UCR

Department of Botany & Plant Sciences



Faculty


Mikeal Roose

Mikeal L. Roose

Chair, Department of Botany and Plant Sciences
Professor of Genetics (Ph.D., 1979, University of California, Davis)

Office: 4121 Batchelor Hall
Phone: (951) 827-4137
Fax: (951) 827-4437
E-mail: mikeal.roose@ucr.edu

Chair's Office: 2118 Batchelor Hall
Chair's phone: (951) 827-4413
Chair's e-mail:bpschair@citrus.ucr.edu


Research Interests:

The major focus of my research program is on the development and implementation of improved methods for crop improvement, particularly for citrus and asparagus. This research uses a wide variety of techniques and ranges from genetic engineering to hybridization-selection and field trials of new varieties.

Some current projects include the following:

Development of high-density genetic maps of citrus including genes for disease resistance and other traits.

The objective of this project is to develop dense genetic linkage maps of important varieties, including sweet orange (Citrus sinensis L.), mandarins, and trifoliate orange (Poncirus trifoliata L. Raf.). Trifoliate orange is used as a rootstock for citrus. Progeny of several different crosses between the varieties are being analyzed for SSR and SNP markers. DNA microarrays and sequencing are used to develop dense NSP maps.

Fig 1Segregation of SSR marker GT03 in progeny of sweet orange x trifoliate orange. Several progeny, with 3 bands, are triploids that will be excluded from map analysis.

 

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Use of molecular markers to understand phylogeny and genetic diversity of citrus.

Fig 2We have used various types of DNA markers, including RFLPs, RAPDs, ISSRs, and SSRs to characterize citrus germplasm and relationships. We have identified putative hybrid accessions based on high heterozygosity and lack of unique alleles, and studied their probable parentage. ISSR (inter-simple sequence repeat) markers are useful for distinguishing hybrid seedlings from apomictic seedlings because they provide a complex "DNA fingerprint" that targets rapidly evolving sequences. A graduate student, Noelle Barkley, studied 24 SSR markers in 370 mostly sexually derived accessions from the Citrus Variety Collection and determined population structure and identified putative hybrid accessions. DNA sequencing is also being used to characterize diversity and phylogeny.

Primers for SSR markers are listed on the link below. Current work is focused on sequencing a set of dispersed genes in diverse accessions.

PCR Primers for Citrus Germplasm Characterization

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Development of EST resources in citrus.

Fig 4To develop public resources for citrus genomics research, we collaborated with Dr. T. J. Close (UCR) to develop cDNA libraries from various citrus tissues, sequence clones, assemble these sequences into contigs, and annotate assemblies. The project target of 100,000 ESTs was reached in January 2005. HarvEST: Citrus (http://harvest.ucr.edu/) provides a free, PC-compatible EST database and sequence viewer for all public EST sequences from citrus. A web version of HarvEST: Citrus is also available at http://www.harvest-web.org/. In 2006, an Affymetrix microarray for analysis of citrus gene expression and mapping was released. Funding was from the California Citrus Research Board and the UC Discovery grant program.

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Breeding and evaluation of new citrus rootstocks.

Fig 5Citrus is propagated on rootstocks to improve yield, disease resistance, environmental stress tolerance and other traits. This project develops new rootstocks by hybridization-selection and evaluates these and other rootstocks in field trials in central and southern California. Particular traits of interest include resistance or tolerance to Phytophthora, citrus tristeza virus, and citrus nematode, good fruit quality, adaptation to calcareous soils, and high yield relative to tree size. Field research is supported by laboratory research on development of marker-assisted selection for various traits. Funding is from the California Citrus Research Board and California Citrus Nursery Board.

View trial summaries

Summary of New Rootstocks (Bitters, Carpenter and Furr)

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Breeding of new citrus fruit varieties.

Fig 6The fruit breeding project emphasizes development of new, low-seeded mandarin and grapefruit cultivars by hybridization-selection methods, and development of low-seeded forms of mandarins and other types by selection of induced mutations. Several new mandarin cultivars have been released in since 2000, and many others are in trials around the state. Descriptions of some recent releases are given below. Funding is from the California Citrus Research Board and California Citrus Nursery Board.

 

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Breeding and evaluation of new asparagus cultivars.

Fig 7We focus on development of new, high-yielding asparagus cultivars that maintain good spear quality in the warm production environment of California. Asparagus, a member of the lily family, is dioecious (separate male and female plants). Selected male and female plants are clonally propagated in tissue culture and planted together to produce the F1 hybrid seed used by growers. The breeding program produces experimental hybrids, test them for yield, quality, and disease resistance first in Riverside, and then later in the San Joaquin delta area where much commercial asparagus is produced. The program includes efforts to expand the germplasm base by hybridization and backcrossing with selected plants from European and New Jersey cultivars. DePaoli, a new hybrid cultivar was released in February 2006. Funding is from the California Asparagus Commission and Eurosemillas, S.A.

Fact Sheet on DePaoli asparagus hybrid (pdf file)

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Some Representative Publications:

Chandrika Ramadugu, Manjunath L. Keremane, Xulan Hu, David Karp, Claire T. Federici, Tracy Kahn, Mikeal L. Roose, Richard F. Lee, Genetic analysis of citron (Citrus medica L.) using simple sequence repeats and single nucleotide polymorphisms, Scientia Horticulturae, Volume 195:124-137. DOI: 10.1016/j.scienta.2015.09.004. (link)

Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, et al.: Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology 2014, 32:656–662. (link)

Zhao, H., Sun, R., Albrecht, U., Padmanabhan, C., Wang, A., Coffey, M. D., Girke, T., Wang, Z., Close, T. J., Roose, M., Yokomi, R. K., Folimonova, S., Vidalakis, G., Rouse, R., Bowman, K. D., and Jin, H. 2013. Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus Huanglongbing disease. Molecular Plant; DOI: 10.1093/mp/sst002 (link)

Ferrante, S. P. and Roose, M. L. 2013. Identification of Citrus sinensis BAC clones containing genes relevant to fruit quality by two-dimensional overgo hybridization. Tree Genetics & Genomes. DOI: 10.1007;s11295-013-0621-0.

Ramadugu, C., Pfeil, B. E., Manjunath, K. L., Lee, R. F., Maureira-Butler, I. J. and Roose, M. L. 2013. A six nuclear gene phylogeny of Citrus (Rutaceae) taking into account hybridization and lineage sorting. PLoS One. DOI: 10.1371/journal.pone.0068410. (link)

Xu, Q., Chen, L-L., Ruan, X., Chen, D., Zhu, A., Chen, C., Bertrand, D., Jiao, W-B., Hao, B-H., Lyon, M. P., Chen, J., Gao, S., Xing, F., Lan, H., Chang, J-W., Ge, X., Lei, Y., Hu, Q., Miao, Y., Wang, L., Xiao, S., Biswas, M. K., Zeng, W., Guo, F., Cao, H., Yang, X., Xu, X-W., Cheng, Y-J., Xu, J., Liu, J-H., Luo, O. J., Tang, Z., Guo, W-W., Kuang, H., Zhang, H-Y., Roose, M. L., Nagarajan, N., Deng, X-X., and Ruan, Y. 2013. The draft genome of sweet orange (Citrus sinensis). Nature Genetics doi:10.1038/ng.2472. (link)

Ollitrault, P., Terol J.,Chen, C., Federici, C. T., Lotfy S., Hippolyte I., Ollitrault, F., Bérard, A., Chauveau, A., Cuenca A., Costantino, G., Kacar, Y., Mu, L., Garcia-Lor, A.,Froelicher, Y., Aleza, P., Boland, A., Billot, C., Navarro, L., Luro, F., Roose, M. L.,Gmitter, F. G.,Talon, M. and Brunel, D. 2012. A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC Genomics 13:593.

Aprile, A., Federici, C. T., Close, T.. Roose, M. L., De Bellis, L and Cattivelli L. 2011. High and low acid lemons: origin and transcriptome comparisons. Acta Horticulturae 892:37-42.

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

Kupper, R. S., Federici, C. T. and Roose, M. L. 2010. Citrus rootstock breeding and evaluation. Citrograph 1 (6): 30-36.

Kepiro, J. L and M. L. Roose.  2009. AFLP markers closely linked to a major gene essential for nucellar embryony (apomixis) in Citrus maxima x Poncirus trifoliata. Tree Genetics and Genomes 6:1-11.

Barkley, N. A., R. R. Krueger, C. T. Federici and M. L. Roose. 2009. What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles. Plant Systematics and Evolution 282:71-86.

Caruso, M., G. Distefano, X. Ye, S. La Malfa, A. Gentile, E. Tribulato, and M. L. Roose. 2008. Generation of expressed sequence tags from carob (Ceratonia siliqua L.) flowers for gene identification and marker development. Tree Genetics and Genomes 4: 869-879.

Caruso, M., C. T. Federici and M. L. Roose. 2008. EST-SSR markers for asparagus genetic diversity evaluation and cultivar identification. Molec. Breeding 21: 195-204.

Chen, C., Lyon, M.T., O'Malley, D., Federici, C.T., Gmitter, J., Grosser, J. W., Chaparro, J. X., Roose, M. L., and Gmitter, F. G. Jr. 2008. Origin and frequency of 2n gametes in Citrus sinensis X Poncirus trifoliata and their reciprocal crosses. Plant Science 174: 1-8.

Stone, N. K. and M. L. Roose. 2008. Update on asparagus breeding program at the University of California, Riverside. Acta Horticulturae 776: 387-395. (refereed).

Roose, M. L. and T. J. Close. 2008. Genomics of Citrus, a Major Fruit Crop of Tropical and Subtropical Regions. In: Moore, P. H. and Ming, R. (eds.). Genomics of Tropical Crop Plants. Springer, pp 187-200.

Close, T.J., S. Wanamaker, M. L. Roose and M. Lyon. 2007. HarvEST: an EST database and viewing software. In: Edwards, D. (ed). Plant Bioinformatics, Methods in Molecular Biology 406:161-178, Humana Press (USA).

Roose, M. L. 2007. Mapping and marker assisted selection in Citrus. In: Khan, I.A. (ed). Citrus Genetics, Breeding and Biotechnology. CAB International, Wallingford, U.K., pp 275-286.

Roose, M. L. and T. E. Williams. 2007. Mutation breeding in Citrus. In: Khan, I. A. (ed.). Citrus Genetics, Breeding and Biotechnology. CAB International, Wallingford, U.K., pp 345-352.

Kepiro, J. L. and M. L. Roose. 2007. Nucellar embryony. In: Khan, I. A. (ed.). Citrus Genetics, Breeding and Biotechnology. CAB International, Wallingford, U.K., pp 141-150.

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

Yang, Z. N., X. R. Ye, J. Molina, M. L. Roose, and T. E. Mirkov. 2003. Sequence analysis of 282-kb region surrounding the Citrus tristeza virus resistance gene (Ctv) locus in Poncirus trifoliata. Plant Physiology 131: 482-490.

Krueger, R. R. and M. L. Roose. 2003. Use of molecular markers in the management of citrus germplasm resources. J. Amer. Soc. Hort. Sci. 128:827-837.

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Recent Teaching:

BIOL 102. Introductory Genetics (4). An introductory course, including classical Mendelian genetics, linkage and recombination, sex-linked traits, cytogenetics, developmental genetics, and molecular genetics. Also includes some probability theory and statistics.

BPSC 221. Advanced Plant Breeding (4) S, Even Years. Advanced treatment of plant breeding theory and practice including development and use of information on inheritance of traits; choice of breeding plans; breeding for yield, quality, and disease and stress resistance; and use of biotechnology.

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Current Laboratory Personnel and Projects:

Molecular markers for citrus, rootstock breeding.
Dr. Claire Federici, Staff Research Associate.

Citrus rootstock breeding and evaluation.
Ms. Ricarda Kupper, Staff Research Associate.

Asparagus breeding.
Mr. Neil Stone, Staff Research Associate.
Mr. Zach Thomas, Lab Assistant

Citrus scion breeding.
Marc Moragues, Associate Project Scientist.

Molecular genetic analysis of citrus evolution and diversity.
Dr. Chandrika Ramadugu, Project Scientist.

Dr. Sai Zadgaonkar, Postdoctoral Scholar.  Protein-protein interaction between Liberobacter and Citrus.

Plant care and field data collection.
Mr. Juan Alvarez, Agricultural Technician.

Molecular analysis of induced mutation in citrus.
Mr. Yi Zhu, Ph.D. student.

Genome-wide association mapping in citrus.
Ms. Yoko Eck, Ph.D.

Effects of citrus rootstocks on fruit gene expression and small RNAs
Ms. Rachel Rattner, Ph.D. student

The Roose Lab says goodbye to

Mr. David McGrath, Lab Assistant

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More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Career OpportunitiesUCR Libraries
Campus StatusDirections to UCR

Department & Program Information

Department of Botany & Plant Sciences
2150 Batchelor Hall

Tel: (951) 827-4619
Fax: (951) 827-4437
E-mail: bpschair@ucr.edu

Plant Biology Graduate Program
CNAS Grad Student Affairs Office
1140 Batchelor Hall

Tel: (800) 735-0717
Fax: (951) 827-5688
E-mail: jammy.yang@ucr.edu

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