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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

2015 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 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 cotton, oilseed rape, camelina and guayule, a genomics lab has been established. The genomics lab is a Center-wide shared space equipped with machines to extract genetic material from plant tissue samples; liquid handlers to process and prepare extracted genetic material for genotyping-by-sequencing, and a plate reader to verify genetic markers identified from genome-wide association studies (GWAS). This lab enables samples to be processed in a semi-automated, high-throughput capacity, which saves time and minimizes error, for GWAS and other genetic mapping studies. The genetic mapping studies processed through this lab will provide genomic resources for the cotton, oilseed rape, and guayule communities to improve production in a changing environment. In prior years, studies were completed to develop genomics-based breeding tools for cotton, where regions of the genome sequence were determined for large populations of cotton plants. These “genotyping by sequencing” (or GBS) approaches provide large amounts of DNA sequence information that can be used to learn about population structure and diversity, as well as provide tools that underpin molecular breeding efforts. In collaboration with scientists at Cornell University, these GBS technologies were recently applied to a diverse collection of approximately 800 Brassica napus oilseed lines. Comparison of the DNA sequences between these various lines allowed for characterization of the evolutionary history within the Brassica population, and also provides important information for future molecular breeding programs. This is one of the largest studies ever done on an oilseed crop. GBS technologies were also recently applied to guayule, which is a natural source of rubber. Understanding the genetic diversity in guayule will be essential for increasing rubber yields and stress tolerance using molecular breeding approaches. In collaboration with scientists at Cornell University, GBS data were obtained for a diverse, natural population of guayule plants. By comparing the DNA sequence data of these accessions, significant insight to the evolutionary history of the plant population was obtained. The degree of genetic variation among the guayule accessions was also informative about which lines might be most useful for breeding efforts to improve rubber and other traits. This effort will also underpin future studies to determine the entire genome sequence of one of the guayule lines. A draft genome sequence has recently been developed as a result of collaborative work between scientists at Cornell University, the ARS lab in Maricopa, Arizona, the International Maize and Wheat Improvement Center (CIMMYT), Kansas State University, and West Virginia University. Availability of GBS data and a full genome sequence will undoubtedly accelerate breeding efforts to select plants with higher rubber content and better response to changing environmental conditions. The primary 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 and the University of Arizona in Maricopa, Arizona, research has focused on developing and testing tractor-mounted ultrasonic distance sensors, infrared sensors, and CropCircle sensors to measure canopy height, temperature, and normalized difference vegetation index, respectively. A regional breeders testing network cotton population, grown under well-watered and drought conditions, is being phenotyped for the third year with these sensors. A National Science Foundation intern is taking “ground-truthing” measurements to help improve accuracy and optimize the sensors. These measurements provide information on how cotton is responding to heat and drought stresses, which can lead to improved cotton varieties through GWAS and marker-assisted selection breeding efforts. The primary goal for Objective 3 is to identify regions of the plant genome associated with important agricultural traits, including stress tolerance, in crops such as oilseed rape and cotton. To study the effects drought has on cotton fiber wax, a trait important for spinning and dye quality of cotton fiber, a recombinant inbred line population developed by scientists at Cornell University, was grown over three years under well-watered and drought conditions. Fiber samples were hand harvested then tested for variations in wax amount and composition using a previously developed laboratory protocol. Statistical analyses for significant differences in traits and trait heritability are ongoing. Association of these traits to genetic markers, previously identified by scientists at Cornell University, are forthcoming. In an effort to identify chromosomal segments/genes involved in seed yield and/or other morphological and physiological traits in oilseed crops, ARS scientists at in Maricopa, Arizona, are collaborating with ARS scientists in Peoria, Illinois, Morris, Minnesota, Sidney, Montana, Mandan, North Dakota, Temple, Texas, Ames, Iowa, Akron, Colorado, Pendleton, Oregon, as well as scientists at Idaho State University and Cornell University, to study large populations of B. napus plants cultivated at three different locations under different environmental conditions. Plants are being monitored for their growth and development, and seeds are being harvested for analyzing. Once these phenotypic data are available, genomics-based approaches will be used to identify regions of the genome responsible for seed quality traits. In addition, six different oilseed crops species including B. napus, B. rapa, B. juncea, B. carinata, Sinapis alba, and Camelina sativa are being subjected to stress trials, including elevated temperature and non-irrigated conditions. Collectively, these efforts provide a foundation for not only identifying genes involved in seed yield, but also the genes and mechanisms that influence oil yield during abiotic stress response.

1. Characterization of the genetic diversity in guayule, a natural source of rubber. Guayule is a perennial shrub native to the southwestern United States and Mexico that holds great promise as a sustainable source of natural rubber and hypoallergenic latex. The yields of rubber in guayule, however, are quite low, and thus research is required to increase overall productivity. Modern plant breeding offers a powerful approach to increase rubber yields, but any successful breeding program requires diverse, well-defined accessions that can serve as parental lines. In an effort to characterize the genetic diversity guayule, ARS scientists at the Arid-Land Agricultural Research Center, Maricopa, Arizona, in collaboration with Cornell University, the International Maize and Wheat Improvement Center, Kansas State University, and West Virginia University, used “genotyping-by-sequencing” technologies to determine the DNA sequences of approximately 70 guayule lines and closely related species. An analysis of the DNA sequences revealed the evolutionary relationships between the individuals and also identified many subtle differences in DNA sequence that could be used as “markers” in plant breeding experiments. The results of these studies provide the most detailed description yet for guayule diversity and can be used in future efforts to increase rubber content of guayule through modern plant breeding.

Review Publications
Yurchenko, O., Singer, S.D., Satinder, G., Mullen, R.T., Weselake, R.J., Nykiforuk, C.L., Moloney, M.M. 2014. Production of a Brassica napus low-molecular mass acyl-coenzyme A-binding protein in Arabidopsis alters the acyl-coenzyme A pool and acyl composition of oil in seeds. Plant Physiology. 165(2):550-560.
Yurchenko, O., Park, S., Ilut, D., Inmon, J.J., Millhollon, J.C., Leichty, Z., Page, J.T., Jenks, M.A., Chapman, K.D., Udall, J.A., Gore, M.A., Dyer, J.M. 2014. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. Biomed Central (BMC) Plant Biology. 14:312-315. doi: 10.1186/s12870-014-0312-5.