Research Areas:
Comparative genomics; physical mappingIn order to fully exploit the genome sequence data that is being generated for several plant species, we are integrating genetic and physical maps. Genetic maps are statistical representations of sequence arrangements on chromosomes whereas physical maps portray the physical location of a sequence on a chromosome. By linking the genetic map to the physical chromosomes and thereby the genome sequence data, it is possible to locate specific genes that condition an observable trait. BAC (bacterial artificial chromosome) libraries and FISH (fluorescence in situ hybridization) are the main techniques used to integrate these maps for the cloning of genes and characterization of plant genomes.
- Interphase nuclear architectureThe arrangement of chromosomes in transcriptionally active nuclei is a highly regulated process and is correlated with gene activity. Using 3-dimensional microscopy and chromatin mutants in Arabidopsis, we are characterizing the arrangement of chromosomes in interphase nuclei in both normal and mutant backgrounds. Understanding how chromosomes are actively positioned for gene transcription and what DNA sequences condition this response will permit the engineering of stably expressed transgenes and the eventual construction of plant artificial chromosomes.
- Soybean geneticsSoybean is one of the most important crops in the U.S. Using molecular genetic and cytogenetic approaches, we are characterizing the genome of Glycine max (soybean) to build the infrastructure for the eventual sequencing of the genome of soybean. Currently, we are integrating the genetic and physical maps using molecular cytogenetic techniques. This will aid in the cloning and characterization of genes that control traits such as seed development, oil content and quality and disease/pest resistances.
Investigators:
Front row (left to right): Chang-Hyu Bae, Mirayda Torres, Trulie Thorley, Navdeep Gill, Christian Hans, Rachel Teat, Sarah CurtisBack row (left to right): Abhijit Sanyal, Brian Abernathy, Jianxin Ma, Carly Carroll, Montona Futrell-Griggs, Jessica Schlueter, Scott Jackson, Will Teat
Recent Publications:
Z. Tian, Y. Yu, F. Lin, Y. Yu, P. SanMiguel, R.A. Wing, S. McCouch, J. Ma, S.A. Jackson. 2011. Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. BMC Genomics 2011 12:142. [PDF]
M. Chen, F. Lu, S.A. Jackson, R.A. Wing. 2010. Dynamic Genome Evolution of Oryza - A Genus-Wide Comparative Analysis. 76-83. [PDF]
Lin, J-Y., R.M Stupar, C. Hans, D.L. Hyten, and S.A. Jackson. 2010. Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to Phaseolus vulgaris. Plant Cell. 22: 2545-2561. [PDF]
Hurwitz, B.L., D. Kudrna, Y. Yu, A. Sebastian, A. Zuccolo, S.A. Jackson, D. Ware, R.A. Wing, L. Stein. 2010. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J. 63: 990-1003. [PDF]
Jetty, S., C. Fan, Y. Yu, X. Song, K. Cranston, A. Pontaroli, F. Lu, A. Sanyal, N. Jiang, T. Rambo, J. Currie, K. Collura, J. Talag, J. Bennetzen, M. Chen, S.A. Jackson, R. Wing. 2010. Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant J. 63: 430-442. [PDF]
Jianchang, Z. Tian, C. Hans, H. Laten, S.A. Jackson, S. Cannon, R. Shoemaker, J. Ma. 2010. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: new insights from genome-wide analysis and multi-specific comparison. Plant J. 63: 584-598. [PDF]
Sanyal, A., A. Jetty, F. Lu, Y. Yu, T Rambo, J. Currie, K. Kollura, HR. Kim, J. Ma, R. Wing and S.A. Jackson. 2010. Orthologous comparisons of the Hd1 region across genera reveal Hd1 genelability within diploid Oryza species and disruptions to microsynteny in sorghum. Mol. Biol and Evol. doi:10.1093/molbev/msq133 2010: 27(11): 2487-2506. [HTML]
Roulin, A., C. Chaparro, B. Piegu, S.A. Jackson, R. Wing and O. Panaud. Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rice. Genome Biol. Evol. 2010: 132 - 139. [PDF]
Jackson, S.A. and J. Chen. 2010. Genomic and Expression Plasticity of Polyploidy. Current Opinions in Plant Biol. 13: 1-7. [PDF]
Schmutz, J., S.B. Cannon, J. Schlueter, J. Ma, D. Hyten, Q. Song, T. Mitros, W. Nelson, G.D. May, N. Gill, M. Peto, D. Goodstein, J.J. Thelen, J. Cheng, T. Sakurai, T. Umezawa, J. Du, M. Bhattacharyya, D. Sandhu, D. Grant, T. Joshi, M. Libault, X-C. Zhang, D. Xu1 M. Futrell-Griggs, B. Abernathy, U. Hellsten K. Berry, J. Grimwood, R.A. Wing, P. Cregan, G. Stacey, J. Specht, D. Rokhsar, R.C. Shoemaker, S.A. Jackson. 2010. Genome sequence of the paleopolyploid soybean (Glycine max (L.) Merr.). Nature 463: 178-183. [PDF]
N. Gill, P. SanMiguel, B.D.S. Dhillon, B. Abernathy, H. Kim, L. Stein, D. Ware, R.A. Wing, S.A. Jackson. 2009. Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents. RICE. DOI 10.1007/s12284-010-9054-7. [PDF]
Tian, Z., C. Rizzon, J. Du, B.S. Gaut, J.L. Bennetzen, S.A. Jackson, and J. Ma. 2009. Genetic recombination shapes the genome-wide pattern of DNA acquisition and elimination mediated by LTR-retrotransposons in rice. Genome Res. doi/10.1101/gr.083899.108. [PDF]
Birney, B., T.J. Hudson, E.D. Green, C. Gunter, S. Eddy, J.R. Harris S. D. Ehrlich...S.A. Jackson ...(many other authors). 2009. Benefits and Best Practices of Rapid Pre-Publication Data Release. Nature 461, 168-170. [PDF]
Gill, N., S. Findley, J.G. Walling, J. Ma, G. Stacey, J. Doyle and S.A. Jackson. 2009. Molecular and chromosomal evidence for allopolyploidy in soybean, Glycine max (L.) Merr. Plant Physiol. 0.1104/pp.109.137935. [PDF]
Varshney, R.K., S.N. Nayak, G.D. May and S.A. Jackson. 2009. Next generation sequencing technologies and their application for crop genetics and breeding. Trends in Biotech. [PDF]
Cannon, S.B., G. D. May and S.A. Jackson. 2009. Update on comparative genomics of legumes. Three sequenced legume genomes and many crop species: rich opportunities for translational genomics. Plant Physiol. doi10.1104/pp.109.144659. [PDF]
Varshney, R.K., N.K. Singh, P.L. Kulwal, R.V. Penmetsa, R.K. Saxena, S. Datta, B. Rosen, A.D. Farmer, A. Dubey, K.B. Saxena, B. Fakrudin, M.N. Singh, K.B. Wanjari, A. Killian, G.D. May, R. McCombie, S.A. Jackson, D.R. Cook. 2009. Pigeonpea genomics initiative (PGI): an international effort towards improving crop productivity of pigeonpea (Cajanus cajan L.). Mol. Breeding DOI10.1007/s11032-009-9327-2. [PDF]
Gao, D., N. Gill, H-R. Kim, J. Walling, W. Zhang, C. Fan, Y. Yu, J. Ma, P. SanMiguel, N. Jiang, Z. Cheng, R. Wing, J. Jiang, S.A. Jackson. 2009. A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J. DOI10.1111/j.1365-313X.2009.04005.x. [PDF]
Lu, F, J.S.S. Ammiraju, A. Sanyal, S. Zhang, R. Song, J. Chen, G. Li, Y. Sui, Z. Cheng, A. Costa de Oliveira, J.L. Bennetzen, S.A. Jackson*, R.A. Wing*, M. Chen*. 2009. Comparative Sequence Analysis of the MONOCULM1 Orthologous Regions in 14 Oryza Genomes. Proc. Natl. Acad. Sci. USA. 106:2071-2076. [PDF]
Jetty*, S.S.A., F. Lu*, A. Sanyal*, Y. Yu, X. Song, N. Jiang, A. Clara Pontaroli, T. Rambo, J. Currie, K. Collura, J. Talag, C. Fan, J-L. Goicoechea, A. Zuccolo, J.L. Bennetzen, M. Chen, S.A. Jackson, and R.A. Wing. 2009. Dynamic Evolution of Oryza Genomes Revealed by Comparative Genomic Analysis of a Genus-wide Vertical Dataset. Plant Cell in press. 20:3191-3209. [PDF]
Innes, R.W., C. Ameline-Torregrosa, T. Ashfield, E. Cannon, S.B. Cannon, B. Chacko, N.W. G. Chen, A. Couloux, A. Dalwani, R. Denny, S. Deshpande, A.N. Egan, N. Glover, C.S. Hans, S. Howell, D. Ilut, S. Jackson, H Lai, J. Mammadov, S. Martin del Campo, M. Metcalf, A. Nguyen, M. O'Bleness, B.E. Pfeil, R. Podicheti, M.B. Ratnaparkhe, S. Samain, I. Sanders, B. Segurens, M. Sevignac, S. Sherman-Broyles, V. Thareau, D. M. Tucker, J. Walling, A. Wawrzynski, J. Yi, J.J. Doyle, V. e Geffroy, B.A. Roe, M.A. S. Maroof and N.D. Young. 2008. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol. 10.1104/pp.108.127902. 148: 1740-1759. [PDF]
Zuccolo, A., J.S.S. Ammiraju, H-Y. Kim, A. Sanyal, S.A. Jackson, and R.A. Wing. Rapid and differential proliferation of the Ty3-gypsy LTR-retrotransposon Atlantys in the genus Oryza. RICE. DOI 10.1007/s12284-008-9002-y. [PDF]
Gill, N, C. Hans and S.A. Jackson. 2008. An overview of plant chromosome structure. Cytogenetic and Genome Res. 120: 194-201. [HTML]
Schlueter, J.A., B.E. Scheffler, S.A. Jackson and R.C. Shoemaker. 2008. Fractionation of synteny in a genomic region containing tandemly duplicated genes across Glycine max, Medicago truncatula and Arabidopsis thaliana. J. Hered. 99: 390-395. [PDF]
Kim, H.K, B. Hurwitz, Y. Yu, K. Collura, N. Gill, P. SanMiguel, J.C. Mullikin, C. Maher, W. Nelson, M. Wissotski, M. Braidotti, D. Kudrna, J.L. Goigochia, L. Stein, D. Ware, S.A. Jackson, C. Soderlund and R.A. Wing. 2008. Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza. Genome Biol. 9: R45. [PDF]
Schlueter, J.A., J.L. Goicoechea, K. Collura, N. Gill, J-Y Lin, Y.Yu, D. Kudrna, A. Zuccolo, C.E. Vallejos, M. Munoz-Torres, M.W. Blair, J. Tohme, J. Tomkins, P. McClean, R.A. Wing and S.A. Jackson 2008. BAC-end sequence analysis and a draft physical map of the common bean (Phaseolus vulgaris L.) genome. Trop. Plant Biol. DOI 10.1007/s12042-007-9003-9. 1: 40-48. [PDF]
Randy Shoemaker, David Grant, Terry Olson, Wesley C. Warren, Rod Wing, Yeisoo Yu, HyeRan Kim, Perry Cregan, Bindu Joseph, Montona Futrell-Griggs, Will Nelson, Jon Davito, Jason Walker, John Wallis, Colin Kremitski, Debbie Scheer, Sandy Clifton, Tina Graves, Henry Nguyen, Xiaolei Wu, Mingcheng Luo, Jan Dvorak, Rex Nelson, Steven Cannon, Jeff Tomkins, Jeremy Schmutz, Gary Stacey, and Scott Jackson. Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps. 51: 294-302. [PDF]
Schlueter, J.A., J-Y Lin, S.D. Schlueter, I.F. Vasylenko-Sanders, S. Deshpande, J. Yi, M. Siegfried, B.A. Roe, R.T. Nelson, B.E. Scheffler, S.A. Jackson and R.C. Shoemaker. 2007. Genome duplication in soybean and the implications for whole genome sequencing. BMC Genomics 8:330. [PDF]
Ma, J., R.A. Wing, J. Bennetzen and S.A. Jackson. Evolutionary history and positional shift of a rice centromere. Genetics 177: 12171220. [PDF]
Jetty, S., A. Zuccolo, Y. Yu, X. Song, B. Piegu, F. Chevalier, J. Walling, J. Ma, J. Talag, D. Brar, P. SanMiguel, N. Jiang, S.A. Jackson, O. Panaud, R. Wing. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J. 52: 342-351. [PDF]
R.A. Wing, H.R. Kim, J.L. Goicoechea, Y. Yu, D. Kudrna, A. Zuccolo, S. S. A. Jetty, M. Luo, W. Nelson, J. Ma, P. SanMiguel, B. Hurwitz, D. Ware, D. Brar, D. Mackill, C. Soderlund, L. Stein, and S. Jackson. 2006. Resource for Comparative Genome Studies within Oryza. In N.M. Upadhyaya (ed.) Rice Functional Genomics. Springer (395-410). 2007. DOI 10.1007/0-387-48912-2 [PDF]
Kim, H-R., P. SanMiguel, W. Nelson, K. Collura, M. Wissotski, J. G. Walling, J. P. Kim, S. A. Jackson, C. Soderlund, R. A. Wing. 2007. Comparative physical mapping between O. sativa (AA genome type) and O. punctata (BB genome type). Genetics 176: 379-390. [PDF]
Ma, J., R.A. Wing, J.L. Bennetzen and S.A. Jackson. Plant Centromere Organization: Conserved Functions within a Dynamic Structure. Trends in Genetics 23: 134-139. [PDF]
Jackson, S.A., D. Rokhsar, G. Stacey, R. Shoemaker, J. Schmutz and J. Grimwood. 2006. Toward a reference sequence of the soybean genome: a multi-agency effort. The Plant Genome in press. [PDF]
Piegu, B., R. Guyot, N. Picault, A. Roulin, A. Sanyal, HR. Kim, K. Collura, D.S. Brar, S.A. Jackson, R.A. Wing and O. Panaud. 2006. Doubling genome size without polyploidization : dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 2006;16 1262-1269. [PDF]
Hass-Jacobus, B., M. Futrell-Griggs, B. Abernathy, R. Westerman, J-L. Goiocechea, J. Stein, P. Klein, B. Hurwitz, B. Zhou, F. Rakhshan, A. Sanyal, N. Gill, J-Y. Lin, J.G. Walling, M.Z. Luo, J.S.S. Ammiraju, D. Kudrna, H-R. Kim, D. Ware, R.A. Wing, P. SanMiguel and S.A. Jackson. 2006. Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. BMC Genomics 2006, 7:199. [PDF]
Jackson, S.A., S. Rounsley and M. Purugganan. 2006. Comparative sequencing of plant genomes: choices to make. Plant Cell 18: 1100-1104. [PDF]
Walling, J.G., R.C. Shoemaker, N.D. Young, J. Mudge and S.A. Jackson. 2006. Chromosome level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 172: 1893-1900. [PDF]
Ma, J and S.A. Jackson. 2006. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res 16: 251-259. [PDF]
Sanyal, A. and S.A. Jackson. 2006. Comparative genomics in the genus Arabidopsis of a 789-kilobase region surrounding the FLC locus. Mol. Genet. Genomics 275: 26-34. [PDF]
Lin, J-Y., B. Hass-Jacobus, P. SanMiguel, J.G. Walling, Y. Yuan, J. Doyle, R.C. Shoemaker, N.D. Young and S.A. Jackson. 2005. Molecular and cytogenetic characterization of gene-poor, heterochromatic regions of Glycine max L. Merr. Genetics 170: 1221-1230. [PDF]
Ammiraju, J.S.S., M. Luo, W. Wang, D. Kudrna, J.L. Goicoechea, C. Mueller, J. Talag, H-R. Kim, NB. Sisneros, B. Blackmon, E. Fang, J. Tomkins, D. Brar, D. MacKill, S. McCouch, N. Kurata, G. Lambert, D.W. Galbraith, K. Arumuganathan, K. Rao, J.G. Walling, N. Gill, P. SanMiguel, C. Soderlund, S.A. Jackson and R. A. Wing. The Oryza Map Alignment Project (OMAP) bacterial artificial chromosome library resource: unveiling a new era in whole genome comparative genomics to study monocot plant evolution, development and physiology. Genome Res.16: 140-147. [PDF]
The Rice Chromosome 3 Sequencing Consortium. 2005. Sequence, Annotation, and Analysis of Synteny Between Rice Chromosome 3 and Diverged Grass Species. Genome Research 15:1284-1291. [PDF]
Susanta K.B., F.H. Valicente, S.D. Rider, S-C. Ming, S.A. Jackson and J.J. Stuart. 2004. A physically anchored genetic map and linkage to avirulence reveals recombination suppression over the proximal region of Hessian fly chromosome 2. Genetics 167:343-355. [PDF]
Wing, R.A., J. Ammiraju, M. Luo, H. Kim, Y. Yu, D. Kudrna, J.L. Goicoechea, W. Wang, W. Nelson, C. Soderlund, D. Brar, D. Mackill, B. Han, L. Stein, P. SanMiguel and S. Jackson. 2005. The Oryza Map Alignment Project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol. Biol. 59: 53-62. [PDF]
Walling, JG, Pires, J.C. and S.A. Jackson. 2005. Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods. In Molecular evolution: producing the biochemical data, part B. Methods in Enzymology Vol 395: 442-459. Elsevier. The Netherlands. [PDF]
Pagel, J., J. Walling, N. Young, R. Shoemaker, S.A. Jackson. 2004. BAC FISH reveals segmental duplications within the Glycine max (soybean) genome. Genome 47:764-768. [PDF]
van der Knapp, E., A. Sanyal, S.A. Jackson, S.D. Tanksley. 2004. Toward cloning of the SUN locus of tomato. Genetics 168:2127-2140. [PDF]
Hass-Jacobus, B. and S.A. Jackson. (2005) Physical analysis of Plant Genomes. In. K. Meksem and Gunter Kahl (eds.) Handbook of Genome Mapping in Plants. Wiley-VCH Verlag GmbH & Co., Weinheim. pp. 133-146.
Hass-Jacobus, B.L., J.C. Pires, R. Porter, R.L. Phillips and S.A. Jackson. 2003. Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris). Theor. Appl. Genet. 107: 773-782. [PDF]
Pagel, J. and S.A. Jackson. 2004. Identifying Gene-Rich Regions within the Soybean Genome. In. C. Brummer and R. Wilson (eds.) Genomics for Legume Crops. AOCS Press, Champaign, IL.
Wing, R.A., S.A. Jackson and L. Stein. 2003. The Oryza map alignment project: toward a closed experimental system for the genus Oryza. Proceedings of the International Workshop on Genetic Resources for the Genus Oryza. (Eds. S. Nakayama, N. Tomooka, M. Hisada, D.A. Vaughn and K. Kadowaki). Tsukuba, Japan.
Jackson, S.A., P. SanMiguel, J.G. Walling, B. Hass Jacobus, R.M Westerman. 2003. Comparative cytogenomics and physical mapping in the Oryzeae. Proceedings of the International Workshop on Genetic Resources for the Genus Oryza. (Eds. S. Nakayama, N. Tomooka, M. Hisada, D.A. Vaughn and K. Kadowaki). Tsukuba, Japan.
Jackson, S.A., R. Stupar, J. Jiang. (2003) Fiber-FISH application in higher plants. In. R. Singh (ed.) Plant Cytogenetics. CRC Press, London. pp 31-35.
Lilly, J. W., M. Havey, S.A. Jackson, J. Jiang. 2001. Plasticity of plastid genomes as revealed by cytogenomic analysis. Plant Cell 13:245-254. [PDF]
Jackson, S.A., P. Zhang, P. Chen, R.L. Phillips, B. Friebe, S. Muthukrishnan, B. S. Gill. 2000. High-resolution structural analysis of biolistic transgene integration into the nuclear genome of wheat. Theor. Appl. Genet. 103: 56-62. [PDF]
Jackson, S.A., J.W. Lilly, R.L. Phillips, W.C. Kennard and R.A. Porter. 2000. Comparative genomics in the Oryzeae. Proceedings of the IV Rice Genetics Symposium. (Eds. D. Brar and G. Kush). Manila, The Philippines. 355-357. [PDF]
Phillips, R.L., S.A. Jackson, J.W. Lilly, W.C. Kennard and R.A. Porter. 2000. Genetic and physical comparative mapping in the Oryzeae. Proceedings of Integration of Biodiversity and Genome Technology for Crop Improvement. (Ed. Kiyoharu Oono). Japan. 1-4. [PDF]
Jackson, S.A., Z. Cheng, M-L. Wang, H.M. Goodman and J. Jiang. 2000. Comparative FISH mapping of a 431-kb Arabidopsis thaliana BAC contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome. Genetics 156: 833-838. [PDF]
Jackson, S.A., F. Dong and J. Jiang, 1999. Digital mapping of bacterial artificial chromosomes by fluorescence in situ hybridization. Plant J. 17: 581-587. [PDF]
Jackson S.A. and R.E. Hanneman, Jr., 1999. Crossability among cultivated and wild tuber and non-tuber-bearing Solanums. Euphytica 109: 51-67. [PDF]
Miller, J.T., F. Dong, S.A. Jackson, J. Song and J. Jiang, 1998. Retrotransposon- related DNA sequences in the centromeres of grass chromosomes. Genetics 150: 1615-1623. [PDF]
Jackson, S.A., M. Wang, H. Goodman and J. Jiang, 1998. Fiber-FISH analysis of repetitive DNA elements in Arabidopsis thaliana. Genome 41: 566-572. [PDF]
Dong, F., J.T. Miller, S.A. Jackson and J. Jiang, 1998. Rice centromeres consist of complex DNA. Proc. Natl. Acad. Sci. USA 95: 8135-8140. [PDF]
Miller, J.T., S.A. Jackson, S. Nasuda, B.S. Gill, R.A. Wing and J. Jiang, 1998. Cloning and characterization of a centromere-specific repetitive DNA element from Sorghum bicolor. Theor. Appl. Genet. 96: 832-839. [PDF]
Jackson, S.A., B. Friebe, B.S. Gill and J. Jiang, 1997. Structure of the rye midget chromosome analyzed by FISH and C-banding. Genome 40: 782-784. [HTML]
More publications
Teaching:
Molecular Cytogenetics - AGRY 598B Course Website
Advanced Plant Genetics (co-taught with Cliff Weil and Dan Szymanski)
Genomics
Education:
M.S./Ph.D. University of Wisconsin-Madison, 1996/1999
Date joined staff: 2001