2012 Annual Report
1a.Objectives (from AD-416):
Objective 1: Improve crop stress tolerance by determining, and developing technology to ameliorate, metabolic limitations by biological processes most sensitive to abiotic stress factors common in arid southwestern U.S. cropping systems. [NP 301, C4, PS 4A]
Sub-objective 1a: Improve crop tolerance to heat stress by devising approaches to improve the ability of Rubisco activase to activate Rubisco at leaf temperatures above the optimum for photosynthesis.
Sub-objective 1b: Develop new approaches to improve chilling tolerance by identifying metabolic mechanisms that limit biochemical/physiological processes most sensitive to chilling temperatures.
Objective 2: Develop improved germplasm resources for abiotic stress resistance and fiber quality in Gossypium barbadense and G. hirsutum utilizing and integrating classical and biotechnology-based methodologies. [NP 301, C3, PS 3C]
Sub-objective 2a: Develop improved germplasm resources for abiotic stress resistance and fiber quality in G. hirsutum utilizing and integrating classical and biotechnology-based methodologies.
Sub-objective 2b: Develop improved germplasm resources for abiotic stress resistance and fiber quality in G. barbadense utilizing and integrating classical and biotechnology-based methodologies.
1b.Approach (from AD-416):
The genetic potential of cotton, and crop species in general, for producing of abundant high quality economic yield is severely compromised by specific abiotic stresses, like temperature and water, that are endemic to the arid-southwestern U.S. In addition, early season chilling stress impacts yield by stunting growth and delaying planting date. The negative impact of these stresses is likely to intensify as the global climate changes and water availability becomes more limiting. The mission of this research unit is to use a multidisciplinary approach to improve stress tolerance and yield in cotton. Fundamental approaches that integrate physiology, biochemistry, biotechnology and classical plant breeding will be used to identify and modify the response of cotton to environmental stress. Through this research, new sources of cotton germplasm will be developed with improved stress tolerance, as well as higher fiber quality and enhanced yield. The basic biochemical strategies developed for improving stress tolerance in cotton will have broad application to the variety of crop plants cultivated in arid environments.
This report documents progress for Project Number 5347-21000-011-00D, which started in April 2010. Progress on this project focuses on Problem 3C, the need for enhanced germplasm and improved crops that are tolerant to abiotic stresses and have superior agronomic characteristics, and Problem 4A, the need for leveraging knowledge of fundamental biological processes in model plant systems to enhance crop productivity. Under Sub-objective 1b, we continued to make significant progress in the identification and cloning of omega-3 fatty acid desaturase (FAD) genes from both diploid progenitors and commercial tetraploid species of cotton. To date, we have identified five different FAD genes that are each present in the genome of the diploid species. Some of these genes, however, were present as multiple copies in the genome and, as such, we are performing a detailed DNA sequence analysis to reveal the exact nature of these duplicated genes. Under Sub-objective 2a, we successfully transformed cotton callus tissue with a FAD gene derived from Brassica napus (canola), and regenerated mature plants. All of the plants examined to date, however, were sterile. Given the labor-intensive nature of this work, we have recently established a collaborative project with the University of North Texas to further explore the role of FADs in conferring temperature stress tolerance in cotton. Under Sub-objective 2a, we made significant progress towards examining levels of molecular diversity in a diverse collection of upland cotton lines. Collectively, the 384 lines included in this collection form the genetic foundation of upland cotton breeding programs. In collaboration with North Carolina State University, we have completed genotyping these lines with 120 genetic markers. Currently, these marker data are being analyzed with population genetics methods to reveal patterns of genetic structure and diversity. Under Sub-objective 2b, we continued to make significant progress in understanding the biological mechanisms responsible for the tolerance and sensitivity of pima cotton to heat and drought stress. Using a high-throughput phenotyping platform and hand-held instruments, we established a temporal pattern for the onset of heat and drought stress in sensitive and tolerant pima cotton cultivars. Measurements conducted in the field under natural conditions of heat and drought showed that plants recovered overnight from drought and heat stress, but that leaf temperatures increased and stomatal conductance, photosynthesis and relative water content decreased as the day progressed. These changes occurred earlier in the day and were of greater magnitude for the more sensitive cultivars. Taken together, these results demonstrated that stomatal limitations to photosynthesis occur earlier in the day for drought-sensitive compared with drought tolerant cultivars, causing higher canopy temperatures and an earlier incidence of the metabolic limitations associated with heat stress.
Factors inhibiting photosynthesis under heat and drought stress. Heat and drought stress reduce crop yield by inhibiting photosynthesis. In collaboration with a scientist at University of Arizona, ARS scientists in Maricopa, AZ, used high-throughput phenotyping methods to determine which photosynthesis related mechanisms in pima cotton are most sensitive to a combination of heat and drought stress in the field. The data showed that pima cotton varieties differed in their response to drought and that the more drought sensitive varieties exhibited greater susceptibility to heat stress. The biochemical basis for this increased susceptibility to heat stress was identified as a metabolic limitation caused by inactivation of the carbon dioxide fixing enzyme Rubisco. The insights gained from the high-throughput methods developed in this study can be used to guide breeding and selection for more heat and drought tolerant cotton.
Development of community resources for cotton genetic improvement. There are a very limited number of publically available genetic and genomic resources for transferring the superior fiber qualities of pima cotton to higher yielding upland cotton. In collaboration with scientists at Monsanto Company and New Mexico State University, ARS scientists in New Orleans, LA, College Station, TX, and Maricopa, AZ, registered an interspecific cotton recombinant inbred mapping population with the National Plant Germplasm System. Seed packets for the population were deposited at two ARS germplasm centers, and associated phenotypic and genotypic information submitted to the public cotton genomics database, CottonGen. Registering this mapping population has increased its accessibility to the global cotton community, thus better facilitating the genetic improvement of fiber quality in upland cotton.
Atomic structure of a key enzyme of photosynthesis. Heat stress reduces crop yield by inhibiting a key enzyme of photosynthesis called Rubisco activase. In collaboration with colleagues at Arizona State University, ARS scientists in Maricopa, AZ, used X-ray bombardment of protein crystals to determine the three-dimensional structure of Rubisco activase. The information about the structure of this enzyme is being used to gain insights into how the protein can be modified to improve its tolerance to heat. Based on this information, new, more heat tolerant germplasm can be developed to ensure that the next generation of crops will be more tolerant to heat stress.
Gore, M.A., Percy, R.G., Zhang, J., Fang, D.D., Cantrell, R.G. 2012. Registration of the TM-1/NM24016 cotton recombinant inbred mapping population. Journal of Plant Registrations. 6(1). 1:4.
Chia, J., Song, C., Bradbury, P., Costich, D., De Leon, N., Doebley, J., Elshire, R., Gaut, B., Geller, L., Glaubitz, J., Gore, M.A., Guill, K., Holland, J., Hufford, M., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J.A., Prasanna, B., Phyajarvi, T., Rong, T., Sekhon, R., Sun, Q., Tenaillon, M., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S.M., Ross-Ibarra, J., McMullen, M.D., Buckler IV, E.S., Zhang, G., Xu, Y., Ware, D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. 40:803-807. DOI: 10.1038/ng.2313.
Do Carmo Silva, A., Gore, M.A., Andrade-Sanchez, P., French, A.N., Hunsaker, D.J., Salvucci, M.E. 2012. Decreased CO2 availability and inactivation of Rubisco limit photosynthesis in cotton plants under heat and drought stress in the field. Environmental and Experimental Botany. 83:1-11.
Do Carmo Silva, A., Salvucci, M.E., 2011. The activity of Rubisco's molecular chaperone, Rubisco activase, in leaf extracts. Photosynthesis Research. 108:143-155.
Henderson, J.N., Kuriata, A., Fromme, R., Salvucci, M.E., Watcher, R.M., 2011. Atomic resolution x-ray structure of the substrate recognition domain of higher plant rubisco activase. Journal of Biological Chemistry. 286:35683-35688.
Lipka, A.E., Feng, T., Wang, Q., Peiffer, J., Li, M., Bradbury, P., Gore, M.A., Buckler IV, E.S., Zhang, Z. 2012. GAPIT: genome association and prediction integrated tool. Bioinformatics. 28(18):2397-2399.
White, J.W., Andrade-Sanchez, P., Gore, M.A., Bronson, K.F., Coffelt, T.A., Conley, M.M., Feldman, K.A., French, A.N., Heun, J.T., Hunsaker, D.J., Jenks, M.A., Kimball, B.A., Roth, R., Strand, R.J., Thorp, K.R., Wall, G.W., Wang, G. 2012. Field-based phenomics for plant genetics research. Field Crops Research. 133:101-112.
Scafaro, A.P., Yamori, W., Do Carmo Silva, A., Salvucci, M.E., Von Caemmerer, S., Atwell, B.J., 2012. Rubisco activity is associated with photosynthetic thermotolerance in a wild rice (Oryza meridionalis). Physiologia Plantarum, 146:99-109.
Do Carmo Silva, A., Salvucci, M.E., 2012. The temperature response of CO2 assimilation, photochemical activities and rubisco activation in camelina sativa, a potential bioenergy crop with limited capacity for acclimation to heat stress. Planta, DOI:10.1007/s00425-012-1691-1.