Objective 1: Identify and characterize genetic diversity in economically important agricultural crop plants for biochemical, physiological, and metabolic processes that condition plants for tolerance to drought and heat extremes. Subobjective 1A: Identify the range of drought tolerance that exists within a diverse core reference set of entries from the National Cotton Germplasm Collection. Subobjective 1B: Contribute to the broadening of the genetic base of cotton for improved drought tolerance by developing Recombinant Inbred populations, breeding lines, and mutant populations using fast-neutron and ethyl methanesulfonate (EMS) mutagenesis. Subobjective 1C: Identify the range of heat stress tolerance in corn germplasm. Subobjective 1D: Evaluate the usefulness of a stress visualization computer software platform that can present and compare environmental and plant stress information in an interactive and manipulative environment to provide novel insights into the relationships between environmental cues and plant responses. Objective 2: Determine genetic mechanisms controlling biochemical and physiological processes that contribute to water-deficit and thermal stress avoidance and/or tolerance in agricultural crops. Subobjective 2A: Evaluate the differential onset of water stress in pre- and post-flowering sorghums via metabolite changes. Subobjective 2B: Characterize genetic and molecular mechanisms contributing to contrasting stress tolerance responses in peanuts. Subobjective 2C: Identification of major QTLs and/or genomic loci that are associated with heat tolerance/sensitive traits in maize and characterization of genetic and molecular mechanisms contributing to heat tolerant traits in maize. Subobjective 2D: Identify plant genes associated with improved abiotic stress tolerance in Arabidopsis; and functionally characterize crop ftsh11 protease homologs in maintaining chloroplast thermostability and photosynthesis at elevated temperatures. Subobjective 2E: Investigate small RNA regulation of plant stress responses and impact on transgene activity in genetically engineered plants. Objective 3: Use integrated marker-assisted breeding methods to develop stress-tolerant cotton germplasm or cultivars with high fiber quality and resistance to Fusarium oxysporium f. sp. Vasinfectum (FOV).
A multidisciplinary research approach will be utilized because of the complexity of the problems to be addressed. Genetic diversity will be identified for biochemical, physiological, and metabolic processes that condition plants for tolerance to drought and heat extremes. Genetic mechanisms controlling biochemical and physiological processes that contribute to water-deficit and thermal stress avoidance and/or tolerance will be determined. Marker-assisted breeding methods will be used to develop stress-tolerant cotton germplasm with high fiber quality and resistance to Fusarium oxysporium f. sp. Vasinfectum (FOV).
This is the final report for Project 3096-21000-019-00D, which terminated in May 2018 and replaced with new Project 3096-21000-022-00D. Objective 1. Development of combined thermographic and visual crop sensor approaches using fixed sensors and unmanned aerial vehicles (UAV). A second year rainfed cotton experiment was completed using 6 planting dates and 4 rain simulations. At the end of the season a UAV was used to collect yield data. Open source software was used to develop a method for measuring cotton yield. The method produced good yield estimates (within 10% of hand harvested values) across a range of yield from 0.5 to 5 bales/acre (280 kg/ha to 2,800 kg/ha). The method was additionally tested and verified using aerial images collected in cooperation with Australian collaborators at yields of 5 bales/acre. Objective 1. In Cropping Year 2018 a procedure has been developed to provide for stand establishment and development rate estimates in cotton based on aerial imagery. The methods have been developed using open source software in an effort to make the methods accessible at a low-cost relative to many current methods. The OZCOT cotton simulation model was implemented using Southern High Plains weather and cultural conditions in cotton. Slight modifications were made to the model inputs and the early modeling results suggest that the model can be used for yield estimation in rainfed cotton in the region. Seasonal canopy temperature data was collected in a rainfed cotton experiment involving 6 planting dates and 4 rain simulations. These data are being used to “drive” the OZCOT model (in place of air temperatures) in an effort to improve yield estimates. Canopy temperature data were collected on a range of peanut and cotton canopies grown under different rain/irrigation regimes. This information is being used to test its ability to improve performance of the OZCOT model. Objective 1. Development of new data analytics and experimental cropping designs to study rainfed crop production: Development, implementation and demonstration of the utility of a rainfed matrix approach to the study of genotype x environment x managementinteractions. Two years of a 7-planting date: 4 rainfall simulation rainfed matrix have been carried out using cotton on the Southern High Plains of Texas. Results indicate that such an approach can significantly improve the ability to understand rainfed crop production and to identify approaches to improvement. Two undergraduate students were used to create a workflow protocol for large-scale data analysis of climate and crop data. This approach allows for large-scale crop modelling for water use, cotton fiber quality traits, and yield. Currently the model is being tested with large data sets from ARS at Lubbock, Texas, and Australia Commonwealth Scientific and Industrial Research Organization (CSIRO). Objective 1. Testing diverse cotton lines for yield improvement under low input irrigation. Replicated studies were performed using two irrigation regimes to confirm the yield advantage observed under water deficit stress conditions and to further evaluate additional morphological and fiber quality traits of a diverse core-set of cotton lines. A total of 142 recombinant inbred lines derived from a cross between Phytogen 72 and NM 67 from the USDA cotton collection and germplasm from the Lubbock, Texas, cotton breeding program were used in the study. Cotton lines from this diverse set of material were identified with improved yield under mid- and late-season water-deficit compared to commercial cotton cultivars. Objective 2. Identification of major quantitative trait loci (QTL) and/or genomic loci that are associated with heat tolerance/sensitive traits in maize. We have completed the field phenotyping analysis for 2 recombinant inbred lines (RILs) and identified several QTL regions associated with 3 heat tolerant traits. A manuscript reporting the identification of heat tolerance QTLs has been submitted for publication. In addition, we are currently generating double hypoid (DH) lines for a new mapping cross between a known heat sensitive and heat tolerant maize inbred. The DH lines will be evaluated for variations in heat tolerance traits under field conditions. Genomic DNA of leaf tissues of individual DH lines, along with the bi-parental lines will be sequenced and analyzed for marker variations. The association of heat tolerance traits with specific markers will be analyzed once we have both phenotyping and marker data. Objective 3. Improved resistance for Fusarium wilt (FOV) race 4 was identified by screening more than 400 upland cotton germplasm entries. Approximately 10% of these entries were selected for FOV4 resistance and seed was increased for additional FOV4 field and greenhouse evaluations. Additionally, crosses were created from some of these accessions and planted FOV4 infested nurseries in California and Texas in Cropping Year 2018 for selection and further evaluation. These entries represent a wide range of diverse genetic upland cotton backgrounds. Improved upland and pima germplasm lines with FOV race 4 tolerance/resistance are expected to be released in 2019.
1. Characterization of ftsh11 protease homologs reveals its role in the maintenance of chloroplast thermostability and photosynthesis at elevated temperatures. ARS research scientists in Lubbock, Texas, have characterized the ftsh11 mutant and published a manuscript underlining mechanisms of the protein (FtsH11) in maintaining photosynthetic efficiency at elevated temperatures. The conserved role of FtsH11 homologs in other plants, including in crop species were characterized in 2 transgenic ftsh11 mutant lines. We also used the sorghum mutant library developed at Lubbock, Texas, to identify a mutant homolog (sbFtsH11). Preliminary results from sbFtsH11 mutant characterization indicate a similar function of sbFtsH11 in thermotolerance as seen in other species. This work establishes a new functional mechanism that directly impacts crop thermotolerance and presents the potential to directly manipulate or improve thermotolerance by breeding or engineering this trait into crop plants. Two manuscripts about this study are being drafted and will be submitted either by end of FY18 or in early FY19.
2. Exploring Ethyl Methane Sulfonate (mutagen EMS) treated cotton (Gossypium hirsutum L.) to improve drought tolerance. The current levels of cotton production are under threat by the fact that the climate is getting hotter and drier, and aquifers, such as the Ogallala, are being depleted faster than they can be replenished. In addition, on the Texas High Plains, often unpredictable and extended periods between rainfall events can lead to a reduction in yield and fiber quality. Therefore, there is a need for drought resistant upland cotton germplasm. However, there may be insufficient genetic diversity among current cotton lines. ARS scientists from Lubbock, Texas, along with researchers from Texas Tech University created three populations of mutant cotton. This research established the importance of examining different traits for the selection of drought tolerant lines and identified a few lines with potential for possible public germplasm release.
3. Comparison of hydrocarbon yields in four cotton accessions: regular vs. limited irrigation. As water for irrigation from the Ogallala Aquifer decreases, farms on the Southern High Plains will need new sources of income. Alternative sustainable renewable sources of petrochemicals and fuels from arid and semi-arid land crops may be one source of income. Recently, it was reported that cotton presents a new possibility as a hydrocarbon source because of its growth habit as a perennial crop and adaptation to long and hot growing seasons. ARS scientists from Lubbock, Texas and Baylor University studied four upland cotton cultivars grown in limited and regular irrigated field conditions to compare water stress effects on hydrocarbon (HC) production. The yields of HC were higher when grown under water stress. The results suggest that cotton grown for HC may be a supplemental income to cotton fiber production. Further research is needed to more fully understand these trends.
4. Development of molecular markers for Fusarium wilt races 1 and 4 resistance. The soil-borne fungal pathogen Fusarium oxysporum f. sp. vasinfectum (FOV), causes one of the most devastating vascular diseases in many cash crops, especially in cotton. Fusarium types represent expanding threats to cotton production in the U.S. and in other countries of the world. Resistant cultivars are highly effective in preventing crop loss from FOV infection. However, new resistant germplasm is needed as new races of the fungi evolve. Progeny and breeding lines developed between Pima and Upland cottons were used to identify/validate molecular markers associated with FOV resistance. Some of the breeding lines showed resistance to both fusarium wilt types, providing multiple resistance sources for breeding. In addition, these new trait-linked markers provide a valuable resource for marker assisted selection of FOV resistance during the breeding process.
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Wang, C., Ulloa, M., Duong, T., Robert, P. 2017. Analysis of transgressive nematode resistance in tetraploid cotton reveals complex interactions in chromosome 11 regions. Frontiers in Plant Science. 8:1979.
Abdullaev, A.A., Salakhutdinov, I.B., Egamberdiev, S.S., Khurshut, E.E., Rizaeva, S.M., Ulloa, M., Abdurakhmonov, I.Y. 2017. Genetic diversity, linkage disequilibrium, and association mapping analyses of gossypium barbadense l. germplasm and cultivars. PLoS One. 12(11):1-30. doi:10.1371/pone.0188125.
Chen, J., Burke, J.J., Xin, Z. 2018. Chlorophyll fluorescence analysis revealed essential roles of FtsH 11 protease in regulation of the adaptive responses of photosynthetic systems to high temperature. Biomed Central (BMC) Plant Biology. doi:10.1186/s12870-018-1228-2.
Zhu, X., Sun, L., Kuppu, S., Hu, R., Mishra, N., Smith, J., Esmaeili, N., Herath, M., Gore, M., Payton, P.R., Shen, G., Zhang, H. 2018. The yield difference between wild-type cotton and transgenic cotton that expresses IPT depends on when water-deficit stress is applied. Nature Scientific Reports. 8:2538.
Zurweller, B., Rowland, D., Tillman, B., Payton, P.R., Migliaccio, K., Wright, D., Erickson, J. 2018. Assessing above-and below-ground traits of disparate peanut genotypes for determining adaptability to soil hydrologic conditions. Field Crops Research. 219:98–105.
Witt, T.W., Ulloa, M., Pelletier, M.G., Mendu, V., Ritchie, G.L. 2018. Exploring ethyl methaneSulfonate (EMS) treated cotton (Gossypium hirsutum L.) to improve drought tolerance. Euphytica. 214:123.
Adams, R.P., Ulloa, M., Witt, T.W., Burke, J.J. 2018. Comparison of hydrocarbon yields in four cotton accessions: regular vs. limited (induced dryland) irrigation. Phytologia. 100(1):6-11.
Adams, R., Frelichowski, J.E., Hinze, L.L., Ulloa, M. 2018. Survey of cotton (Gossypium sp.) for non-polar, extractable hydrocarbons for use as petrochemicals and liquid fuels. Phytologia. 100(1):37-44.
Wang, C., Ulloa, M., Duong, T., Robert, P. 2018. Quantitative trait loci mapping of multiple independent loci for resistance to fusarium oxysporum f. sp. vasinfectum races 1 and 4 in an interspecific cotton population. Journal of Phytopathology. 108:759-767.
Kushanov, F., Buriev, Z.T., Shermatov, S.E., Turaev, O.S., Norov, T., Pepper, A.E., Saha, S., Ulloa, M., Yu, J., Jenkins, J.N., Abdukarimov, A., Abdurakhmonov, I.Y. 2017. QTL mapping for flowering-time and photoperiod insensitivity of wild cotton Gossypium darwinii Watt. PLoS One. https://doi.org/10.1371/journal.pone.0186240.
Burke, J.J., Ulloa, M. 2017. Stress responses of commercial cotton cultivars to reduced irrigation at flowering and maximization of yields under sub-optimal subsurface drip irrigation. Journal of Cotton Science. 21:290241.
Adams, R.P., TeBeest, A.K., Ulloa, M., Witt, T.W., Burke, J.J., Frelichowski, J.E., Hinze, L.L. 2017. Comparison of hydrocarbon yields in cotton from field grown vs. greenhouse grown plants. Phytologia. 99(3):200-207.
Xin, Z., Chen, J., Jiao, Y., Gladman, N., Hayes, C.M., Burow, G.B., Emendack, Y., Burke, J.J. 2018. Registration of BTx623ms8 - a new and easily identifiable nuclear male sterile mutant in sorghum. Journal of Plant Registrations. https://doi.org/10.3198/jpr2017.09.0063crgs.
Wang, M.L., Xin, Z., Burow, G.B., Chen, J., Vankus, P.J., Pinnow, D.L., Tonnis, B.D., Cuevas, H.E., Yu, J. 2017. Evaluation of sweet sorghum accessions for seedling cold tolerance using both lab and field cold germination test. Journal of Agricultural Science and Botany. 1(1):1-8.
Jiao, Y., Burow, G.B., Gladman, N., Acosta Martinez, V., Chen, J., Burke, J.J., Ware, D., Xin, Z. 2018. Efficient identification of causal mutations through sequencing of bulked F2 from two allelic bloomless mutants. Frontiers in Plant Science. doi.org/10.3389/fpls.2017.02267.
Burke, J.J., Emendack, Y., Hayes, C.M., Chen, J. 2018. Genetic diversity in the environmental conditioning of two sorghum (Sorghum bicolor L.) hybrids. American Journal of Plant Sciences. 9:817-831.
Gitz, D.C., Baker, J.T., Echevarria-Laza, H., Payton, P.R., Mahan, J.R., Lascano, R.J. 2017. CO2 and chamber effects on epidermal development in field grown peanut (Arachis hypogaea L.). American Journal of Plant Sciences. 8:349-362.