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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Research Project #424775

Research Project: Enhancing Plant Resistance to Water-Deficit and Thermal Stresses in Economically Important Crops

Location: Plant Stress and Germplasm Development Research

2015 Annual Report

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).

Progress Report
Cotton lines from the USDA germplasm collection were evaluated for yield enhancements under mid- and late-season water-deficit stresses compared with commercial cotton varieties. A line was identified that exhibited better yields than the commercial checks in the study. Additional studies are underway to confirm the yield advantage observed and to further evaluate additional lines from the USDA Cotton Collection. The differential onset of water stress in pre- and post-flowering drought tolerant sorghums was identified via metabolite changes. The research was completed and manuscript published. (See Publication.) More than 300 Upland entries/germplasm were evaluated under a Fusarium wilt (FOV) race 4 infested field in California. These entries represent a wide range and diverse genetic backgrounds of germplasm material. We continue to follow our established breeding scheme or strategy for identifying, selecting, and developing FOV race 4 resistant/tolerant germplasm. Selected breeding lines were examined and targeted for the introgression of FOV race 4 resistance/tolerance genes from entries such as Pima-S6, Upland TM-1, and Acala FBCX2 (original pedigree-parental line of Acala NemX). In addition, after evaluation for FOV race 4 tolerance/response-infection of more than 200 entries from the Cotton Collection (USDA-ARS) under field conditions in 2014, around 24 Upland entries were identified with good levels of tolerance. These entries were self-pollinated for seed increase, and plants were evaluated from these entries in 2015 for additional selection to FOV race 4 tolerance/resistance. Moreover, progeny F1 and parents from different crosses-combinations of approximately 5 entries used as parents of the above 24 entries were also evaluated for tolerance/response-infection. Results from research studies of evaluations of different crosses-combinations for resistance to FOV race 4 indicated activity of resistance gene(s) varied within progeny. DNA isolation has been done for more than 1,300 single plants/family lines from leaf tissue for molecular marker-evaluations. Forty previously identified molecular markers associated to FOV races 1 and 4, and root-knot nematode resistance were assayed on cotton chromosome substitution lines to validate chromosomes gene locations of these diseases. The previously developed GIS-based time surface visualization system has been incorporated into an open source software system (R). The new platform provides a web-based interface that allows other users to access the platform. A 10-year period of weather and plant data from 3 locations has been added to the system. Climate data from the US and Australian cotton regions is currently being assemble for analysis. Additional efforts this year will focus on the application of pattern recognition for cross-year and cross-region comparisons. The subobjectives of 1C and 2C are to identify 1) the range of heat stress tolerance in corn germplasm and 2) the major QTLs and/or genomic loci associated with heat tolerance/sensitive traits in maize. We have just completed 2-years’ field-based evaluation for heat tolerance traits of 537 maize accessions. The 2-years’ field data will be compiled. The genotype data of these maize accessions will be assembled into the same version (currently in different release versions) by our collaborators. Genome-wide association analysis will be performed to identify genomic loci that are associated with the observed heat tolerance traits. In addition, several crosses have been made between maize lines of distinct heat tolerant traits to produce F1 seeds. F2 seeds of these crosses will be produced during the winter. The F2/F3 populations will be used for QTL mapping of major heat tolerance traits. We also initiated a field-based study to determine and distinguish if a particular abiotic stress tolerance/sensitive trait is caused by high temperature extremes or a combination of drought and heat stresses. We evaluated 537 maize accessions for a range of stress phenotypes under either well-watered or deficit irrigation condition in 2015 field study. The responses of maize plants to heat stress and combined heat and drought stresses were visually evaluated 7-10 days after each major heat wave event had occurred. Major stress sensitive/tolerant traits of maize plants were recorded. Preliminary field observation indicated diverse responses of maize accession to these stresses: Tolerance to both stresses, Sensitive to both stresses; Tolerance/Sensitive only to heat stress; Tolerance/Sensitive only to drought stress, etc. The responses of 537 maize accessions to the combined drought/heat stresses will be reevaluated in 2016 season. Maize lines with specific stress tolerant traits in both years’ studies will be further evaluated under controlled environments to confirm stress tolerance/sensitive of those accessions. Crosses between selected parents will be made in 2017 season to generate mapping populations for genetic studies. Furthermore, we also evaluated one sorghum diversity panels and two maize RIL populations for heat tolerance traits in 2015 field study. The subobjective of 2Db is to functionally characterize if crop ftsh11 protease homologs plays a role in the maintenance of chloroplast thermostability and photosynthesis at elevated temperatures. We have cloned 3 full-length cDNAs of atFtsH11 homologous genes from three plant species. These cDNA clones have been introduced into the binary vector respectively. The resulting constructs will be introduced into the Arabidopsis ftsh11 mutant via Agrobacterium-mediate transformation approach. Relational databases for cotton and peanut transcriptome and proteome data are being developed. The finished product will be available to the public and allow for comparative searches for all transcriptome and proteome experiments in cotton and peanut. Additionally, all data and sequence information will be freely available for download. Currently, the first draft of the runner and Valencia peanut transcriptomes are being annotated for the database. A cotton fiber transcriptome and root drought transcriptome are also being annotated.

1. Heat tolerance developed in pollen. Pollen is the most heat sensitive organ in higher plants. ARS researchers at the USDA-ARS Cropping Systems Research Laboratory in Lubbock, TX have inserted and expressed in pollen a gene known to contribute to vegetative heat tolerance. Laboratory, greenhouse and field studies confirmed improved heat tolerance in cotton pollen expressing the gene. This research serves as a foundation to improve reproductive heat tolerance of crops to better cope with drought and global warming.

2. Visual indicators of genes controlling cotton fiber development. Environmental stresses, such as drought, high temperature and combination of both, not only reduce the overall growth of cotton plants, but also greatly decrease cotton lint yield and fiber quality. The impact of environmental stresses on fiber development is poorly understood due to technical difficulties associated with the study of developing fiber tissues and lack of genetic materials to study fiber development. ARS researchers at the USDA-ARS Cropping Systems Research Laboratory in Lubbock, TX have inserted reporter genes attached to fiber developmental gene switches to allow scientists to see when specific developmental genes are turned on. These newly developed materials provide new molecular tools for studying the effects of abiotic stresses on fiber development and may be used in study of cotton fiber development genes and eventually in the genetic manipulation of fiber quality.

3. New pima cotton germplasm resistance to fusarium wilt race 4. Over the past 12 years, the race 4 of the fungus causing Fusarium wilt (FOV) disease has impacted cotton production in California. Cotton varieties resistant to FOV race 4 have been effective in controlling yield losses, and an economical approach for dealing with this fungal disease. To continue providing germplasm with good levels of resistance to FOV race 4 to cotton researchers and breeders, ARS researchers in Texas developed and jointly released in collaboration with researchers at the University of California five Pima cotton germplasm lines (SJ-FR05, SJ-FR06, SJ-FR07, SJ-FR08, and SJ-FR09) with resistance to FOV race 4 combined with good yield and fiber quality properties. The SJ-FR05-FR09 lines provide needed alternative sources of FOV race 4 resistance to cotton breeders, and they should be helpful to speed efforts to broaden the genetic base, which is critical to maintaining a healthy Pima cotton industry in the San Joaquin Valley of California.

4. Creation of open source visualization tool. Visualization of large data sets of plant and climate measurements has been difficult. Initial efforts by ARS researchers at the USDA Cropping Systems Research Laboratory in Lubbock, TX demonstrated the creation of climate/plant data in the form of time surfaces using the ARCGIS software platform. This year ARS researchers developed a custom visualization platform in an open source “R” environment. This tool now has web-based functionality and can be freely distributed.

Review Publications
Burke, J.J., Payton, P.R., Chen, J., Xin, Z., Burow, G.B., Hayes, C.M. 2015. Metabolic responses of two contrasting sorghums to water-deficit stress. Crop Science. 55:344-353.
Yu, J., Ulloa, M., Hoffman, S.M., Kohel, R.J., Pepper, A.E., Fang, D.D., Percy, R.G., Burke, J.J. 2014. Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. x G. barbadense L.) RIL population. Molecular Genetics and Genomics. 289:1347-1367.
Wubben, M., Callahan, F.E., Velten, J.P., Burke, J.J., Jenkins, J.N. 2015. Overexpression of MIC-3 indicates a direct role for the MIC gene family in mediating Upland cotton (Gossypium hirsutum) resistance to root-knot nematode (Meloidogyne incognita). Theoretical and Applied Genetics. 128:199-209.
Chen, J., Burke, J.J. 2015. Developing fiber specific promoter-reporter transgenic lines to study the effect of abiotic stresses on fiber development in cotton. PLoS One. 10(6):1-17.
Hulse-Kemp, A.M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D.D., Frelichowski, J.E., Giband, M., Hague, S., Hinze, L.L., Kochan, K., Riggs, R., Scheffler, J.A., Udall, J.A., Ulloa, M., Wang, S., Zhu, Q., Bag, S.K., Bhardwaj, A., Burke, J.J., Byers, R.L., Claverie, M., Gore, M.A., Harker, D.B., Islam, M.S., Jenkins, J.N., Jones, D.C., Lacape, J., Llewellyn, D.J., Percy, R.G., Pepper, A.E., Poland, J.A., Rai, K., Sawant, S.V., Singh, S., Spriggs, A., Taylor, J.M., Wang, F., Yourstone, S.M., Zheng, X., Lawley, C.T., Ganal, M.W., Van Deynze, A., Wilson, L.W., Stelly, D.M. 2015. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.). Genes, Genomes, Genetics. 5:1187-1209. doi:10.1534/g3.115.018416.
Abdullaev, A.A., Salakhutdinov, I.B., Egamberdiev, S.S., Kuryazov, Z., Glukhova, L.G., Adilova, A.T., Rizaeva, S.M., Ulloa, M., Abdurakhmonov, I.Y. 2015. Analyses of Fusarium wilt race 3 resistance in upland cotton (Gossypium hirsutum L.). Genetica. 143(3):385-392.
Brauer, D.K., Baumhardt, R.L., Gitz, D.C., Gowda, P., Mahan, J.R. 2015. Characterization of trends in reservoir storage, streamflow and precipitation in the Canadian River Watershed in New Mexico and Texas. Lake and Reservoir Management. 31:64-79.
Goebel, T.S., Lascano, R.J., Payton, P.R., Mahan, J.R. 2015. Rainwater use by irrigated cotton measured with stable isotopes of water. Agricultural Water Management. 158:17-25.
Gitz, D.C., Baker, J.T., Mahan, J.R. 2015. Evaluation of a metabolic cotton seedling emergence model. American Journal of Plant Sciences. 6:1727-1733.
Burke, J.J., Chen, J. 2015. Enhancement of reproductive heat tolerance in plants. PLoS One. 10(4):1-23.
Mahan, J.R., Burke, J.J. 2015. Active management of plant canopy temperature as a tool for modifying plant metabolic activity. American Journal of Plant Sciences. 6:249-259.