions. In collaboration with scientists at West Virginia University, ARS researchers in Maricopa, Arizona, characterized the leaf waxes from seventeen Camelina species. The various plant lines exhibited a wide range of wax contents, which revealed significant variation for this trait in camelina species. This work lays the foundation for future breeding efforts that aim to increase camelina wax with the end-goal of improving drought tolerance of the crop.

Review Publications
Tomasi, P., Wang, H., Lohrey, G.T., Park, S., Dyer, J.M., Jenks, M.A., Abdel-Haleem, H.A. 2017. Characterization of leaf cuticular waxes and cutin monomers of Camelina sativa and closely-related Camelina species. Industrial Crops and Products. 98:130-138. doi: 10.1016/j.indcrop.2017.01.030.
Thompson, A.L., Pauli, D., Tomasi, P., Yurchenko, O., Jenks, M.A., Dyer, J.M., Gore, M.A. 2017. Chemical variation for fiber cuticular wax levels in upland cotton (Gossypium hirsutum) evaluated under contrasting irrigation regimes. Industrial Crops and Products. 100:153-162.