Department of Botany & Plant Sciences


CloseTimothy 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



Agricultural Plant Genomics and Breeding

The current goals in my laboratory are to:

  • Create and utilize genomic resources for research and teaching, and conduct outreach in crop plant genomics
  • Promote environmental tolerance in crop plants through breeding and efficient cultural and post-harvest practices
  • Develop biomarkers, especially SNPs, for plant traits

As a Professor, and as a Geneticist in the Agricultural Experiment Station, my efforts are distributed between research, teaching and public service. The majority of my research is in Agricultural Plant Genomics,  summed up as the identification and use of genetic variation in crop plant germplasm to enhance tolerance of, or resistance to, abiotic and biotic environmental stresses. My group is presently active with cowpea (Vigna unguiculata (L). Walp), barley and Citrus. This includes development of fundamental genome resources including SNP marker assays, coupled genetic and physical maps, and genome sequence assemblies, as well as the use of these resources for applied purposes. We provide software (HarvEST) for genome database browsing and batch export of sequences, markers, annotations and associated information. We previously conducted 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 and the basis of acidity in lemons. In more recent years we have developed high-throughput SNP genotyping resources and SNP-based genetic maps for barley and cowpea, and applied them to the localization of numerous trait determinants. In cowpea these include resistance to Fusarium and Macrophomina, heat tolerance during reproductive development, seedling-stage drought tolerance, heat-induced browning of seed coats, seed size, resistance to foliar thrips and aphids, and leaf shape. Some continuing effort is also underway to understand the group of proteins known as dehydrins, and the genes that encode them. These are exciting times in biological research, as we now live in the light of the "genome era", wherein each organism can be studied directly, its significance determined by economic and social relevance, or as part of an ecosystem. Research is currently funded by grants from the US Agency for International Development Feed the Future Program, the US Department of Agriculture National Institute of Food and Agriculture, the University of California Agriculture Experiment Station, and the Consultative Group on International Agricultural Research. The work on cowpea is partnered with leading breeders in sub-Saharan Africa, mainly West Africa.

Some web resources from our projects:

HarvEST. Browsing Software and Online Databases. Portable Windows-based HarvEST viewers are available from http://harvest.ucr.edu. We maintain versions for barley, cowpea and citrus. Earlier versions that are no longer regularly updated are available for Brachypodium, cassava, coffee, Musa, rice, soybean and wheat. The graphical user interface provides comparative genome (synteny) views for barley  versus rice, Brachypodium and the wheat D genome, and cowpea versus soybean, common bean and Medicago truncatula. Details and annotations of Affymetrix microarray probe sets are also provided (barley, citrus, rice, soybean, wheat), along with several sequence alignment, expression filtering and batch export functions.

Barley and Cowpea Draft Genome Sequences, Physical Maps and BAC Sequences. The barley genome is ~5300 Mbp total size.  An estimated 70% of all transcribed barley genes are contained in ~1700 Mb of sequenced gene-bearing BACs representing a minimal tiling path of gene-containing BAC contigs from a physical map. These sequences can be searched via our BLAST server. Likewise, the cowpea genome is ~620 Mbp total size, sequences of an estimated 97% of all cowpea genes are available in a 60X genome coverage assembly from our BLAST server, and an estimated 10X depth of coverage physical map of the entire cowpea genome is available.

Programs for Linkage Map Construction from High-Density Biallelic Marker Data. We provide time-efficient programs to generate a genetic linkage map from a single mapping population (MSTMap) or a consensus linkage map  from two or more individual maps (MergeMap). These tools can be operated online up to a modest input size limit,  or locally after downloading the programs and installing them to run under Windows, Linux or MacOSX.

Other Tools Supporting Marker-Assisted Breeding. We post various additional tools that address recurrent needs of genotoype-informed breeding activities on breedit.org.

Some Representative Publications:

Muñoz-Amatriaín, M., Lonardi, S., Luo, M.C., Madishetty, K.,  Svensson, J.T., Moscou, M.J., Wanamaker, S., Jiang, T., Kleinhoifs, A., Muehlbauer, G.J., Wise, R.P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bhat, P.R., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H.N., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J.,  Šimková, H., Dolezel, J., Grimwood, J., Schmutz, J., Duma, D., Altschmied, L., Blake, T., Bregitzer, P., Cooper, L., Dilbirligi, M., Falk, A., Feiz, L., Graner, A., Gustafson, J.P., Hayes, P.M., Lemaux, P., Mammadov, J., Close, T.J. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal 84:216-227.

Huynh, B., Ehlers, J.D., Ndeve, A., Wanamaker, S., Lucas, M.R., Close, T.J., Roberts, P.A. 2015. Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California. Molecular Breeding 35: 36.

Lucas, M.R., Huynh, B., Roberts, P.A., Close, T.J. 2015. Introgression of a rare haplotype from Southeastern Africa to breed California blackeyes with larger seeds. Frontiers in Plant Science 6: 126.

Pottorff, M., Li, G., Ehlers, J.D., Close, T.J., Roberts, P.A. 2014. Genetic mapping, synteny, and physical location of two loci for Fusarium oxysporum f. sp. tracheiphilum race 4 resistance in cowpea [Vigna unguiculata (L.) Walp]. Molecular Breeding 33: 779-791.

Bozdag, S., Close, T.J., Lonardi, S. 2013. A graph-theoretical approach to the selection of the minimum tiling path from a physical map. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 352-360.

Lonardi, S., others, Close, T.J. 2013. Combinatorial pooling enables selective sequencing of the barley gene space. PLOS Computational Biology. Vol. 9: e 1003010

Lucas, M.R., Huynh, B., Diop, N., Roberts, P.A., Close, T.J. 2013. Markers for breeding heat tolerant cowpea. Molecular Breeding 31:529-536.

Huynh, B., Close, T.J., Roberts, P.A., Hu, Z., Wanamaker, S., Lucas, M.R., Chiulele, R., Cisse, N., David, A., Hearne, S., Fatokun, C., Diop, N.N., Ehlers, J.D. 2013. Genepools and the genetic architecture of domesticated cowpea [Vigna unguiculata (L.) Walp.]. The Plant Genome 6: doi: 0.3835/plantgenome2013.03.0005.

Muchero, W., Roberts, P.A., Diop, N.N., Drabo, I., Cisse, N., Close, T.J., Muranaka, S., Boukar, O., Ehlers, J.D. 2013. Genetic architecture of delayed senescence, biomass, and grain yield under drought stress in cowpea. PLOS ONE 8: e70041

International Barley Sequencing Consortium. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711-716.

Aprile, A., Federici, C., Close, T.J., De Belllis, L., Cativelli, L., Roose, M.L. 2011. Expression of the H+-ATPase AHA10 proton pump is associated with citric acid accumulation in lemon juice sac cells. Functional & Integrative Genomics 11:551-563.

Lucas, M.R., Diop, N., Wanamaker, S., Ehlers, J.D., Roberts, P.A., Close, T.J. 2011. SNP consensus mapping and comparative genomics of cowpea [Vigna unguiculata (L. Walp)]. The Plant Genome. 4:218-225.

Muñoz-Amatriaín, M., Moscou, M.J., Bhat, P.R., Svensson, J.T., Bartoš, J., Suchánková, P., Šimková, H., Endo, T.R., Fenton, R.D., Lonardi, S., Castillo, A.M., Chao, S., Cistué, L., Cuesta-Marcos, A., Forrest, K.L., Hayden, M.J., Hayes, P.M., Horsley, R.D., Makato, K., Moody, D., Sato, K., Vallés, M.P., Wulff, B.B., Muehlbauer, G.J., Dolezel, J., Close, T.J. 2011. An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers. The Plant Genome 4:238-249.

Wu, Y., Close, T.J., Lonardi, S. 2010. Accurate construction of consensus genetic maps via integer linear programming. IEEE/ACM Transactions on Computational Biology & Bioinformatics 8:381-394.

Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato, K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582.

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.

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

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.

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.

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.


  • Plants and Human Affairs (BPSC011)
  • Genes, Selections and Populations (BPSC150)
  • Genes of Crop Plant Domestication (BPSC225K, BPSC240)
  • Advanced Plant Breeding (BPSC221)

Current Laboratory Personnel and Projects:

Timothy J. Close, Professor of Genetics and Geneticist in the Agricultural Experiment Station. Cowpea, citrus and barley genetics and genome resources. Development of markers for cowpea breeding. The structure and function of dehydrins.

Steve Wanamaker, Programmer. Informatics for cowpea, barley and citrus.

Bao-Lam Huyhn, Assistant Professional Researcher. Cowpea genetics, breeding and germplasm.

Yi-Ning Guo, Staff Research Associate. General laboratory, greenhouse and field assistance, artwork.

Jasmine Dixon, Laboratory Assistant. Cowpea operations.

Hamid Mirebrahim, Ph.D. student in Computer Science, Barley BACs, cowpea SNP discovery, cowpea genome.

Rachid Ounit, Ph.D. student in Computer Sciences. Classifiication algorithms using discriminative k-mers (CLARK).

Sassoum Lo,  Ph.D. student in Plant Biology. Cowpea genetics and breeding, seed size and nutritional composition.

Maria Munoz-Amatriain, Assistant Project Scientist. Cowpea genetics and breeding, barley genome resources.

Eric Castillo, Farm Laborer, cowpea operations.

Ira Herniter, Ph.D. student in Plant Biology, cowpea genetics: seed coat patterns, abiotic stress tolerance.

More Information

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University of California, Riverside
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Department of Botany & Plant Sciences
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Fax: (951) 827-4437
E-mail: bpschair@ucr.edu

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