Department of Botany & Plant Sciences

 

Timothy J. Close

Professor of Genetics and Geneticist (Ph.D., 1982, University of California, Davis)
Office: 4157 Batchelor Hall
Phone: (951) 827-3318
Fax: (951) 827-4437
Email: timothy.close@ucr.edu

 

 

Genetics of Environmental Stress Tolerance

The goals in my laboratory are to:

1. Create and utilize genomic resources for research and teaching, and conduct educational outreach in crop plant genomics
2. Promote environmental tolerance in plants through genetics and efficient cultural and post-harvest practices
3. Develop biomarkers including SNPs and immunological assays from genomic studies of plant traits
4. Determine the properties of plant stress proteins to understand mechanisms

My group is active in barley, cowpea (Vigna unguiculata), Citrus, cassava, and Musa genomics. This includes library production, EST assemblies, content definition for microrarrays, software (HarvEST) for EST database browsing, genetic and physical mapping, and genome sequencing. We have conducted microarray-based transcriptome analyses of abiotic stresses in rice and barley, and several traits relevant to citrus such as easy-peeling, the effect of storage on flavor, citrus tristeza virus response. We have developed high-throughput SNP genotyping resources for barley and cowpea and applied them to the localization of a number of trait determinants and to the anchoring of physical maps to genetic maps. Research is currently funded by grants from the USDA/CSREES Agriculture and Food Research Initiative, University of California Agriculture Experiment Station and the CGIAR Generation Challenge Program.

Research goals in environmental stress are unified by the question, "What are the fundamental biochemical processes within which there exists genetic diversity related to tolerance of low temperature, drought, and salinity and resistance to pests and pathogens?" One example is the family of proteins known as "dehydrins" (a.k.a. LEAD11). Dehydrins are "intrinsically unstructured proteins" that are produced in plants in response to low non-freezing temperatures or any environmental influence with a dehydration component, including seed development, drought stress, freeze-thaw, and osmotic stress. We found that dehydrins associate, through an amphipathic alpha helical region, with unilamellar vesicles containing anionic phospholipids (Koag et al. 2003, Koag et al. 2009). We demonstrated in the 1990's by immunocytochemical methods that plant dehydrins can be present in the nucleus, and are associated with endomembrane-rich areas of the cytoplasm. We found 13 dehydrin (Dhn) genes in barley, dispersed at eight genetic map locations on five chromosomes. Some of these locations, as well as Dhn loci in maize and other plants, seem to coincide with QTL for low temperature or drought tolerance. The Vigna unguiculata (cowpea) Dhn1 gene, associated with chilling tolerance during seedling emergence, is one such example (Ismail et al. 1999).

Software and databases from our projects:

HarvEST: EST database viewers for barley, Brachypodium, citrus, coffee, cowpea, Musa, rice, soybean and wheat. Graphical user interface functions include comparative genome views for barley and cowpea, details of microarray probe sets and enhanced annotations for Affymetrix genome arrays for barley, citrus, rice, soybean and wheat.
(Windows versions) (online versions)

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. Upload a FASTA file and then receive an output of overlapping 22-mers to create templates for synthesis of labeled 36-mers. (online access to OligoSpawn) (barley overgo probes generate by OligoSpawn)

Barley and Cowpea Physical Maps. The barley genome is 5300 Mb total size. The majority of genes are in 1700 Mb of BAC contigs contained in the barley physical map. The cowpea genome is 600 Mb total size. A 10X depth of coverage physical map of the entire cowpea genome.

Some Representative Publications:

Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ. 2009. A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc. Natl. Acad. Sci. (USA) 106: 19159-18164.

Koag M-C, Wilkens S, Fenton RD, Resnik J, Vo E, Close TJ. 2009. The K-segment of maize DHN1 mediates binding to anionic phospholipid vesicles and concommitant structural changes. Plant Physiology 150: 1503-1514.

Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N. 2009. International Barley Sequencing Consortium (IBSC) - at the threshold of efficient access to the barley genome. Plant Physiology 149: 142-147.

Wu Y, Bhat PR, Close TJ, Lonardi S. 2008. Efficient and accurate constructioin of genetic linkage maps from the minimum spanning tree of a graph. PLOS Genetics 4: e000212.

Wu Y, Liu L, Close TJ, Lonardi S. 2008. Deconvoluting BAC-gene relationships using a physical map. Journal of Bioinformatics & Computational Biology 6: 603-622.

Walia H, Wilson C, Condamine P, Wahid A, Cui X, Close TJ. 2006. Expression analysis of barley (Hordeum vulgare L.) during salinity stress. Functional and Integrative Genomics 6:143-156.

Zheng J, Svensson JT, Madishetty K, Close TJ, Jiang T, Lonardi S. 2006. OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BioMed Central Bioinformatics 7:7.

Close TJ. 2005. The barley microarray: a community vision and application to abiotic stress. Czech Journal of Genetics and Plant Breeding 41:144-152.

Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ. 2005. Comparative transcriptional profiling of two contrasting rice (Oryza sativa L.) genotypes under salinity stress during vegetative growth stage. Plant Physiology 139: 822-835.

Cui X., Xu J, Asghar R, Condamine P, Svensson JT, Wanamaker S, Stein N, Roose M, Close TJ. 2005. Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit. Bioinformatics 21: 3852-3858.

Rodriguez EM, Svensson JT, Malatrasi M, Choi DW, Close TJ. 2005. Barley Dhn13 encodes a KS-type dehydrin with constitutive and stress responsive expression. Theoretical and Applied Genetics 110:852-858.

Close TJ, Wanamaker S, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. 2004. A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiology 134: 960-968.

Koag MC, Fenton RD, Wilkens S, Close TJ. 2003. The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity. Plant Physiology 131: 309-316.

Choi DW, Rodriguez E, Close TJ. 2002. Barley Cbf3 gene identification, expression pattern, and map location. Plant Physiology 129: 1781-1787.

Svensson J, Ismail AM, Palva ET, Close TJ. 2002. Dehydrins. In Cell and Molecular Responses to Stress (Storey, K.B. and Storey, J.M., eds.), Vol. 3: Sensing, Signaling and Cell Adaptation. Elsevier Press, Amsterdam, 2002, pp. 155-171.

Zhu B, Choi DW, Close TJ. 2000. Expression of the barley dehydrin multigene family and the development of freezing tolerance. Molecular & General Genetics 264:145-153.

Choi DW, Koag MC, Close TJ. 2000. Map locations of barley Dhn genes determined by gene-specific PCR. Theor. and Appl. Genet. 101: 350-354.

Ismail AM, Hall AE, Close TJ. 1999. Allelic variation of a dehydrin gene co-segregates with chilling tolerance during seedling emergence. Proc. Natl. Acad. Sci. USA. 23: 13569-13573.

Teaching:

• Plant Genomics & Biotechnology Lab
• Plants and Human Affairs
• Molecular Genetics of Plant Domestication
• Genomics & Bioinformatics

Current Laboratory Personnel and Projects:

Timothy J. Close, Professor of Genetics and Geneticist in the Agricultural Experiment Station. Barley, cowpea and citrus genomics and bioinformatics. The structure and function of dehydrins. Development of nearby markers for cowpea breeding.

Raymond D. Fenton, Staff Research Associate. Laboratory management. New cDNA libraries, combinatorial pooling, curation of barley genetic resources, purification and biochemical analyses of dehydrins.

Steve Wanamaker, Programmer. HarvEST software (Windows and online).

Jessica Nguyen, Undergraduate Student. Crop plant genomics.

Marti Pottorff, PhD Student in Plant Biology. Crop plant genomics & bioinformatics, biomarker development.

Ndeye Diop, Post-Doc. Cowpea genomics and breeding.

Wellington Muchero, Post-Doc. Cowpea genomics and breeding.

Stephanie Chiueh, Junior Specialist, Barley genomics.

Eric Manley, Undergraduate Student. Cowpea chilling tolerance during seedling emergence.

Andrew Flores, Undergraduate Student from Riverside Community College, STEM program. Unequal recombination in barley.

Hana Abughoush, Undergraduate Student from Riverside Community College, STEM program. Unequal recombination in barley.

AJ Salehi, Undergraduate Student. Cowpea germplasm diversity, association genetics.

Yi-Ning Guo, Undergraduate Student. Cowpea chilling tolerance during seedling emergence.

Andy Snipes, PhD Rotation Student in Plant Biology. Cowpea chilling tolerance during seedling emergence.