Faculty
Mikeal L. Roose
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, Department of Botany and Plant Sciences 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.
Job Posting: Assistant/Associate Specialist in Citrus Breeding
Some current projects include the following:
- Development of high-density genetic maps of Citrus and Poncirus
- Use of molecular markers to understand phylogeny and genetic diversity of citrus
- Positional cloning of a gene for resistance to citrus tristeza virus
- Development of EST resources and microarrays in citrus (with T. J. Close)
- Breeding and evaluation of new citrus rootstocks for improved stress tolerance and other traits
- Development of new seedless mandarins and early-maturing grapefruit by hybridization and mutation breeding
- Breeding and evaluation of new asparagus cultivars
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 two important varieties, sweet orange (Citrus sinensis L.) 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. We are exploring use of DNA microarrays for mapping large numbers of SNPs.
Segregation 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.
Use of molecular markers to understand phylogeny and genetic diversity of citrus.
We 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, recently completed a study of 24 SSR markers in 370 mostly sexually derived accessions from the Citrus Variety Collection and determined population structure and identified putative hybrid accessions.
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
Positional cloning of a gene for citrus tristeza virus resistance.
A collaborative project with Dr. T. E. Mirkov (Texas A&M University) is directed toward cloning a Poncirus trifoliata gene that causes resistance to citrus tristeza virus. We developed high-density linkage maps of the region surrounding this gene and sequenced a 282 kb BAC contig that should contain the gene. Candidate genes are now being tested by transformation. Most funding was from USDA-CSREES grants.
Portion of 282 kb sequence assembly in citrus tristeza virus resistance gene region showing CC-NSB-LRR type R genes (green), transposable elements (red and blue), and hypothetical genes (black).
Development of EST resources in citrus.
To 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.
Breeding and evaluation of new citrus rootstocks.
Citrus 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.
Summary of New Rootstocks (Bitters, Carpenter and Furr)
Breeding of new citrus fruit varieties.
The 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.
- Description of Gold Nugget Mandarin Hybrid (pdf file)
- Description of TDE2 Mandarin Hybrid (pdf file)
- Description of TDE3 Mandarin Hybrid (pdf file)
- Description of TDE4 Mandarin Hybrid (pdf file)
- Solids:acid data on TDE hybrids at various California locations (pdf file)
- Description of Tango Mandarin (pdf file)
- Description of DaisySL Mandarin (pdf file)
- Seed Problems in DaisySL Mandarin (pdf file)
- Description of FairchildLS Mandarin (pdf file)
- Description of KinnowLS Mandarin (pdf file)
Breeding and evaluation of new asparagus cultivars.
We 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)
Some Representative Publications:
Kupper, R. S., Federici, C. T. and Roose, M. L. 2010. Citrus rootstock breeding and evaluation. Citrograph 1 (6): 30-36.
Close, T. J., Bhat, P. R., Lonardi, S., Wu, Y. H., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J. T., Wanamaker, S., Bozdag, S., Roose, M. L., Moscou, M. J., Chao, S. A. M., Varshney, R. K., Szucs, P., Sato, K., Hayes, P. M., Matthews, D. E., Kleinhofs, A.., Muehlbauer, G. J., DeYoung, J., Marshall, D. F.,.Madishetty, K., Fenton, R. D., Condamine, P., Graner, A., Waugh, R. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582.
Aguilar-Melendez, A., P. L. Morrell, M. L. Roose, and S. Kim. 2009. Genetic diversity and structure in semi-wild and domesticated chiles (Capsicum annuum L.) from Mexico. Amer. J. Bot. 96:1190-1202.
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.
Rostoks, N., L. Ramsay, K. MacKensie, L. Cardle, P. R. Bhat, M. L. Roose, J. T. Svensson, N. Stein, R. K. Varshney, D. Marshall, A. Graner, T. J. Close and R. Waugh. 2006. A recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc. Nat. Acad. Sci. USA 103:18656-18661.
Barkley, N. A., M. L. Roose, R. R. Krueger, and C. T. Federici. 2006. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor. Appl. Genet. 112:1519-1531.
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.
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.
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.
Ms. Maria Kostecki, Agricultural Technician
Citrus scion breeding.
Mr. Timothy Williams, Staff Research Associate.
Molecular genetic analysis of citrus evolution and diversity.
Dr. Chandrika Ramadugu, Research Scientist.
Plant care and field data collection.
Mr. Juan Alvarez, Agricultural Technician.
Molecular analysis of induced mutation in citrus.
Ms. Jennifer Crowley, Ph.D. student.
Chemical genomic approaches to Liberibacter diseases.
Ms. Sai Patne, Ph.D. student.
The Roose Lab says goodbye to
Ms. Rui Fan, visiting Ph.D. student. (2008-2009)
Ms. Lihua (Lisa) Mu, Lab Assistant. (2000-2009)