Ecological genetics and genomics of plant defences: Evidence and approaches

Functional Ecology

Volumn 25, Issue 2, 2011, Pages 312-324

  Anderson, Jill T ^a   Mitchell Olds, Thomas ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Candidate gene; Genome wide association studies; Plant defence; Population genomics; Quantitative trait loci; Transgenics

Indexed keywords

ALLELE; ANTIHERBIVORE DEFENSE; BIOINFORMATICS; DICOTYLEDON; EVOLUTIONARY BIOLOGY; FITNESS; GENE EXPRESSION; GENERALIST; GENETIC ANALYSIS; GENETIC STRUCTURE; GENOMICS; HERBIVORY; INTERDISCIPLINARY APPROACH; NATURAL SELECTION; PLANT-HERBIVORE INTERACTION; SPECIALIST; TOLERANCE;

ARABIDOPSIS;

EID: 79952662416     PISSN: 02698463     EISSN: 13652435     Source Type: Journal    
DOI: 10.1111/j.1365-2435.2010.01785.x     Document Type: Article

References (153)

1. Agrawal, A. (2011) Plant defense evolution: synthesis and future directions. Functional Ecology, 25, 420-432.
2. Agrawal, A.A. & Fishbein, M. (2006) Plant defense syndromes. Ecology, 87, S132-S149.
3. Atwell, S., Huang, Y., Vilhjalmsson, B., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A., Hu, T. & Al, E. (2010) Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines. Nature, 465, 627-631.
4. Bae, K.M., Kwom, Y.S., Cho, I.H. & Yi, S.I. (2006) Use of cDNA-AFLP for transcript profiling in narrow genetic pools; for example, cucumber (Cucumis sativus L.). Plant Breeding, 125, 488-492.
5. Bakker, E., Toomajian, C., Kreitman, M. & Bergelson, J. (2006) A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell, 18, 1803-1818.
6. Balasubramanian, S., Sureshkumar, S., Agrawal, M., Michael, T.P., Wessinger, C., Maloof, J.N., Clark, R., Warthmann, N., Chory, J. & Weigel, D. (2006) The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nature Genetics, 38, 711-715.
7. Baldwin, I.T., Halitschke, R., Paschold, A., Von Dahl, C.C. & Preston, C.A. (2006) Volatile signaling in plant-plant interactions: "Talking trees" in the genomics era. Science, 311, 812-815.
8. Barakat, A., Bagniewska-Zadworna, A., Choi, A., Plakkat, U., DiLoreto, D.S., Yellanki, P. & Carlson, J.E. (2009) The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression. BMC Plant Biology, 9, 26.
9. Basten, C., Weir, B. & Zeng, Z.-B. (2004) QTL Cartographer., Department of Statistics, North Carolina State University, Raleigh, NC.
10. Benedito, V., Visser, P., Angenent, G. & Krens, F. (2004) The potential of virus-induced gene silencing for speeding up functional characterization of plant genes. Genetics and Molecular Research, 3, 323-341.
11. Bergelson, J., Dwyer, G. & Emerson, J.J. (2001) Models and data on plant-enemy coevolution. Annual Review of Genetics, 35, 469-499.
12. Bottcher, C., Westphal, L., Schmotz, C., Prade, E., Scheel, D. & Glawischnig, E. (2009) The multifunctional enzyme CYP71B1 (PHYTOALEXIN DEFICIENT3) converts cysteine-indole-3-acetonitrile to camalexin in the indole-3-acetonitrile metabolic network of Arabidopsis thaliana. The Plant Cell, 21, 1830-1845.
13. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C.P., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J. & Vingron, M. (2001) Minimum information about a microarry experiment (MIAME)-toward standards for microarray data. Nature Genetics, 29, 365-371.
14. Broekgaarden, C., Poelman, E., Steenhuis, G., Voorrips, R.E., Dicke, M. & Vosman, B. (2007) Genotypic variation in genome-wide transcription profiles induced by insect feeding: Brassica oleracea - Pieris rapae interactions. BMC Genomics, 8, 239.
15. Broekgaarden, C., Poelman, E.H., Steenhuis, G., Voorrips, R.E., Dicke, M. & Vosman, B. (2008) Responses of Brassica oleracea cultivars to infestation by the aphid Brevicoryne brassicae: an ecological and molecular approach. Plant Cell and Environment, 31, 1592-1605.
16. Broekgaarden, C., Poelman, E.H., Voorrips, R.E., Dicke, M. & Vosman, B. (2010) Intraspecific variation in herbivore community composition and transcriptional profiles in field-grown Brassica oleracea cultivars. Journal of Experimental Botany, 61, 807-819.
17. Broman, K.W. & Sen, S. (2009) A guide to QTL Mapping wtih R/qtl. Springer, New York.
18. Burch-Smith, T., Anderson, J.C., Martin, G. & Dinesh-Kumar, S.P. (2004) Applications and advantages of virus-induced gene silencing for gene function studies in plants. The Plant Journal, 39, 734-746.
19. Butaye, K.M.J., Cammue, B.P.A., Delaure, S.L. & De Bolle, M.F.C. (2005) Approaches to minimize variation of transgene expression in plants. Molecular Breeding, 16, 79-91.
20. Caldwell, K.S. & Michelmore, R.W. (2009) Arabidopsis thaliana genes encoding defense signaling and recognition proteins exhibit contrasting evolutionary dynamics. Genetics, 181, 671-684.
21. Carmona, D., Lajeunesse, M. & Johnson, M. (2011) Plant traits that predict resitance to herbivores. Functional Ecology 25, 358-367.
22. Chan, E.K.F., Rowe, H.C. & Kliebenstein, D.J. (2010) Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping. Genetics, 185, 991-1007.
23. Chen, H., Wilkerson, C.G., Kuchar, J.A., Phinney, B. & Howe, G. (2005) Jasmonate-inducible plant enzymes degrade essential amino acids in the herbivore midgut. Proceedings of the National Academy of Sciences of the United States of America, 102, 19237-19242.
24. Chuaqui, R.F., Bonner, R.F., Best, C.J.M., Gillespie, J.W., Flaig, M.J., Hewitt, S.M., Phillips, J.L., Krizman, D.B., Tangrea, M.A., Ahram, M., Linehan, W.M., Knezevic, V. & Emmert-Buck, M.R. (2002) Post-analysis follow-up and validation of microarray experiments. Nature Genetics, 32, 509-514.
25. Collard, B.C.Y., Jahufer, M.Z.Z., Brouwer, J.B. & Pang, E.C.K. (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica, 142, 169-196.
26. Dallas, P.B., Gottardo, N.G., Firth, M.J., Beesley, A.H., Hoffmann, K., Terry, P.A., Freitas, J.R., Boag, J.M., Cummings, A.J. & Kees, U.R. (2005) Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR - how well do they correlate. BMC Genomics, 6, 59.
27. De Meaux, J. & Mitchell-Olds, T. (2003) Evolution of plant resistance at the molecular level: ecological context of species interactions. Heredity, 91, 345-352.
28. Dean, A.M. & Thornton, J.W. (2007) Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics, 8, 675.
29. Diatchenko, L., Lau, Y.F., Campbell, A.P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S., Lukyanov, K., Gurskaya, N., Sverdlo, E.D. & Siebert, P.D. (1996) Suppression substractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proceedings of the National Academy of Sciences of the United States of America, 93, 6025-6030.
30. Donson, J., Fang, Y., Espiritu-Santo, G., Xing, W., Salazar, A., Miyamoto, S., Armendarez, V. & Volkmuth, W. (2002) Comprehensive gene expression analysis by transcript profiling. Plant Molecular Biology, 48, 75-97.
31. Drigalenko, E. (1998) How sib pairs reveal linkage. American Journal of Human Genetics, 63, 1242-1245.
32. Ekblom, R., Balakrishnan, C.N., Burke, T. & Slate, J. (2010) Digital gene expression analysis of the zebra finch genome. BMC Genomics, 11, 219.
33. Erickson, D.L., Fenster, C.B., Stenoien, H. & Price, D. (2004) Quantitative trait locus analyses and the study of evolutionary processes. Molecular Ecology, 13, 2505-2522.
34. Faris, J.D., Li, W.L., Liu, D.J., Chen, P.D. & Gill, B.S. (1999) Candidate gene analysis of quantitative disease resistance in wheat. Theoretical and Applied Genetics, 98, 219-225.
35. Feder, M.E. & Mitchell-Olds, T. (2003) Evolutionary and ecological functional genomics. Nature Reviews Genetics, 4, 651-657.
36. Fornoni, J. (2011) Ecological and evolutionary implications of plant tolerance to herbivory. Functional Ecology, 25, 399-407.
37. Freeman, J.S., O'reilly-Wapstra, J.M., Vaillancourt, R.E., Wiggins, N. & Potts, B.M. (2008) Quantitative trait loci for key defensive compounds affecting herbivory of eucalypts in Australia. New Phytologist, 178, 846-851.
38. Fridman, E., Carrari, F., Liu, Y., Fernie, A. & Zamir, D. (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science, 305, 1786-1789.
39. Fulker, D.W. & Cherny, S.S. (1996) An improved multipoint sib-pair analysis of quantitative traits. Behavior Genetics, 26, 527-532.
40. Gardner, K.M. & Latta, R.G. (2007) Shared quantitative trait loci underlying the genetic correlation between continuous traits. Molecular Ecology, 16, 4195-4209.
41. Gelvin, S.B. (2003) Agobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiology and Molecular Biology Reviews, 67, 16-37.
42. Gilardoni, P.A., Schuck, S., Jungling, R., Rotter, B., Baldwin, I.T. & Bonaventure, G. (2010) SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses. BMC Plant Biology, 10, 66.
43. Gonzalez-Martinez, S.C., Wheeler, N.C., Ersoz, E., Nelson, C.D. & Neale, D.B. (2007) Association genetics in Pinus taeda L.I. wood property traits. Genetics, 175, 399-409.
44. Gould, B. & Kramer, E.M. (2007) Virus-induced gene silencing as a tool for functional analyses in the emerging model plant Aquilegia (columbine, Ranunculaceae). Plant Methods, 3, 6.
45. Gupta, P., Rustgi, S. & Kulwal, P. (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology, 57, 461-485.
46. Halitschke, R. & Baldwin, I.T. (2003) Antisense LOX expression increases herbivore performance by decreasing defense responses and inhibiting growth-related transcriptional reorganization in Nicotiana attenuata. The Plant Journal, 36, 794-807.
47. Halkier, B.A. & Gershenzon, J. (2006) Biology and biochemistry of glucosinolates. Annual Review of Plant Biology, 57, 303-333.
48. Hamada, H., Matsumura, H., Tomita, R., Terauchi, R., Suzuki, K. & Kobayashi, K. (2008) SuperSAGE revealed different classes of early resistance response genes in capsicum chinense plants harboring L-3-resistance gene infected with pepper mild mottle virus. Journal of General Plant Pathology, 74, 313-321.
49. Hardy, J. & Singleton, A. (2009) Genomewide association studies and human disease. The New England Journal of Medicine, 360, 1759-1768.
50. Herrera, C.M. & Bazaga, P. (2009) Quantifying the genetic component of phenotypic variation in unpedigreed wild plants: tailoring genomic scan for within-population use. Molecular Ecology, 18, 2602-2614.
51. Hohenlohe, P.A., Bassham, S., Etter, P.D., Stiffler, N., Johnson, E.A. & Cresko, W.A. (2010) Population genomics of parallele adaptation in Threespine Stickleback using sequenced RAD tags. Public Library of Science Genetics, 6, e1000862.
52. Holeski, L.M., Chase-Alone, R. & Kelly, J.K. (2010) The genetics of phenotypic plasticity in plant defense: Trichome production in Mimulus guttatus. American Naturalist, 175, 391-400.
53. Hudson, M.E. (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources, 8, 3-17.
54. Iliadou, A., Evans, D.M., Zhu, G., Duffy, D.L., Frazer, I.H., Montgomery, G.W. & Martin, N.G. (2007) Genomewide scans of red cell indices suggest linkage on chromosome 6q23. Journal of Medical Genetics, 44, 24-30.
55. Jain, N., Thatte, J., Braciale, T., Ley, K., O'connell, M. & Lee, J.K. (2003) Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics, 19, 1945-1951.
56. Jermstad, K.D., Bassoni, D.L., Jech, K.S., Wheeler, N.C. & Neale, D.B. (2001) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir I. Timingo f vegetative bud flush. Theoretical and Applied Genetics, 102, 1142-1151.
57. Juenger, T. & Bergelson, J. (2000) The evolution of compensation to herbivory in scarlet gilia, Ipomopsis aggregata: herbivore-imposed natural selection and the quantitative genetics of tolerance. Evolution, 54, 764-777.
58. Kaeppler, S.M., Kaeppler, H.F. & Rhee, Y. (2000) Epigenetic aspects of somaclonal variation in plants. Plant Molecular Biology, 43, 179-188.
59. Kammenga, J., Herman, M.A., Ouborg, N.J., Johnson, L. & Breitling, R. (2007) Microarray challenges in ecology. Trends in Ecology & Evolution, 22, 273-279.
60. Kao, C.-H., Zeng, Z.-B. & Teasdale, R.D. (1999) Multiple interval mapping for quantitative trail loci. Genetics, 152, 1203-1216.
61. Karban, R. (2011) The ecology and evolution of induced resistance against herbivores. Functional Ecology 25, 339-347.
62. Karban, R. & Baldwin, I.T. (1997) Induced responses to herbivory. University of Chicago Press, Chicago.
63. Kessler, A., Halitschke, R. & Baldwin, I.T. (2004) Silencing the jasmonate cascade: induced plant defenses and insect populations. Science, 305, 665-668.
64. Kivimaki, M., Karkkainen, K., Gaudeul, M., Loe, G. & Agren, J. (2007) Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata. Molecular Ecology, 16, 453-462.
65. Kleensang, A., Franke, D., Alcais, A., Abel, L., Muller-Myhsok, B. & Ziegler, A. (2010) An extensive comparison of quantitative trait loci mapping methods. Human Heredity, 69, 202-211.
66. Kliebenstein, D.J. (2009) Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. Annual Review of Plant Biology, 60, 93-114.
67. Kliebenstein, D.J., Figuth, A. & Mitchell-Olds, T. (2002a) Genetic architecture of plastic methyl jasmonate responses in Arabidopsis thaliana. Genetics, 161, 1685-1696.
68. Kliebenstein, D.J., Pedersen, D., Barker, B. & Mitchell-Olds, T. (2002b) Comparative analysis of quantitative trait loci controlling glucosinolates, myrosinase and insect resistance in Arabidopsis thaliana. Genetics, 161, 325-332.
69. Kliebenstein, D.J., West, M., Van Leeuwen, H., Loudet, O., Doerge, R.W. & St. Clair, D.A. (2006) Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics, 7, 308.
70. Knight, C.A., Vogel, H., Kroymann, J., Shumate, A., Witsenboer, H. & Mitchell-Olds, T. (2006) Expression profiling and local adaptation of Boechera holboellii populations for water use efficiency across a naturally occurring water stress gradient. Molecular Ecology, 15, 1229-1237.
71. Kollner, T.G., Held, M., Lenk, C., Hiltpold, I., Turlings, T.C.J., Gershenzon, J. & Degenhardt, J. (2008) A maize (E)-beta-caryophyllene synthase implicated in indirect defense responses against herbivores is not expressed in most American maize varieties. Plant Cell, 20, 482-494.
72. Korth, K.L. (2003) Profiling the response of plants to herbivorous insects. Genome Biology, 4, 221.
73. Kroymann, J. & Mitchell-Olds, T. (2005) Epistasis and balanced polymorphism influencing complex trait variation. Nature, 435, 95-98.
74. Kroymann, J., Donnerhacke, S., Schnabelrauch, D. & Mitchell-Olds, T. (2003) Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proceedings of the National Academy of Sciences of the United States of America, 100, 14587-14592.
75. Krügel, T., Lim, M., Gase, K., Halitschke, R. & Baldwin, I.T. (2002) Agrobacterium-mediated transformation of Nicotiana attenuata, a model ecological expression system. Chemoecology, 12, 177-183.
76. Lambrix, V., Reichelt, M., Mitchell-Olds, T., Kliebenstein, D.J. & Gershenzon, J. (2001) The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and influences Trichoplusia ni herbivory. Plant Cell, 13, 2793-2807.
77. Lawrence, S.D. & Novak, N.G. (2004) Maize genes induced by herbivory and volicitin. Journal of Chemical Ecology, 30, 2543-2557.
78. Leung, Y.F. & Cavalieri, D. (2003) Fundamentals of cDNA microarray data analysis. Trends in Genetics, 19, 649-659.
79. Li, J., Brader, G. & Palva, E.T. (2004) The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell, 16, 319-331.
80. Lou, P., Zhao, J., He, H., Hanhart, C., Del Carpio, D.P., Verkerk, R., Custers, J., Koornneef, M. & Bonnema, G. (2008) Quantitative trait loci for glucosinolate accumulation in Brassica rapa leaves. New Phytologist, 179, 1017-1032.
81. Mackay, T.F.C. (2001) The genetic architecture of quantitative traits. Annual Review of Genetics, 35, 303-339.
82. Mackay, T.F.C., Stone, E.A. & Ayroles, J.F. (2009) The genetics of quantitative traits: challenges and prospects. Nature Reviews Genetics, 10, 565-577.
83. Mannerlof, M. & Tenning, P. (1997) Variability of gene expression in transgenic tobacco. Euphytica, 98, 133-139.
84. Matsumura, H., Reich, S., Ito, A., Saitoh, H., Kamoun, S., Winter, P., Kahl, G., Reuter, M., Kruger, D.H. & Terauchi, R. (2003) Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proceedings of the National Academy of Sciences of the United States of America, 100, 15718-15723.
85. Matsumura, H., Bin Nasir, K.H., Yoshida, K., Ito, A., Kahl, G., Kruger, D.H. & Terauchi, R. (2006) SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nature Methods, 3, 469-474.
86. Mauricio, R. (2005) Ontogenetics of QTL: the genetic architecture of trichome density over time in Arabidopsis thaliana. Genetica, 123, 75-85.
87. Mckay, J.K. & Stinchcombe, J.R. (2008) Ecological genomics of model eukaryotes. Evolution, 62, 2953-2957.
88. Meyers, B.C., Galbraith, D.W., Nelson, T. & Agrawal, V. (2004) Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiology, 135, 637-652.
89. Mitchell-Olds, T. (2001) Arabidopsis thaliana and its wild relatives: a model system for ecology and evolution. Trends in Ecology & Evolution, 16, 693-700.
90. Mitchell-Olds, T. (2010) Complex-trait analysis in plants. Genome Biology, 11, 113.
91. Mitchell-Olds, T. & Schmitt, J. (2006) Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature, 441, 947-952.
92. Mitchell-Olds, T., Willis, J.H. & Goldstein, D.B. (2007) Which evolutionary processes influence natural genetic variation for phenotypic traits? Nature Reviews Genetics, 8, 845-856.
93. Mitra, S., Wunsche, H., Giri, A.P., Hivrale, V. & Baldwin, I.T. (2008) Silencing 7 herbivory-regulated proteins in Nicotiana attenuata to understand their function in plant-herbivore interactions. Functional Ecology, 22, 606-615.
94. Moeller, D.A. & Tiffin, P. (2005) Genetic diversity and the evolutionary history of plant immunity genes in two species of Zea. Molecular Biology and Evolution, 22, 2480-2490.
95. Molina, C., Rotter, B., Horres, R., Udupa, S.M., Besser, B., Bellarmino, L., Baum, M., Matsumura, H., Terauchi, R., Kahl, G. & Winter, P. (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics, 9, 553.
96. Morozova, O. & Marra, M.A. (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics, 92, 255-264.
97. Mortazavi, A., Williams, B., McCue, K.A., Schaeffer, L. & Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5, 621-628.
98. Nikova, V., Palakarcheva, M., Pundeva, R. & Krusteva, D. (1998) Somaclonal variation in cultured in vitro tobacco plants from the hybrid Nicotiana gossey Domain. x N-tabacum L. Israel Journal of Plant Sciences, 46, 35-40.
99. Nordborg, M. & Weigel, D. (2008) Next-generation genetics in plants. Nature, 456, 720-723.
100. Obermeier, C., Hosseini, B., Friedt, W. & Snowdon, R. (2009) Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus. BMC Genomics, 10, 295.
101. O'Neil, S.T., Dzurisin, J.D., Carmichael, R.D., Lobo, N.F., Emrich, S.J. & Hellmann, J.J. (2010) Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics, 11, 310.
102. Ouborg, N.J. & Vriezen, W.H. (2007) An ecologist's guide to ecogenomics. Journal of Ecology, 95, 8-16.
103. Payne, C.T., Zhang, F. & Lloyd, A.M. (2000) GL3 encodes a bHLH protein that regulates trichome development in Arabidopsis through interaction with GL1 and TTG1. Genetics, 156, 1349-1362.
104. Philippe, R.N., Ralph, S.G., Kulheim, C., Jancsik, S.I. & Bohlmann, J. (2009) Poplar defense against insects: genome analysis, full-length cDNA cloning, and transcriptome and protein analysis of the poplar Kunitz-type protease inhibitor family. New Phytologist, 184, 865-884.
105. Pritchard, J., Stephens, M., Rosenberg, N.A. & Donnelly, P. (2000) Association mapping in structure populations. American Journal of Human Genetics, 67, 170-181.
106. Purkayastha, A. & Dasgupta, I. (2009) Virus-induced gene silencing: a versatile tool for discovery of gene functions in plants. Plant Physiology and Biochemistry, 47, 967-976.
107. Ralph, S.G., Oddy, C., Cooper, D., Yueh, H., Jancsik, S., Kolosova, N., Philippe, R., Aeschliman, D., White, R., Huber, D., Ritland, C., Benoit, F., Rigby, T., Nantel, A., Butterfield, Y., Kirkpatrick, R., Chun, E., Liu, J., Palmquist, D., Wynhoven, B., Stott, J., Yang, G., Barber, S., Holt, R.D., Siddiqui, A., Jones, S., Marra, M., Ellis, B., Douglas, C., Ritland, K. & Bohlmann, J. (2006) Genomics of hybrid poplar (Populus trichocarpa X deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defenses in poplar. Molecular Ecology, 15, 1275-1297.
108. Rasmann, S. & Agrawal, A.A. (2009) Plant defense against herbivory: progress in identifying synergism, redundancy, and antagonism between resistance traits. Current Opinion in Plant Biology, 12, 473-478.
109. Restrepo, S., Myers, K.L., Del Pozo, O., Martin, G.B., Hart, A.L., Buell, C.R., Fry, W.E. & Smart, C.D. (2005) Gene profiling of a compatible interaction between Phytophthora infestans and Solanum tuberosum suggests a role for carbonic anhydrase. Molecular Plant-Microbe Interactions, 18, 913-922.
110. Reymond, P., Weber, H., Damond, M. & Farmer, E.E. (2000) Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. The Plant Cell, 12, 707-719.
111. Reymond, P., Bodenhausen, N., Van Poecke, R.M.P., Krishnamurthy, V., Dicke, M. & Farmer, E.E. (2004) A conserved transcript pattern in response to a specialist and a generalist herbivore. The Plant Cell, 16, 3132-3147.
112. Salvi, S. & Tuberosa, R. (2005) To clone or not to clone plant QTLs: present and future challenges. Trends in Plant Science, 10, 297-304.
113. Schenk, P.M., Kazan, K., Wilson, I., Anderson, J.P., Richmond, T., Somerville, S. & Manners, J.M. (2000) Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proceedings of the National Academy of Sciences of the United States of America, 97, 11655-11660.
114. Schmidt, D.D., Kessler, A., Kessler, D., Schmidt, S., Lim, M., Gase, K. & Baldwin, I.T. (2004) Solanum nigrum: a model ecological expression system and its tools. Molecular Ecology, 13, 981-995.
115. Schmidt, D.D., Voelckel, C., Hartl, M., Schmidt, S. & Baldwin, I.T. (2005) Specificity in ecological interactions attack from the same lepidopteran herbivore results in species-specific transcriptional responses in two solanaceous host plants. Plant Physiology, 138, 1763-1773.
116. Schnee, C., Kollner, T.G., Held, M., Turlings, T.C.J., Gershenzon, J. & Dengenhardt, J. (2006) The products of a single maize sesquiterpene synthase form a volatile defense signal that attracts natural enemies of maize herbivores. Proceedings of the National Academy of Sciences of the United States of America, 103, 1129-1134.
117. Schranz, M.E., Manzaneda, A.J., Windsor, A.J., Clauss, M.J. & Mitchell-Olds, T. (2009) Ecological genomics of Boechera stricta: identification of a QTL controlling the allocation of methionine- vs branched-chain amino acid-derived glucosinolates and levels of insect herbivory. Heredity, 102, 465-474.
118. Schwachtje, J., Kutschbach, S. & Baldwin, I.T. (2008) Reverse genetics in ecological research. PLoS One, 3, e1543.
119. Shiu, S.-H. & Borevitz, J.O. (2008) The next generation of microarray research: applications in evolutionary and ecological genomics. Heredity, 100, 141-149.
120. Shonle, I. & Bergelson, J. (2000) Evolutionary ecology of the tropane alkaloids of Datura stramonium L(Solanaceae). Evolution, 54, 778-788.
121. Stamp, N. (2003) Out of the quagmire of plant defense hypotheses. The Quarterly Review of Biology, 78, 23-55.
122. Steppuhn, A. & Baldwin, I.T. (2007) Resistance management in a native plant: nicotine prevents herbivores from compensating for plant protease inhibitors. Ecology Letters, 10, 499-511.
123. Steppuhn, A., Gase, K., Krock, B., Halitschke, R. & Baldwin, I.T. (2004) Nicotine's defensive function in nature. Public Library of Science Biology, 2, e217.
124. Stinchcombe, J.R. & Hoekstra, H.E. (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity, 100, 158-170.
125. Storey, J.D. & Tibshirani, R. (2003) SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays. The Analysis of Gene Expression Data: Methods and Software (eds G. Parmigiani, E.S. Garrett, R.A. Irizarry & S.L. Zeger). pp. 272-290, Springer, New York City.
126. Storz, J.F. (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671-688.
127. Stracke, R., Werber, M. & Weisshaar, B. (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Current Opinion in Plant Biology, 4, 447-456.
128. Sun, C., Li, Y., Wu, Q., Luo, H., Sun, Y., Song, J., Lui, E.M. & Chen, S. (2010) De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics, 11, 262.
129. Thomas, M.A. & Klaper, R. (2004) Genomics for the ecological toolbox. Trends in Ecology & Evolution, 19, 439-445.
130. Thompson, G.A. & Goggin, F.L. (2006) Transcriptomics and functional genomics of plant defence induction by phloem-feeding insects. Journal of Experimental Biology, 57, 755-766.
131. Tian, D., Traw, M., Chen, J., Kreitman, M. & Bergelson, J. (2003) Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature, 423, 74-77.
132. Tiffin, P. (2000) Mechanisms of tolerance to herbivore damage: what do we know? Evolutionary Ecology, 14, 523-536.
133. Tiffin, P., Hacker, R. & Gaut, B.S. (2004) Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea. Genetics, 168, 425-434.
134. Tittiger, C. (2004) Functional genomics and insect chemical ecology. Journal of Chemical Ecology, 30, 2335-2358.
135. Tuinstra, M.R., Ejeta, G. & Goldsbrough, P.B. (1997) Heterogeneous inbred family (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci. Theoretical and Applied Genetics, 95, 1005-1011.
136. Turner, T.L., Bourne, E.C., Von Wettberg, E.J., Hu, T. & Nuzhdin, S. (2010) Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics, 42, 260-263.
137. Van Poecke, R.M.P., Posthumus, M.A. & Dicke, M. (2001) Herbivore-induced volatile production by Arabidopis thaliana leads to attraction of the parasitoid Cotesia rubecula: chemical, behavioral, and gene-expression analysis. Journal of Chemical Ecology, 27, 1911-1928.
138. Vardhanabhuti, S., Blakemore, S.J., Clark, S.M., Ghosh, S., Stephens, R.J. & Rajagopalan, D. (2006) A comparison of statistical tests for detecting differential expression using Affymetrix oligonucleotide microarrays. OMICS, 10, 555-566.
139. Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. (1995) Serial Analysis of Gene-Expression. Science, 270, 484-487.
140. Vera, J.C., Wheat, C.W., Fescemyer, H.W., Frilander, M.J., Crawford, D.L., Hanski, I. & Harden, J. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology, 17, 1636-1647.
141. Voelckel, C. & Baldwin, I.T. (2004) Generalist and specialist lepidopteran larvae elicit different transcriptional responses in Nicotiana attenuata, which correlated with larval FAC profiles. Ecology Letters, 7, 770-775.
142. Volkmuth, W., Turk, S., Shapiro, A., Fang, Y., Kiegle, E., Van Haaren, M. & Donson, J. (2003) Technical advances: genome-wide cDNA-AFLP analysis of the Arabidopsis transcriptome. OMICS, 7, 143-159.
143. Wang, S.M. (2007) Understanding SAGE data. Trends in Genetics, 23, 42-50.
144. Wang, Z., Gerstein, M. & Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57-63.
145. Wang, X.-L., He, R.-F. & He, G.-C. (2005) Construction of suppression subtractive hybridization libraries and identification of brown planthopper-induced genes. Journal of Plant Physiology, 162, 1254-1262.
146. Wei, C., Li, J. & Bumgarner, R.E. (2004) Sample size for detecting differentially expressed genes in microarray experiments. BMC Genomics, 5, 87.
147. Weinig, C., Stinchcombe, J.R. & Schmitt, J. (2003) QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments. Molecular Ecology, 12, 1153-1163.
148. Wouters, L., Gohlmann, H.W., Bijnens, L., Kass, S.U., Molenberghs, G. & Lewi, P.J. (2003) Graphical exploration of gene expression data: a comparative study of three multivariate methods. Biometrics, 59, 1131-1139.
149. Wu, R.L. (1998) Genetic mapping of QTLs affecting tree growth and architecture in Populus: implication for ideotype breeding. Theoretical and Applied Genetics, 96, 447-457.
150. Xu, Z.W., Escamilla-Trevino, L.L., Zeng, L.H., Lalgondar, M., Bevan, D.R., Winkel, B.S.J., Mohamed, A., Cheng, C.L., Shih, M.C., Poulton, J.E. & Esen, A. (2004) Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1. Plant Molecular Biology, 55, 343-367.
151. Zavala, J., Patankar, A., Gase, K., Hui, D. & Baldwin, I.T. (2004) Manipulation of endogenous trypsin proteinase inhibitor production in Nicotiana attenuata demonstrates their function as antiherbivore defenses. Plant Physiology, 134, 1181-1190.
152. Zheng, S.J., Snoeren, T.A.L., Hogewoning, S.W., Van Loon, J.J.A. & Dicke, M. (2010) Disruption of plant carotenoid biosynthesis through virus-induced gene silencing affects oviposition behaviour of the butterfly Pieris rapae. New Phytologist, 186, 733-745.
153. Zhou, X., Su, Z., Sammons, R.D., Peng, Y., Tranel, P.J., Stewart C.N., Jr & Yuan, J.S. (2009) Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinformatics, 10, S16.