Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences
Start Date:
September 1, 2004
Expires:
August 31, 2008 (Estimated)
Awarded Amount to Date:
$5584982
Investigator(s):
Loren Rieseberg lriesebe@indiana.edu (Principal Investigator)
Kent Bradford (Co-Principal Investigator) Richard Michelmore (Co-Principal Investigator) Richard Kesseli (Co-Principal Investigator) Steven Knapp (Co-Principal Investigator)
Sponsor:
Indiana University
P O Box 1847
Bloomington, IN 47402 812/855-0516
NSF Program(s):
PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):
BIOT, 9109, 7462
Program Element Code(s):
1329
ABSTRACT
This collaborative multi-disciplinary research project will develop resources for functional, comparative, and evolutionary genomics of the Compositae, particularly lettuce (Lactuca sativa) and sunflower (Helianthus annuus). Six domestication and ten escape and naturalization events are being investigated to elucidate the genetic bases and evolutionary forces underlying the domestication of crops and evolution of weeds. These data will build on the Compositae Genome Project (CGP, http://compgenomics.ucdavis.edu) as well as capitalize on the wealth of knowledge being developed for Arabidopsis and other model species.
Specifically, (i) 450,000 EST sequences will be deposited in GenBank and the CGP web site with an emphasis on allelic diversity (covering 18 plant species); (ii) the study of phenotypic and molecular variation in seven genera is being examined for patterns of selection and sequence or expression differences associated with domestication or weed traits, (iii) quantitative traits and gene expression patterns for seed oil profiles in lettuce and sunflower are being detected, and (iv) gene order and chromosome rearrangements in lettuce, sunflower, and Arabidopsis are being characterized. This research will investigate a broad range of genes involved in evolution of cultivated plants and weeds and will evaluate of the relative importance of changes in gene sequence versus changes in gene expression for the evolution of different traits such as flowering time, seed production and quality and clonal growth among others. The genetic bases of parallel evolutionary trends (e.g. changes to short life cycles, or changes from annual to perennial growth) will be assessed and will provide a basis for future functional analyses.
The data and resources developed with this project will be readily available to the scientific community through the CGP web site and commercial distributors of clones and arrays. Multiple national and international interactions with the academic and private sectors will allow for rapidly released agriculturally useful information and genetically diverse accessions. Our project is complementary to downstream programs in the private sector.
The CGP will have significant economic impact and generate permanent resources for the Compositae, one of the largest and ecologically successful families. Lettuce is one of the top ten US crops and sunflower ranks #14 worldwide. The family also includes many minor crops, important weeds, and species with novel biochemistries. The CGP funnels basic genomics information to crop improvement by efficiently leveraging information from the sequencing and functional genomics of model organisms. The project contributes to the genetic data being developed across all plants.
The CGP emphasizes multidisciplinary teams with expertise drawn from multiple universities. The CGP integrates genetics, biochemistry, physiology, and bioinformatics and will provide broad training in these areas. In addition, an effective outreach program that impacts all levels of students is in place. The CGP will provide research experience to minorities, especially at Cal Poly Pomona and U. Mass., Boston and introduce computer science majors to biology.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Argyris, J., Dahal, P., Truco, M.J., Ochoa, O., Still. D.W., Michelmore, R.W., and Bradford, K.J.. "Genetic analysis of lettuce seed thermoinhibition," Acta Horticulturae, v.782, 2007, p. 23.
Argyris, J., M.J. Truco, O. Ochoa, S.J. Knapp, D.W. Still, G. Lenssen, J. Schut, R.W. Michelmore, and K.J. Bradford. "Quantitative trait loci associated with seed and seedling traits in Lactuca," Theoretical and Applied Genetics, v.111, 2005, p. 1365.
Argyris, J.M., Dahal, P., Hayashi, E., Still, D.W., and Bradford, K.J.. "Genetic variation for lettuce seed thermoinhibition is associated with temperature-sensitive expression of abscisic acid, gibberellin and ethylene biosynthesis, metabolism and response genes," Plant Physiology, v.148, 2008.
Baack, E.J., Y. Sapir, M.A. Chapman, J.M. Burke, and L.H. Rieseberg.. "Selection on domestication traits and QTLs in crop-wild sunflower hybrids.," Molecular Ecology, v.17, 2008, p. 666.
Barker, M.S., N.C. Kane, A. Kozik, R.W. Michelmore, M. Matvienko, S.J. Knapp, and L.H. Rieseberg. "Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years," Molecular Biology and Evolution, v.25, 2008, p. 2445.
Bethke PC, Libourel IGL, Aoyama N, ChungY-Y, Still DW, and Jones R.L.. "The Arabidopsis aleurone layer responds to nitric oxide, gibberellin, and abscisic acid and is
sufficient and necessary for seed dormancy.," Plant Physiology, v.143, 2007, p. 1173.
Burke, J.M., S.J. Knapp, and L.R. Rieseberg. "Genetic consequences of a recent selective sweep in cultivated sunflower," Genetics, v.171, 2005, p. 1933.
Burke, J.M., Z. Lai, M. Salmaso, T. Nakazato, S. Tang, A. Heesacker, S.J. Knapp, and L.H. Rieseberg. "Comparative mapping and rapid karyotypic evolution in Helianthus," Genetics, v.167, 2004, p. 449.
Bushman, B.S., Scholte, A.A., Cornish, K., Scott, D.J., Brichta, J.L., Vederas, J.C., Ochoa, O., Michelmore, R.W., Shintani, D., Knapp, S.J.. "Identification and characterization of natural rubber from two Lactuca species.," Phytochemistry, v.67, 2006, p. 2590.
Chapman, M., J. C. Chang, D. Weisman, R. Kesseli and J. Burke.. "Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae," Theoretical and Applied Genetics, v.115, 2007, p. 747.
Church, S.A., K. Livingstone, Z. Lai, A. Kozik, S.J. Knapp, R.W. Michelmore, and L.H. Rieseberg. "Using variable rate models to identify genes under selection in pairwise comparisons: its
validity and limitations for EST sequences.," Journal of Molecular Evolution, v.64, 2007, p. 171.
Dempewolf, H., L.H. Rieseberg, and Q. Cronk. "Crop domestication in the Compositae: a family-wide trait assessment," Genetic Resources and Crop Evolution, 2008.
Dussel, C.M., V. Hahn, S.J. Knapp, and E. Bauer. "PlArg from Helianthus argophyllus is unlinked to other known downy mildew resistance
genes in sunflower," Theoretical and Applied Genetics, v.2004, 2004, p. 1083.
Filichkin S, Slabaugh MB, Knapp SJ. "Thioesterases isolated from Cuphea calophylla, a high laurate species, have broad substrate
specificities and complement an Arabidopsis fatb mutant.," European Journal of Lipid Science and Technology, v.108, 2006, p. 979.
Gandhi S., A.F. Heesacker, C.A. Freeman, J. Argyris, K. Bradford, and S.J. Knapp. "The self-incompatibility locus (S) and quantitative trait loci for self-pollination and seed
dormancy in sunflower," Theoretical and Applied Genetics, v.111, 2004, p. 619.
Hajduch M, Castell JE, Tang S, Hearne LB, Knapp SJ, Thelen JJ. "Protoemic analysis of near-isogenic sunflower varieties differing in seed oil content suggests," Journal of Proteome Research, v.6, 2007, p. 323.
Harter, A.V., K.A. Gardner, D. Falush, D.L. Lentz, R. Bye, L.H. Rieseberg. "Origin of extant domesticated sunflowers in eastern North America," Nature, v.430, 2004, p. 201.
Hass, C., Tang, S., Leonard, S., Miller, J.F., Traber, M., and Knapp, S.J.. "Novel tocopherol (vitamin E) profiles are produced by mutations among duplicated
epistatically interacting methyltransferase loci in sunflower," Theoretical and Applied Genetics, v.113, 2006, p. 783.
Hass, C., Tang, S., Leonard, S., Miller, J.F., Traber, M., and Knapp, S.J.. "Three non-allelic epistatically interacting methyltransferase mutations produce novel tocopherol (vitamin E) profiles in sunflower," Theoretical and Applied Genetics, v.113, 2006, p. 783.
Hayashi E., Aoyama N, Wu Y, Chi H-C, Boyer SK, Still DW.. "Multiplexed, quantitative gene expression analysis for lettuce seed germination on
GenomeLab GeXP genetic analysis system.," Application Information Bulletin, v.A-102, 2007, p. 95.
Heesacker A, Gao W, Kishore VK, Kolkman JM, Tang S, Gingle A, Kozik A, Michelmore RW, Lai Z, Rieseberg LH, Knapp SJ. "SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility," Theoretical and Applied Genetics, v.117, 2008, p. 1021.
Kane, N.C., and L.H. Rieseberg. "Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in
common sunflower, Helianthus annuus.," Genetics, v.17, 2007, p. 1803.
Kane, N.C., and L.H. Rieseberg. "Genetics and evolution of weedy Helianthus annuus populations: evidence of multiple origins," Molecular Ecology, v.17, 2008, p. 384.
Kolkman JM, Berry S, Leon A, Burke JM, Knapp SJ. "Single nucleotide polymorphisms and linkage disequilibrium in sunflower.," Genetics, v.177, 2007, p. 457.
Kolkman, J.M., M.B. Slabaugh, J.M. Bruniard, S.T. Berry, S.B. Bushman, G. Abratti, A. Zambelli, J.F. Miller, A. Leon, and S.J. Knapp. "Acetohydroxyacid synthase mutations conferring resistance to imidazolinone or
sulfonylurea herbicides in wild sunflower biotypes," Theoretical and Applied Genetics, v.109, 2004, p. 1147.
Lai, Z., B. Gross, Y. Zou, J. Andrews, and L. H. Rieseberg. "Detecting differential gene expression in homoploid hybrid sunflower species using
microarrays.," Molecular Ecology, v.15, 2006, p. 1213.
Lai, Z., Livingstone, K., Zou, Y. Church, S.A., Knapp, S.J., J. Andrews, and Rieseberg, L.H.. "Identification and mapping of SNPs from ESTs in sunflower.," Theoretical and Applied Genetics, v.111, 2005, p. 1532.
Lai, Z., N.C. Kane, Y. Zou, and L.H. Rieseberg. "Natural variation in gene expression between wild and weedy populations of Helianthus annuus," Genetics, v.179, 2008, p. 1881.
Lai, Z., Nakazato, T., Salmaso, M., Burke, J.M., S. Tang, S., Knapp, S.J., and Rieseberg, L.H.. "Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid
sunflower species," Genetics, v.171, 2005, p. 291.
Lee Timms, Rosmery Jimenez, Mike Chase, Leah McHale, Dean Lavelle, Alex Kosak, Zhao, Richard Michelmore, Loren Rieseberg, Steven Knapp, Rick Kesseli. "Analyses of Synteny between Arabidopsis thaliana and Species in the Compositae Reveal a
Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements," Genetics, v.173, 2006, p. 2227.
Lexer, C., D.M. Rosenthal, O. Raymond, L. Donovan, and L.H. Rieseberg. "Genetics of species differences in the wild annual sunflowers, Helianthus annuus and H.
petiolaris.," Genetics, v.169, 2005, p. 2225.
Micic, Z., V. Hahn, E. Bauer, C.C. Schoen, S.J. Knapp, S. Tang, and A.E. Melchinger. "Identification and validation of QTL for Sclerotinia midstalk rot resistance in sunflower by
selective genotyping," Theoretical and Applied Genetics, v.111, 2005, p. 233.
Micic, Z., V. Hahn, E. Bauer, C.C. Schoen, S.J. Knapp, S. Tang, and A.E. Melchinger.. "QTL mapping of Sclerotinia midstalk rot resistance in sunflower," Theoretical and Applied Genetics, v.109, 2004, p. 1474.
Perez-Vich B, Berry ST, Velasco L, Fernandez-Martinez JM, Gandhi S, Freeman C, Heesacker A, Knapp SJ, and Leon AJ. "Genetic mapping of nuclear male-sterility genes in sunflower," Crop Science, v.45, 2005, p. 1851.
Perez-Vich B., Steven J. Knapp, A.J. Leon, J.M. Fernandez-Martinez, and S.T. Berry. "Mapping minor QTL for increased stearic acid content in sunflower seed oil," Molecular Breeding, v.13, 2004, p. 313.
Perez-Vich, B., B. Akhtouch, S.J. Knapp, A.J. Leon, L. Velasco, J.M. Fernandez-Martinez, and S.T. Berry. "Quantitative trait loci for broomrape (Orobanche cumana Wallr.) resistance in sunflower," Theoretical and Applied Genetics, v.109, 2004, p. 92.
Radwan, O., Ghandi, S., Heesacker, A.F., Whitaker, B., Taylor, C.A., Plozik, A., Kesseli, R., Kozik, A., Michelmore, R.W., and Knapp, S.J.. "Genetic diversity and genomic distribution of homologs encoding NBS-LRR disease resistance proteins in sunflower," Mol Genetics Genomics, v.280, 2008, p. 111.
Rieseberg, L.H., and J.M. Burke. "Molecular evidence and the origin of the domesticated sunflower," Proceedings of the National Academy of Sciences USA, v.105, 2008, p. E46.
Rieseberg, L.H., Kim, S.-C. R.A. Randell, K.D. Whitney, B.L. Gross, C. Lexer, and K. Clay. "Hybridization and the colonization of novel habitats by annual sunflowers," Genetica, v.129, 2007, p. 149.
Schuppert, G.F., Tang, S., Slabaugh, M.B., and Knapp, S.J.. "The sunflower high-oleic mutant Ol carries variable tandem repeats of FAD2-1, a seed-
specific oleoyl-phosphatidyl choline desaturase.," Molecular Breeding, v.17, 2006, p. 241.
Tang, S., A. Leon, and S.J. Knapp. "Quantitative trait loci for genetically correlated seed traits are tightly linked to branching and
pericarp pigment loci in sunflower
in sunflower," Crop Science, v.46, 2006, p. 721.
Tang, S., Hass, C., and Knapp, S.J.. "Ty3/gypsy-like retrotransposon knockout of a 2-methyl-6-phytyl-1,4-benzoquinone
methyltransferase is non-lethal, unmasks a cryptic paralogous mutation, and enhances the
synthesis of ?- and ?-tocopherol in sunflower.," Theoretical and Applied Genetics, v.113, 2006, p. 767.
Tang, S., Hass, C., and Knapp, S.J.. "Ty3/gypsy-like retrotransposon knockout of a 2-methyl-6-phytyl-1,4-benzoquinone methyltransferase is non-lethal, uncovers a cryptic paralogous mutation, and produces novel tocopherol (vitamin E) profiles in sunflower," Theoretical and Applied Genetics, v.113, 2006, p. 767.
Timms, L., Jimenez, R., Chase, M., McHale, L., Lavelle, D., Kosak, A., Lai, Z., Michelmore, R., Rieseberg, L., Knapp, S., Kesseli, R.. "Analyses of Synteny between Arabidopsis thaliana and Species in the Compositae Reveal a," Genetics, v.173, 2006, p. 2227.
Timms, L; Jimenez, R; Chase, M; Lavelle, D; McHale, L; Kozik, A; Lai, Z; Heesacker, A; Knapp, S; Rieseberg, L; Michelmore, R; Kesseli, R. "Analyses of synteny between Arabidopsis thaliana and species in the asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements," GENETICS, v.173, 2006, p. 2227-2235.
Truco, MJ; Antonise, R; Lavelle, D; Ochoa, O; Kozik, A; Witsenboer, H; Fort, SB; Jeuken, MJW; Kesseli, RV; Lindhout, P; Michelmore, RW; Peleman, J. "A high-density, integrated genetic linkage map of lettuce (Lactuca spp.)," THEORETICAL AND APPLIED GENETICS, v.115, 2007, p. 735-746.
Wood, T.E., J.M. Burke, and L.H. Rieseberg. "Parallel genotypic adaptation: when evolution repeats itself," Genetica, v.123, 2005, p. 157.
Yue B, Radi SA, Vick BA, Cai X, Tang S, Knapp SJ, Gulya TJ, Miller JF, Hu J. "Identifying quantitative trait loci for resistance to Sclerotinia head rot in two USDA sunflower germplasms," Phytopathology, v.98, 2008, p. 926.
Zhang, F.Z, Wagstaff, C., Rae, A.M., Kaur, A., Keevil, W.C., Rothwell, S.D., Clarkson, G.J.J., Michelmore, R.W., Truco, M.J., Dixon, M.S., Taylor, G.. "QTLs for shelf life in lettuce co-locate with those for leaf biophysical properties but not with those for leaf developmental traits," Journal of Experimental Botany, v.58, 2007, p. 1433.
