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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

2014 Annual Report


Objectives
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.


Approach
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 primary goal for Objective 1 is to develop genomic resources for studying a variety of important crop species including cotton and various oilseeds. To develop resources for studying Brassica napus, one of the world’s most important oilseed crops, a total of 520 unique spring variety accessions were planted and grown out in Maricopa, Arizona. A collaborating partner, KeyGene, has determined the genome sequences for all Brassica varieties, and a post-doctoral fellow, in collaboration with scientists at Cornell University, is helping to assemble and annotate the genome sequences. A manuscript on the population genetics of B. napus is in preparation. Once assembled, these genome sequences will be used for genome-wide association studies, which aim to identify regions of the B. napus genome that are responsible for various traits such as oil content, composition, and wax content on leaves and stems. In a separate study, extensive resources for genetic and phenotypic analysis of guayule were developed. Guayule is a desert shrub that contains high amounts of latex, or natural rubber, in the bark tissues. One of the major limitations for increasing latex amounts through crop breeding is that very little is known about the genome size and genetic organization of guayule. To address this issue, methods were developed for characterizing genome properties and size, and these values were determined for diverse lines of guayule. The results showed that guayule plants could contain between one and three copies of the genome, and that the size of the single guayule genome was half that of sunflower and lettuce. These data will be helpful for future efforts in guayule breeding. A second major limitation for guayule cultivation is that commercial fields are currently established using greenhouse-grown seedlings that must be hand-planted. This practice is expensive, laborious and very time consuming. To help address this issue, experiments were conducted to develop and test direct seeding methods using “pelletized” seeds. Pelleted and non-pelleted seeds were tested under a variety of conditions including altered water, salinity, and temperature treatment to identify optimal conditions for seed germination and seedling establishment. The results of these studies provide important insights that will guide the selection of optimal seasonal and soil conditions for field establishment with the new direct seeding methods. The major goal for Objective 2 is to develop field-based, high-throughput methods for measuring plant phenotypes, particularly in relation to heat and drought stress. In collaboration with scientists in the Water Management Unit in Maricopa, Arizona, research has focused on developing and testing tractor-mounted ultrasonic distance sensors and infrared (IRT) sensors to measure canopy height and temperature, respectively. These sensors were used to measure phenotypic traits in both oilseed and cotton plots, including plants grown under drought conditions. Technical optimization of the entire platform is currently underway. For Objective 3, the overall goal is to identify regions of the plant genome associated with important agricultural traits, including stress tolerance, in crops such as Brassica napus and cotton. To help facilitate these studies, 520 unique accessions of Brassica napus, representing worldwide diversity, were planted and grown in Maricopa, Arizona, in replicated plots, and scored for various phenotypes. Visual scoring for “glaucousness”, which is the light bluish-gray or bluish-white color associated with surface wax content, revealed significant variation in the surface deposition of waxes on leaves, and flowering time was recorded. A laboratory based high-throughput lipid analysis platform was developed and used to quantify major variation in wax amount and composition. Comparison of these traits to the genomic sequences of the B. napus population are ongoing.


Accomplishments
1. Development of direct seeding methods for guayule, a natural source for rubber. Guayule, Parthenium argentatum, is a desert shrub that produces latex in bark tissues and represents a potential domestic source of natural rubber. One of the major challenges for cultivating guayule, however, is that the plant must be hand-sown using seedlings, which significantly increases the costs and labor associated with crop production. ARS scientists in Maricopa, Arizona, in collaboration with scientists at the University of Arizona, Cornell University, West Virginia University, and Seed Dynamics Incorporated of Salinas, California, developed direct-seeding methods for guayule and optimized conditions for seed germination and seedling establishment. The results of these studies will directly impact the guayule industry and underpin future efforts to further improve guayule cultivation and agronomics.


Review Publications
Sanchez, P.L., Costich, D., Friebe, B., Coffelt, T.A., Jenks, M.A., Gore, M.A. 2014. Genome size variation in guayule and mariola: Fundamental descriptors for polyploid plant taxa. Industrial Crops and Products. 54:1-5.
Sanchez, P.L., Chen, M., Pessarakli, M, Hill, H., Gore, M.A., Jenks, M.A. 2014. Effects of temperature and salinity on germination of non-pelleted and pelleted guayule (Parthenium argentatum A. Gray) seeds. Industrial Crops and Products. 55:90-96.