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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

2016 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 with improved drought tolerance identified: A diverse core-set of cotton lines from the USDA germplasm collection were identified with good yield under mid- and late-season water-deficit stresses when they were compared with commercial cotton varieties. Some of these lines exhibited better yields than the commercial checks in the study. Replicated studies are underway using two irrigation regimes to confirm the yield advantage observed under water stress conditions and to further evaluate additional morphological and fiber quality traits of these lines. (Objective 1) Cotton selection for improved resistance to Fusarium wilt (FOV) race 4: From more than 507 Upland entries/germplasm evaluated under a Fusarium wilt (FOV) race 4 infested field in California, 15% of these entries were selected, and seed was increased for additional FOV4 field and greenhouse evaluations. In addition, 142 crosses (F1’s progeny) were created from some these accessions and planted under FOV4 pressure in the field and greenhouse in 2016 for selection and further evaluation. These entries represent a wide range and diverse genetic backgrounds of germplasm material. (Objective 3) Peanut Transcriptomic and proteomic website developed: Working with colleagues at the Center for Biotechnology and Genomics at Texas Tech University a publically available website ( for peanut transcriptomic and proteome data was developed. All data are from experiments generated under this project (Objective 2, Sub-objective 2B). The website allows download of all raw and processed data, protein and nucleic acid BLAST search, and gene expression analysis. (Objective 2) Cotton pollen sensitivity to low humidity can limit natural outcrossing: Adventitious presence is defined as the unintended presence of unwanted biotechnology traits in a seed lot. With the majority of U.S. commercial cotton cultivars containing proprietary technologies, todays’ cotton breeders must be careful to ensure that the company technologies do not find their way into public cultivars under development. Our research evaluated the genetic diversity in the ability of mature cotton pollen to move to neighboring cotton plants. Six cotton cultivars were studied because of their identified differences in pollen humidity sensitivity. Differences in outcrossing of 5 to 15% were observed under both irrigated and dryland production systems. Year to year variability was larger than genetic differences within a year. The lowest levels of outcrossing were observed for cotton cultivars having pollen with the greatest sensitivity to low humidity. The results suggest that the pollen desiccation in response to low humidity could be used to reduce the amount of cotton outcrossing in the natural environment. Additionally, cultivars with pollen resistant to drying out under low humidity could be used to enhance outcrossing in the development of hybrid cotton. (Objective 1) Controlled environment studies to study the mechanism of abiotic stress acclimation: Three primed acclimation experiments were conducted in a glasshouse environment at the USDA-ARS Cropping Systems Research Laboratory in Lubbock. Experiments 1-2 comprised five selected peanut genotypes (two runner types and three Spanish types) that were subjected to water deficit stress from sowing through the initiation of flowering. For priming, water deficit was maintained at approximately 40% volumetric water content as determined by lysimeters. Pots were irrigated twice weekly to maintain a constant water deficit. Leaf gas-exchange was measured before and after irrigation events to physiologically characterize the water-deficit stress and plant growth measurements were made weekly. At anthsesis, primed plant pots were irrigated to field capacity and pots were maintained at 80-100% VWC for three weeks. Subsequently, pots (primed and non-primed controls) were subjected to a slow-onset water deficit stress (approximately 10% daily decline in VWC) and leaf gas-exchange was measured to characterize the physiological response. After 10 days of water deficit stress, plants were re-watered and the response to irrigation and recovery was monitored by leaf gas-exchange for one week. For all genotypes, priming resulted in a decreased growth rate from sowing to anthesis that was correlated with lower net CO2 assimilation rates and transpiration rates. Following initiation of full irrigation, growth rates of the acclimated plants were similar to control plants. Primed plants showed slower response to the subsequent water deficit stress and had higher photosynthsis rates compared to non-primed plants at the same soil VWC, suggesting that the priming was successful. Primed plants also showed increased rates of recovery of photosynthesis following the return to full irrigation. After 2 weeks, all plants, primed and non-primed, showed similar rates of growth, photosynthesis, and water use as controls. Leaf and root samples were collected during key time-points of priming, the slow-onset water deficit, and recovery phases of the experiments. These samples are currently being processed for RNA isolation for transcriptomic response to priming and water deficit stress. Data was analyzed and presented in two Master’s thesis reports. Manuscript related to these experiments is under preparation. Experiment 3 utilized 4 wild accessions, 2 isolines, and 4 cultivars of cotton selected for drought tolerance in the field (Collaboration with J. Dever, Texas A&M). Experiments were conducted to examine the interaction between heat and drought stress and the impact of elevated growth temperature on the acclimation response. Briefly, two growth conditions were established: control (TC=28/18°C day/night) and elevated (ET=34/22°C day/night). Plants were grown under each temperature regime and then subjected to modeled heatwave (+6/4°C day/night) for 4 days. Leaf gas-exchange was monitored during and after return to the growth temperature, as well as plant growth and water use. At anthesis, plants were subjected to an additional heatwave event in addition to moderate water deficit stress (approximately 50% soil gwc) for 4 days. Again, leaf gas-exchange was monitored during and after the stress event. Leaf and root samples were collected at each timepoint during the stress and recovery periods for RNASeq transcriptome analysis. Data are currently being analyzed. (Objective 1) Identification of the range of heat stress tolerance in corn germplasm and the major QTLs and/or genomic loci associated with heat tolerance/sensitive traits in maize: We have just completed the 3rd year field-based evaluation for heat tolerance traits of 537 maize accessions. The genotype data of these maize accessions of different versions have been assembled into the current V3 version by our collaborators. A preliminary Genome-Wide Association Study (GWAS) analysis for the yearly-summary rating for LF phenotypes was performed and the GWAS outputs were discussed with collaborators at the Maize Genomic Meeting. The consensus formed was to use individual phenotyping ratings instead of yearly summaries when performing GWAS analysis. Additional variables that may influence ratings such as planting to flower date, weather data, planting date, and field locations will be incorporated into the GWAS analysis to identify genomic loci that are associated with the observed heat tolerance traits. This year’s phenotyping data will be compiled together with the 2-previouse years’ data and send to collaborators along with data for other variables. In addition, F2 seeds of several crosses made with maize lines of distinct heat tolerant traits were planted in 2016 field. Phenotype of F2 plants will be used for QTL mapping of major heat tolerance traits. (Objective 1) The subobjective of 2D is to functionally characterize if crop ftsh11 protease homologs plays roles in the maintenance of chloroplast thermostability and photosynthesis at elevated temperatures. We have introduced 3 full-length cDNAs of at FtsH11 into the binary vector respectively and transformed the resulting constructs into the Arabidopsis ftsh11 mutant via Agrobacterium-mediate transformation approach. The transformants containing the crop homologs are being identified. The heat tolerance of transformant will be performed in several thermotolerance assays. (Objective 2)

1. Genetic diversity in cotton pollen outcrossing. Pollen is the most heat and desiccation sensitive organ in higher plants. ARS researchers at the USDA-ARS Cropping Systems Research Laboratory in Lubbock, Texas have identified genetic diversity for natural outcrossing associated with pollen stress sensitivities. Laboratory, greenhouse and field studies confirmed that more desiccation tolerant cotton pollen outcrosses more frequently than stress sensitive pollen. This research serves as a foundation to regulate genetic outcrossing through the basic characteristic of the pollen.

2. Cotton nematode and fungal disease resistance traits identified. Discovering nematode and disease resistance genes in the cotton genome is essential for speeding the development of cotton resistant varieties with improved yields. Using cotton chromosome substitution (CS) entries that carried chromosome segments from other cotton species (G. barbadense or G. tomentosum), ARS researchers and University cooperators confirmed the location of root-knot nematode and fusarium wilt (FOV races 1 and 4) resistance genes. Analyses validated important regions on cotton chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes. This study provides a foundation for effective plant breeding of nematode and disease resistance in cotton.

Review Publications
Ulloa, M., Hutmacher, R., Percy, R.G., Wright, S., Burke, J.J. 2015. Release of Pima SJ-FR05, Pima SJ-FR06, Pima SJ-FR07, Pima SJ-FR08, and Pima SJ-FR09 Pima cotton with improved FOV4 resistance, and good lint yield and fiber quality. Germplasm Release. p. 2.
Ulloa, M., Wang, C., Saha, S., Hutmacher, R.B., Stelly, D.M., Jenkins, J.N., Roberts, P. 2016. Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species. Genetica. 144(2):167-179.
Ulloa, M., Hutmacher, R.B., Percy, R.G., Wright, S.D., Burke, J.J. 2016. Registration of five pima cotton germplasm lines (SJ-FR05 - FR09) with improved resistance to fusarium wilt race 4 and good lint yield and fiber quality. Journal of Plant Registrations. 10:154-158.
Wang, C., Ulloa, M., Shi, X., Yuan, X., Saski, C., Yu, J., Roberts, P. 2015. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens. Frontiers in Plant Science. 6:791.
Shapulatov, U.M., Buriev, Z.T., Ulloa, M., Saha, S., Devor, E.J., Ayubov, M.S., Norov, T.M., Shermatov, S.E., Abdukarimov, A., Jenkins, J.N., Abdurakhmonov, I.Y. 2016. Characterization of small RNAs and their targets of Fusarium oxysporum infected and non-infected cotton seedlings. Plant Molecular Biology Reporter. 34:698-707.
Burke, J.J. 2016. Genetic Diversity of Natural Crossing in Cotton. Crop Science. 56:1059-1066.