2013 Annual Report
1a.Objectives (from AD-416):
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.
1b.Approach (from AD-416):
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.
This is the initial report for this project which was initiated in June of 2013 and continues research from 5347-21410-005-00D entitled, "Commercialization of New Industrial Crop Germplasm and Cropping Systems". This project is currently vacant for the two key scientists positions. Two ARS scientists, though having more minor assignments on this project, have been advancing the goals of the research, nonetheless. The high clearance phenotyping vehicle has entered the cotton field plots in Maricopa, Arizona, and is now collecting data using ultrasonic distance sensors and infrared (IRT) sensors to measure canopy height and canopy temperature, respectively. These same sensors were also used to measure similar phenotypes in oilseed plots. Technical optimization of many aspects of the entire platform is currently underway. Genetic diversity in Guayule has been identified from among wild field-collected seeds, and the genome size and ploidy level of 36 Parthenium species and their interspecific hybrids has been completed, with a paper scheduled for submission soon. A total of 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 revealed significant variation in the surface deposition of waxes on leaves, and flowering time was recorded to show dramatic variation in time to anthesis. A lab based high-throughput lipid analysis platform was developed and used to quantify major variation in wax amount and composition. Analysis of wax content of all plant lines is roughly half completed. The resulting datasets will be used for linking phenotypic differences to specific molecular markers determined by genome sequencing and genome-wide association studies. A collaborating partner, KeyGene, has determined the genome sequences for a portion of the Brassica varieties, and a post-doctoral fellow has just started on the project to initiate statistical genetic analyses. Seeds of each Brassica variety were also collected for oil analysis, which will also be used as a dataset for statistical genetics analysis, but seed yield was very poor due to the hot temperatures during seed development and harvest.
Genome analysis of guayule. Guayule is a woody, desert shrub under development as a domestic source of natural rubber, but improving rubber yields will require a better understanding of the genes involved in regulating rubber synthesis. Scientists at the US Arid Land Agricultural Research Center (ALARC) in Maricopa, Arizona, completed an analysis of genome size, chromosome number, and ploidy on 36 Parthenium (guayule) species and their interspecific hybrids. Wide variation in genomes was observed, with genome size ranging from 1,624 Mb in diploids to 5,756 Mb in tetraploids, and interspecific hybrids ranging from 2,523 to 4,225 Mb. The results of these studies will be useful for genetic and genome-wide population analysis, with the end-goal of identifying genomic markers or individual genes that can be used to improve rubber yields.