Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea

Genetics

Volumn 168, Issue 1, 2004, Pages 425-434

  Tiffin, Peter ^a   Hacker, Robert ^b   Gaut, Brandon S ^b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; COEVOLUTION; CONTROLLED STUDY; DIPLOIDY; DNA POLYMORPHISM; DOMESTICATION; EXON; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; HAPLOTYPE; HM2 GENE; HYPOTHESIS; INTRASPECIFIC VARIATION; INTRON; MAIZE; MOLECULAR EVOLUTION; MPI GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT DEFENSE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STATISTICAL DISTRIBUTION; TETRAPLOIDY; WIP1 GENE;

ALLELES; BASE SEQUENCE; DNA PRIMERS; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HOST-PARASITE RELATIONS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES; PLANT PROTEINS; PROTEINASE INHIBITORY PROTEINS, SECRETORY; PROTEINS; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS); ZEA MAYS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA; ZEA; ZEA DIPLOPERENNIS; ZEA MAYS; ZEA PERENNIS;

EID: 3843128155     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.023028     Document Type: Article

References (63)

1. BERGELSON, J., G. DWYER and J. J. EMERSON, 2001 Models and data on plant-enemy coevolution. Annu. Rev. Genet. 35: 469-499.
2. BITTNER-EDDY, P., C. CAN, N. GUNN, M. PINEL, M. TOR et al., 1999 Genetic and physical mapping of the RPP13 locus in Arabidopsis responsible for specific recognition of several Peronopora parasitca (downy mildew) isolates. Mol. Plant-Microbe Interact. 12: 792-802.
3. BUCKLER, E. S., and T. P. HOLTSFORD, 1996 Zea systematics: ribosomal ITS evidence. Mol. Biol. Evol. 13: 612-622.
4. CAICEDO, A. L., B. A. SCHAAL and B. A. KUNKEL, 1999 Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 96: 302-306.
5. CLARK, R. M., E. LINTON, J. MESSING and J. F. DOEBLEY, 2004 Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc. Natl. Acad. Sci. USA 101: 700-707.
6. CLAUSS, M. J., and T. MITCHELL-OLDS, 2003 Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life histories. Mol. Ecol. 12: 1287-1299.
7. CORDERO, M. J., D. RAVENTOS and B. SAN SEgUNDO, 1994 Expression of a maize proteinase inhibitor gene is induced in response to wounding and fungal infection: systemic wound-response of a monocot gene. Plant J. 6: 141-150.
8. DE MEAUX J., and T. MITCHELL-OLDS, 2003 Evolution of plant resistance at the molecular level: ecological context of species interactions. Heredity 94: 343-352.
9. DE QUIROS, H. C., R. MAGRATH, D. MCCALLUM, J. KROYMANN, D. SCNABELRAUCH et al., 2000 Alpha-keto acid elongation and glucosinolate biosynthesis in Arabidopsis thaliana. Theor. Appl. Genet. 101: 429-437.
10. DOEBLEY, J., 1990 Molecular evidence and the evolution of maize. Econ. Bot. 44: 6-27.
11. DOEBLEY, J., A. STEC and C. GUSTAS, 1995 Teosinte branched 1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141: 333-346.
12. DOEBLEY, J., A. STEC and L. HUBBARD, 1997 The evolution of apical dominance in maize. Nature 386: 485-488.
13. DOEBLEY, J. F., W. RENFROE and A. BLANTON, 1987 Restriction site variation in the Zea chloroplast genome. Genetics 117: 139-147.
14. FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
15. FITCH, W. M., 1976 Molecular evolutionary clocks, pp. 160-178 in Molecular Evolution, edited by F. J. AYALA. Sinauer Associates, Sunderland, MA.
16. FU, Y. X., 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-952.
17. GAUT, B. S., B. R. MORTON, B. M. MCCAIG and M. T. CLEGG, 1996 Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 93: 10274-10279.
18. HILDER, V. A., A. M. R. GATEHOUSE, S. E. SHEERMAN, R. F. BARKER and D. BOULTER, 1987 A novel mechanism of insect resistance engineered into tobacco. Nature 330: 160-163.
19. HILL, R. R., 1971 Selection in autotetraploids. Theor. Appl. Genet. 41: 181-186.
20. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
21. ILTIS, H. H., J. F. DOEBLEY, R. GUZMAN and B. PAZY, 1979 Zea diploperennis (Gramineae): a new teosinte from Mexico. Science 203: 186-188.
22. INNAN, H., and F. TAJIMA, 1999 The effect of selection on the amounts of nucleotide variation within and between allelic classes. Genet. Res. 73: 15-28.
23. JAYAKAR, S. D., 1970 A mathematical model for interaction of gene frequencies in a parasite and its host. Theor. Pop. Biol. 1: 140-164.
24. JOHAL, G. S., and S. P. BRIGGS, 1992 Reductase activity encoded by the HM1 disease resistance gene in maize. Science 258: 985-987.
25. JOHNSON, R., J. NARVAEZ, G. AN and C. A. RYAN, 1989 Expression of proteinase inhibitors I and II in transgenic tobacco plants: effects on natural defense against Manduca sexta larvae. Proc. Natl. Acad. Sci. USA 86: 9871-9875.
26. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "Hitchiking Effect" revisited. Genetics 123: 887-899.
27. KAWABE, A., and N. T. MIYASHITA, 1999 DNA variation in the basic chitinase locus (ChiB) region of the wild plant Arabidopsis thaliana. Genetics 153: 1445-1453.
28. KAWABE, A., and N. T. MIYASHITA, 2002 DNA variation in the acidic chitinase locus (ChiA) region in Arabis gemmifera and its related species. Genes Genet. Syst. 77: 167-175.
29. KAWABE, A., H. INNAN, R. TERAUCHI and N. T. MIYASHITA, 1997 Nucleotide polymorphism in the acidic chitinase focus (ChiA) region of the wild plant Arabidopsis thaliana. Mol. Biol. Evol. 14: 1303-1315.
30. KREITMAN, M., and R. R. HUDSON, 1991 Inferring the evolutionary histories of Adh and the Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics 127: 565-582.
31. KROYMANN, J., S. DONNERHACKE, D. SCHNABELRAUCH and T. MITCHELL-OLDS, 2003 Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc. Natl. Acad. Sci. USA 100: 14587-14592.
32. KUNKEL, B. N., 1996 A useful weed put to work: genetic analysis of disease resistance in Arabidopsis thaliana. Trends Genet. 12: 63-69.
33. KUMAR, S., K. TAMURA, I. JAKOBSEN and M. NEI, 2000 MEGA: molecular evolutionary genetics analyses. Pennsylvania State University/Arizona State University, University Park, PA/Tempe, AZ.
34. LEVIN, D. A., 1983 Polyploidy and novelty in flowering plants. Am. Nat. 122: 1-25.
35. MAURICIO, R., E. A. STAHL, T. KORVES, D. C. TIAN, M. KREITMAN et al., 2003 Natural selection for polymorphism in the disease resistance gene Rps2 of Arabidopsis thaliana. Genetics 163: 735-746.
36. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh1 locus in Drosophila. Nature 351: 652-654.
37. MULTANI, D. S., R. B. MEELEY, A. H. PATERSON, J. GRAY, S. P. BRIGGS et al., 1998 Plant-pathogen micro evolution: molecular basis for the recent origin of a disease in maize. Proc. Natl. Acad. Sci. USA 95: 1686-1691.
38. NELSON, O. E., and A. J. ULLSTRUP, 1964 Resistance to leaf spot in maize. J. Hered. 55: 195-199.
39. NORDBORG, M., J. O. BOREVITZ, J. BERGELSON, C. C. BERRY, J. CHORY et al., 2002 The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30: 190-193.
40. NUISMER, S. L., and J. N. THOMPSON, 2001 Plant polyploidy and non-uniform effects on insect herbivores. Proc. R. Soc. Lond. Ser. B Biol. Sci. 268: 1937-1940.
41. OTTO, S. P., and J. WHITTON, 2000 Polyploid incidence and evolution. Annu. Rev. Genet. 34: 401-437.
42. PRZEWORSKI, M., 2003 Estimating the time since the fixation of a beneficial allele. Genetics 164: 1667-1676.
43. PURUGGANAN, M. D., and J. I. SUDDITH, 1999 Molecular population genetics of floral homeotic loci: departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA gene of Arabidopsis thaliana. Genetics 151: 839-848.
44. ROHRMEIER, T., and L. LEHLE, 1993 WIP1, a wound-inducible gene from maize with homology to Bowman-Birk proteinase inhibitors. Plant Mol. Biol. 22: 783-792.
45. ROSE, L. E., P. D. BITTNER-EDDY, C. H. LANGLEY, E. B. HOLUB, R. W. MICHEMORE et al., 2004 Maintenance of extreme amino acid diversity at the disease resistance gene RPP13 in Arabidopsis thaliana. Genetics 166: 1517-1527.
46. ROZAS, J., and R. ROZAS, 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
47. RYAN, C. A., 1990 Protease inhibitors in plants: genes for improving defenses against insects and pathogens. Annu. Rev. Phytopathol. 28: 425-449.
48. SANCHEZ, G. J. J., T. A. K. YAMAKAKE, M. A. SANMIGUEL, J. M. H. CASILLAS, A. L. RODRIGUEZ et al., 1998 Distribucion y characterization del teocintle. Instituto Nacional de Investigaciones Forestales, Agricolas, y Pecuarias, Mexico City.
49. SEGER, J., 1988 Dynamics of some simple host-parasite models with more than two genotypes in each species. Philos. Trans. R. Soc. Lond. B 319: 541-555.
50. SEGER, J., 1990 Evolution of exploiter-victim relationships, pp. 3-25 in Natural Enemies: The Population Biology of Predators, Parasites and Diseases, edited by M. J. CRAWLEY. Blackwell Scientific, London.
51. SHARBEL, T. F., B. HAUBOLD and T. MITCHELL-OLDS, 2000 Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Mol. Ecol. 9: 2109-2118.
52. STAHL, E. A., G. DWYER, R. MAURICIO, M. KREITMAN and J. BERGELSON, 1999 Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400: 667-671.
53. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
54. TAJIMA, F., 1993 Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135: 599-607.
55. TAMAYO, M. C., M. RUFAT, J. M. BRAVO and B. SAN SEGUNDO, 2000 Accumulation of a maize proteinase inhibitor in response to wounding and insect feeding, and characterization of its activity toward digestive proteinases of Spodoptera littoralis larvae. Planta 211: 62-71.
56. TIAN, D., H. ARAKI, E. A. STAHL, J. BERGELSON and M. KREITMAN, 2002 Signature of balancing selection in Arabidopsis. Proc. Natl. Acad. Sci. USA 99: 11525-11530.
57. TIFFIN, P., 2004 Comparative evolutionary histories of chitinase genes in the genus Zea and family Poaceae. Genetics 167: 1331-1340.
58. TIFFIN, P., and B. S. GAUT, 2001a Molecular evolution of the wound-induced serine protease inhibitor wip1 in Zea and related genera. Mol. Biol. Evol. 18: 2092-2101.
59. TIFFIN, P., and B. S. GAUT, 2001b Sequence diversity in the autotetraploid Zea perennis and the closely related diploid Z. diploperennis: insights from four nuclear loci. Genetics 158: 401-412.
60. WANG, R. L., A. STEC, J. HEY, L. LUKENS and J. DOEBLEY, 1999 The limits of selection during maize domestication. Nature 398: 236-239.
61. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 188-193.
62. WRIGHT, S. I., B. LAUGA and D. CHARLESWORTH, 2003 Subdivision and haplotye structure in natural populations of Arabidopsis lyrata. Mol. Ecol. 12: 1247-1263.
63. ZHANG, L., A. S. PEEK, D. DUNAMAS and B. S. GAUT, 2002 Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis). Genetics 162: 851-860.