Regents Professor Ph.D. (1988) Cornell University Fellow, American Association for the Advancement of Science Lamar Dodd Award for Research, University of Georgia, 2009 Distinguished Agriscience Scientist Award, Christopher Columbus Fellowship Foundation and American Farm Bureau Overall chair, International Cotton Genome Initiative Grant Support - "Adapting to a duplicated genome," NSF "Comparative Evolutionary Genomics of Cotton," NSF "Accelerating deployment of novel alleles in cotton," NSF Accelerating the domestication of Miscanthus," DOE-USDA "Genomic and Breeding Foundations for Bioenergy Sorghum Hybrids," DOE-USDA "Discovery and development of alleles contributing to sorghum drought tolerance," Generation Challenge Program Research Interests - Our laboratory is interested in the identification and implementation of DNA diagnostic tools that are predictive of specific plant characteristics such as disease resistance, improved productivity, or improved quality. We work in close collaboration with scientists in several applied agricultural disciplines; thereby contributing to accelerated improvement of plants to better suit human purposes by traditional means such as classical plant breeding. We are also interested in the identification of specific genes that are responsible for characteristics important to plant development, evolution, or agriculture, and elucidating the function(s) of these genes. Finally, we are interested in elucidating plant biodiversity at the genic and genomic level; gaining better understanding of the 200-million year history of flowering plant diversification from a hypothetical common ancestor, and better understanding specific molecular-level events that have contributed to the ability of flowering plants to colonize much of the Earth. Research Research Areas: Genomics and Bioinformatics Biotechnology Selected Publications Selected Publications: Kim, C., D. Zhang, S.A. Auckland, L.K. Rainville, K. Jakob, B. Kronmiller, E.J. Sacks, M. Deuter and A.H. Paterson. 2012. SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum. Theoretical and Applied Genetics, in press. Wisniewski-Dyé, F., K. Borziak, G. Khalsa-Moyers, G. Alexandre, L.O. Sukharnikov, K. Wuichet, G.B. Hurst, H.W. McDonald, A. Lapidus, V. Barbe, A. Calteau, Z. Rouy, S. Mangenot, C. Prigent-Combaret, P. Normand, M. Boyer, P. Siguier, Yves Dessaux, C. Elmerich, G. Condemine, I. Kennedy, A.H. Paterson, V. González, P. Mavingui and I.B. Zhulin 201#. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. Plos Genetics ##:##-##. Wang, X., M. Torres, G. Pierce, C. Lemke, L. Nelson, B. Yuksel, J. Bowers, B. Marler, Y. Xiao, L. Lin, E. Epps, H. Sarazen, C. Rogers, S. Karunakaran, J. Ingles, E.Giattina, J.-H. Mun, Y.-J. Seol, B.-S. Park, R. Amasino, C. Quiros, T. Osborn, C. Pires, C. Town and A. Paterson. 2011. A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. BMC Genomics 12: 470 (doi: 10.1186/1471-2164-12-470). Thor, S.W., D.A. Hilt, J. Kissinger, A.H. Paterson and M.W. Jackwood. 2011. Recombination in avian gamma-coronaviruses. Viruses 3(9): 1777-1799. Zhang, Z., J. Rong, V. Waghmare, P. Chee, O. May, R. Wright, J. Gannaway and A. Paterson. 2011. QTL alleles for improved fiber quality from a wild Hawaiian cotton, Gossypium tomentosum. Theoretical and Applied Genetics 123(7): 1075-1088. Wang, X., et al (The Brassica rapa Genome Sequencing Project Consortium, including X. Wang, H. Tang, H. Guo, T.-H. Lee, J. Li, H. Jin, X. Tan, Y. Wang and A.H. Paterson. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43: 1035-1039. Paterson, A.H. and Z.-K. Li. 2011. Paleo-Green Revolution for rice. Proceedings of the National Academy of Sciences of the USA 108(27): 10931-10932. Ratnaparkhe, M.B., X. Wang, J. Li, R.O. Compton, L.K. Rainville, C. Lemke, C. Kim, H. Tang and A.H. Paterson. 2011. Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny. New Phytologist 192(1): 164-178. Wang, X., H. Tang and A.H. Paterson. 2011. Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel in major Poaceae lineages. The Plant Cell 23(1): 27-37. Glover, J.D., J.P. Reganold, L.W. Bell, J. Borevitz, E.S. Buckler, C.M. Cox, T.S. Cox, T.E. Crews, S.W. Culman, L.R. DeHaan, D. Eriksson, B.S. Gill, J. Holland, F. Hu, B. Hulke, A.M.H. Ibrahim, S.S. Jones, S.C. Murray, A.H. Paterson, Edmundo Ploschuk, E.J. Sacks, S. Snapp, D. Tao, D.L. Van Tassel, L.J. Wade, D.L. Wyse and Y. Xu. 2010. Increasing Food and Ecosystem Security through Perennial Grain Breeding. Science 328: 1638-1639. Lin, L., G. Pierce, J.E. Bowers, J.C. Estill, R.O. Compton, L.K. Nelson, C. Kim, C. Lemke, J. Rong, H. Tang, X. Wang, M. Braidotti, A.H. Chen, K. Collura, E. Epps, W. Golser, C. Grover, K.L. Herrick, J. Ingles, S. Karunakaran, D. Kudrna, J. Olive, N. Tabassum, E. Um, M. Wissotski, Y. Yu, A. Zuccolo, M. ur Rahman, D.G. Peterson, R.A. Wing, J.F. Wendel and A.H. Paterson. 2010. A draft Physical Map of a D-genome Cotton Species (G. raimondii). BMC Genomics 11: 395. Paterson, A.H., M. Freeling, H. Tang and X. Wang. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 349-372. Tang, H., J.E. Bowers, X. Wang and A.H. Paterson. 2010. Early polyploidy events in the monocotyledon lineage revealed by angiosperm genome comparisons. Proceedings of the National Academy of Sciences of the USA 107: 472-477. Wang, X., H. Tang, J.E. Bowers and A.H. Paterson. 2009. Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Research 19: 1026-1032. Paterson, A.H., J.E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, U. Hellsten, T. Mitros, A. Poliakov, J. Schmutz, M. Spannagl, H. Tang, X. Wang, T.Wicker, A.K. Bharti, J. Chapman, F.A. Feltus, U. Gowik, I. Grigoriev, E. Lyons, C.A. Maher, M. Martis, A. Narechania, R. Otillar, B.W. Penning, A.Salamov, Y. Wang, L. Zhang, N.C. Carpita, Michael Freeling, A.R. Gingle, C.T. Hash, B. Keller, P. Klein, S. Kresovich, M.C. McCann, R. Ming, D.G. Peterson, M. ur Rahman, D. Ware, P. Westhoff, K.F.X. Mayer, J. Messing and D.S. Rokhsar. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556. Tang, H., X. Wang, J.E. Bowers, R. Ming, M. Alam and A.H. Paterson. 2008. Unraveling the Consequences of Ancient Hexaploidy through Multiply-aligned Angiosperm Gene Maps. Genome Research 18: 1944-1954. Doyle J.J., L.E. Flagel, A.H. Paterson, R.A. Rapp, D.E. Soltis, P.S. Soltis and J.F. Wendel. 2008. Evolutionary genetics of genome merger and doubling in plants. Annual Review of Genetics 42: 443-461. Tang, H., J.E. Bowers, X. Wang, R. Ming, M. Alam and A.H. Paterson. 2008. Synteny and colinearity in plant genomes. Science 320: 486-488. Paterson, A.H., P. Felker, S.P. Hubbell and R. Ming. 2008. The fruits of tropical plant genomics. Tropical Plant Biology 1: 3-19. Ray M., S. Hou, Y. Feng, Q. Yu, A. Dionne-Laporte, J. Saw, P. Senin, W. Wang, S.Salzberg, H. Tang, E. Lyons, D. Rice, M. Riley, R. Skelton, J. Murray, C. Chen, M. Eustice, E. Tong, H. Albert, R.E. Paull, M.-L. Wang, Y. Zhu, M. Schatz, N. Nagarajan, R. Agbayani, P. Guan, A. Blas, J. Wang, J.-K. Na, T. Michael, E.V. Shakirov, B. Haas, J. Thimmapuram, D. Nelson, X. Wang, J.E. Bowers, J. Suzuki, S. Tripathi, K. Neupane, H. Wei, R. Singh, B. Irikura, N. Jiang, W. Zhang, K. Wall, G. Presting, A. Gschwend, Y. Li, A. Windsor, R.N. Pérez, M.J. Torres, F.A. Feltus, B. Porter, M. Paidi, M.-C. Luo, L. Liu, D. Christopher, P.H. Moore, T. Sugimura, C. dePamphilis, J. Jiang, M. Schuler, T. Mitchell-Olds, D. Shippen, J. Palmer, M.R. Freeling, A.H. Paterson, D. Gonsalves, L. Wang and M. Alam. 2008. The draft genome of the tropical fruit tree papaya (Carica papaya, Linnaeus). Nature 452: 991-996. Wang, J., P.H. Moore, A.H. Paterson and R. Ming. 2007. Sex chromosomes in flowering plants. American Journal of Botany 94: 141-150. Grover, C.E., H.R. Kim, R.A. Wing, A.H. Paterson and J.F. Wendel. 2007. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant Journal 50: 995-1006. Lohithaswa, H.C., F.A. Feltus, H.P. Singh, C.D. Bacon, C. D. Bailey and A.H. Paterson. 2007. Leveraging rice genome sequence for comparative genomics in monocots. TAG 115: 237-243. Yang, T.J., S.-J. Kwon, J. Kim, K.-B. Lim, J.-A. Kim, M. Jin, J.Y. Park, M.-H. Lim, H.-I. Kim, Y.P. Lim, A.H. Paterson and B.-S. Park. 2007. Characterization and genome-wide comparative analysis of terminal-repeat retrotransposon in miniature (TRIM) families in the Brassicaceae. TAG 114: 627-636. Mei, H., F. Feng, B. Lu, F.A. Feltus, A.H. Paterson, X. Cai, L. Chen, X. Xu, J. Wu, X. Yu, H. Chen, Y. Li and L. Luo. 2007. Experimental validation of inter-subspecific genetic diversity in rice represented by the differences between the DNA sequences of ‘Nipponbare’ and ‘93-11.’ Chinese Science Bulletin 52: 1327-1337. Yu, Q., S. Hou, R. Hobza, F.A. Feltus, X. Wang, W. Jing, R.L. Skelton, A. Blas, C. Lemke, J.H. Saw, P.H. Moore, M. Alam, J. Jiang, A.H. Paterson and R. Ming. 2007. Chromosomal location and gene paucity of the male-specific region on the papaya Y chromosome. Mol. Gen. Genet. 278: 177-185. Rong, J., F.A. Feltus, V.N. Waghmare, G.J. Pierce, P.W. Chee, X. Draye, Y. Saranga, R.J. Wright, T.A. Wilkins, O.L. May, C.W. Smith, J.R. Gannaway, J.F. Wendel and A.H. Paterson. Meta-analysis of polyploid cotton QTLs shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176: 2577-2588. Wei, F., E. Coe, W. Nelson, A. Bharti, F. Engler, E. Butler, H.-R. Kim, J.L. Goicoechea, M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M. McMullen, G. Davis, J. Bowers, A. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund and R. Wing. 2007. Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genetics 3: 1254-1263. Desai, A., P.W. Chee, J. Rong, O.L. May and A.H. Paterson. 2006. Chromosome structural changes in diploid and tetraploid A genomes of Gossypium. Genome 49: 336-345. Paterson, A.H. 2006. Leafing through the genomes of our major crop plants: strategies for capturing unique infomation. Nature Reviews Genetics 7: 174-184. Udall, J.A., J. Swanson, K. Haller, R.A. Rapp, M. Sparks, J. Hatfield, Y. Yu, Y. Wu, D.J. Llewellyn, E. Dennis, A.B. Arpat, B. Sickler, T. A. Wilkins, J. Guo, X. Chen, E. Taliercio, R. Turley, C. Dowd, H. Mcfadden, N. Klueva, P. Payton, R. Allen, D. Zhang, C. Haigler, C. Wilkerson, J. Suo, S. R. Schulze, M. Pierce, M. Essenberg, H. Kim, D. Kudrna, R. Wing, A.H. Paterson, C. Soderlund and J.F. Wendel. 2006. A global assembly of cotton ESTs. Genome Research 16: 441-450. Bethel, C.M., E.B. Sciara, J.E. Bowers, J.C. Estill, W. Hanna and A.H. Paterson. 2006. A framework linkage map of Bermudagrass (Cynodon dactylon x transvaalensis) based on single-dose restriction fragments. Theor. Appl. Genet. 112: 727-737. Chapman, B.A., J.E. Bowers, F.A. Feltus and A.H. Paterson. 2006. Buffering crucial functions by paleologous duplicated genes may impart cyclicality to angiosperm genome duplication. Proceedings of the National Academy of Sciences of the USA 103: 2730-2735. Feltus, F.A., G.E. Hart, K.F. Schertz, A.M. Casa, P. Brown, P. Klein, S. Kresovich and A.H. Paterson. 2006. Genetic map alignment and QTL correspondence between inter- and intra-specific Sorghum populations. Theor. Appl. Genet. 112: 1295-1305. Hamblin, M.T., A.M. Casa, H. Sun, S.C. Murray, A.H. Paterson, C.F. Aquadro and S. Kresovich. 2006. Challenges of detecting directional selection after a domestication bottleneck: lessons from Sorghum bicolor. Genetics 173: 953-954. Feltus, F.A., H.P. Singh, H.C. Lohithaswa, S.R. Schulze, T. Silva and A.H. Paterson. 2006. A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved noncoding sequences in orphan crops. Plant Physiology 140: 1183-1191. Gingle, A.R., H. Yang, P. Chee, O.L. May, J. Rong, D.T. Bowman, E.L. Lubbers and A.H. Paterson. An integrated web resource for cotton. Crop Science 46: 1998-2007. Takamiya, T., A.H. Paterson and H. Okuizumi. 2006. Restriction landmark genomic scanning with isoschizomers (MspI/HpaII) for DNA methylation analysis. Electrophoresis 27: 2846-2856. Jang, C.S., T.L. Kamps, D.N. Skinner, S.R. Schulze, W.K. Vencill and A.H. Paterson. 2006. Functional classification, genomic organization, putative cis-acting regulatory elements, and relationship to quantitative trait loci, of Sorghum genes with rhizome-enriched expression. Plant Physiology 142: 1148-1159. Hamblin, M.T., M.G. Salas-Fernandez, A.M. Casa, S.E. Mitchell, C.F. Aquadro, A.H. Paterson and S. Kresovich. 2005. Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics 171: 1247-1256. Van Becelaere, G., E.L. Lubbers, A.H. Paterson and P.W. Chee. 2005. Pedigree versus DNA marker-based genetic similarity estimates in cotton. Crop Science 45: 2281-2287. Bowers, J.E., (33 authors, A.H. Paterson as corresponding author). 2005. Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc. Natl. Acad. Sci. USA 102: 13206-13211. Yuksel, B., J.C. Estill, S.R. Schulze and A.H. Paterson. 2005. Organization and evolution of resistance gene analogs in peanut. Molecular Genetics and Genomics 274: 248-263. Rong, J.K., G.J. Pierce, V.N. Waghmare, C.A.J. Rogers, A. Desai, P.W. Chee, O.L. May, J.R. Gannaway, J.F. Wendel, T.A. Wilkins and A.H. Paterson. 2005. TAG 111: 1137-1146. Rong J., J.E. Bowers, S.R. Schulze, V.N. Waghmare, C.J. Rogers, G.J. Pierce, H. Zhang, J.C. Estill and A.H. Paterson. 2005. Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy. Genome Research 15: 1198-1210. Paterson, A.H., J.E. Bowers and B.A.Chapman. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. USA 101: 9903-9908. Hamblin, M.T., S.E. Mitchell, G.M. White, W. Gallego, R. Kukatla, R.A. Wing, A.H. Paterson and S. Kresovich. 2004. Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics 167: 471-483. Rong, J.K., C. Abbey, J.E. Bowers, C.L. Brubaker, C. Chang, P.W. Chee, T.A. Delmonte, X.L. Ding, J.J. Garza, B.S. Marler, C.H. Park, G.J. Pierce, K.M. Rainey, V.K. Rastogi, S.R. Schulze, N.L. Trolinder, J.F. Wendel, T.A. Wilkins, T.D. Williams-Coplin, R.A. Wing, R.J. Wright, X.P. Zhao, L.H. Zhu and A.H. Paterson. 2004. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166: 389-417. Ma, H., P.H. Moore, Z.Y. Liu, M.S. Kim, Q.Y. Yu, M.M.M. Fitch, T. Sekioka, A.H. Paterson and R. Ming. 2004. High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166: 419-436. Saranga, Y., C.X Jiang., R.J. Wright, D. Yakir and A.H. Paterson. 2004. Genetic dissection of cotton physiological responses to arid conditions and their inter-relationships with productivity. Plant Cell and Environment 27: 263-277. Liu, Z.Y., P.H. Moore, H. Ma, C.M. Ackerman, M. Ragiba, Q.Y. Yu, H.M. Pearl, M.S. Kim, J.W. Charlton, J.I. Stiles, F.T. Zee, A.H. Paterson, and R. Ming. 2004. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427: 348-352. Bowers, J.E., C. Abbey, S. Anderson, C. Chang, X. Draye, A.H. Hoppe, R. Jessup, C. Lemke, J. Lennington, Z.K. Li, Y.R. Lin, S.C. Liu, L.J. Luo, B.S. Marler, R.G. Ming, S.E. Mitchell, D. Qiang, K. Reischmann, S.R. Schulze, D.N. Skinner, Y.W. Wang, S. Kresovich, K.F. Schertz and A.H. Paterson. 2003. A high-density genetic recombination map of sequence-tagged sites for Sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165: 367-386. Hu, F.Y., D.Y. Tao, E. Sacks, B.Y. Fu, P. Xu, J. Li, Y. Yang, K. McNally, G.S. Khush, A.H. Paterson and Z.K. Li. 2003. Convergent evolution of perenniality in rice and sorghum. Proc. Natl. Acad. Sci. USA 100: 4050-4054. Bowers, J.E., B.A. Chapman, J.K. Rong and A.H. Paterson. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438. Paterson, A.H., J.E. Bowers, M.D. Burow, X. Draye, C.G. Elsik, C.X. Jiang, C.S. Katsar , T.H. Lan, Y.R. Lin, R.G. Ming and R.J. Wright. 2000. Comparative genomics of plant chromosomes. Plant Cell 12: 1523-1539. Jiang, C.X., P.W. Chee, X. Draye, P.L. Morrell, C.W. Smith and A.H. Paterson. 2000. Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton). Evolution 54: 798-814. Wright, R.J., P.M. Thaxton, K.M. El-Zik and A.H. Paterson. 1998. D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (Cotton) suggests that polyploid formation has created novel avenues for evolution. Genetics 149: 1987-1996. Jiang, C.X., R.J. Wright, K.M. El-Zik and A.H. Paterson. 1998. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc. Natl. Acad. Sci. USA 95: 4419-4424. Multani, D.S., R.B. Meeley, A.H. Paterson, J. Gray, S.P. Briggs and G.S. Johal. 1998. Plant-pathogen microevolution: Molecular basis for the origin of a fungal disease in maize. Proc. Natl. Acad. Sci. USA 95: 1686-1691. Paterson, A.H., T.H. Lan, K.P. Reischmann, C. Chang, Y.R. Lin, S.C. Liu, M.D. Burow, S.P. Kowalski, C.S. Katsar, T.A. DelMonte, K.A. Feldmann, K.F. Schertz and J.F. Wendel. 1997. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nature Genetics 14: 380-382. Paterson, A.H., Y.R. Lin, Z.K. Li, K.F. Schertz, J.F. Doebley, S.R.M. Pinson, S.C. Liu, J.W. Stansel, and J.E. Irvine. 1995. Science 269: 1714-1718. Paterson, A.H., E.S. Lander, J.D. Hewitt, S. Peterson, S.E. Lincoln and S.D. Tanksley. 1988. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721-726.