UCR

Department of Botany & Plant Sciences



Faculty


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 focused on cowpea (Vigna unguiculata (L). Walp). This includes development of fundamental genome resources including SNP marker assays, coupled genetic and physical maps, genome and pan-genome sequence assemblies, and 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 and coat patterns, resistance to foliar thrips and aphids, leaf shape, time to flowering, photoperiod sensitivity, climbing habit, pod shattering, flower color, and others. Some 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 Feed the Future Program through the US Agency for International Development (USAID), the US National Science Foundation BREAD program, and the University of California Agriculture Experiment Station. The work on cowpea is partnered with leading breeders in sub-Saharan Africa, mainly West Africa.

Some web resources from our projects:

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.

HarvEST. Browsing Software and Online Databases. Portable Windows-based HarvEST viewers are available from http://harvest.ucr.edu. We maintain a version cowpea. Earlier versions that are no longer regularly updated are available for barley, Brachypodium, cassava, citrus, coffee, Musa, rice, soybean and wheat. The graphical user interface provides comparative genome (synteny) views for barley  versus rice, 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.

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., Mirebrahim, H., Xu, P., Wanamaker, S.I., Luo, M., Alhakami, H., Alpert, M., Atokple, I., Batieno, B.J., Boukar, O., Bozdag, S., Cisse, N., Drabo, I., Ehlers, J.D., Farmer, A., Fatokun, C., Gu, Y.Q., Guo, Y., Huynh, B., Jackson, S.A., Kusi, F., Lawley, C.T., Lucas, M.R., Ma, Y., Timko, M.P., Wu, J., You, F., Barkley, N.A., Roberts, P.A., Lonardi, S., Close, T.J. 2017. Genome resources for climate-resilient cowpea, an essential crop for food security. The Plant Journal. Vol. 89: p.1042-1054.

Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S.O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P.E., Russell, J., Bayer, M., Ramsay, L., Liu, H., Haberer, G., Zhang, X., Zhang, Q., Barrero, R.A., Li, L., Taudien, S., Groth, M., Felder, M., Hastie, A., Šimková, H., Vrána, J., Chan, S., Muñoz-Amatriaín, M., Ounit, R., Wanamaker, S., Bolser, D., Colmsee, C., Schmutzer, T., Aliyeva-Schnorr, L., Grasso, S., Tanskanen, J., Chailyan, A., Sampath, D., Heavens, D., Clissold, L., Cao, S., Chapman, B., Dai, F., Han, Y., Li, H., Li, X., Lin, C., McCooke, J.K., Tan, C., Wang, P., Wang, S., Yin, S., Zhou, G., Poland, J.A., Bellgard, M.I., Borisjuk, L., Houben, A., Doležel, J., Ayling, S., Lonardi, S., Kersey, P., Langridge, P., Muehlbauer, G.J., Clark, M.D., Caccamo, M., Schulman, A.H., Mayer, K.F., Platzer, M., Close, T.J., Scholz, U., Hansson, M., Zhang, G., Braumann, I., Spannagl, M., Li, C., Waugh, R., Stein, N. 2017. A chromosome conformation capture ordered sequence of the barley genome. Nature 544: 427-433.

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.

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

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.

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.

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:

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

Current Personnel and Roles:

Timothy J. Close, Professor of Genetics and Geneticist in the Agricultural Experiment Station. Cowpea, citrus and barley genetics and genome resources. Cowpea breeding and germplasm management..

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

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

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

Eric Castillo, Farm Laborer, cowpea operations.

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

Qihua Liang, Ph.D. student in Genetics, Genomics and Bioinformatics. Cowpea genome annotation and pan-genome, comparative genomics.


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