Agrios, G.N. (2005). Plant Pathology. Burlington, MA: Academic Press.
Ascencio-Ibanez, J., Sozzani, R., Lee, T., Chu, T., Wolfinger, R., Cella, R., et al. (2008). Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiology 148, 436 - 454.
Desprez-Loustau, M.L., Marcais, B., Nageleisen, L., Piou, D., and Vannini, A. (2006). Interactive effects of drought and pathogens in forest trees. Annals of Forest Science 63, 597-612.
Fox, J., and Weisberg, S. (2011). "An R Companion to Applied Regression". 2 ed. (Thousand Oaks, CA: Sage).
Franks, S., Hamann, E., and Weis, A.E. (2018). Using the resurrection approach to understand contemporary evolution in changing environments. Evolutionary Applications 11(1), 17-28.
Franks, S., Kane, N., O'Hara, N., Tittes, S., and Rest, J. (2016). Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools. Molecular Ecology 25(15), 3622-3631.
Franks, S.J. (2011). Plasticity and evolution in drought avoidance and escape in the annual plant Brassica rapa. New Phytologist 190(1), 249-257.
Franks, S.J., Avise, J.C., Bradshaw, W.E., Conner, J.K., Etterson, J.R., Mazer, S.J., et al. (2008). The resurrection initiative: storing ancestral genotypes to capture evolution in action. BioScience 58(9), 870 - 873.
Franks, S.J., Sheina, S., and Weis, A.E. (2007). Rapid evolution of flowering time by an annual plant in response to a climate fluctuation. Proceedings of the National Academy of Sciences 104(4), 1278-1282.
Franks, S.J., Weber, J.J., and Aitken, S.N. (2014). Evolutionary and plastic responses to climate change in terrestrial plant populations. Evolutionary Applications 7(1), 123 -139. doi: doi: 10.1111/eva.12112.
Franks, S.J., and Weis, A.E. (2008). A change in climate causes rapid evolution of multiple life-history traits and their interactions in an annual plant. Journal of Evolutionary Biology 21, 1321-1334.
Garg, R., Tyagi, A., and Jain, M. (2012). Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice Jain Plant Signaling & Behavior 7(8).
Garrett, K., Thomas-Sharma, S., Forbes, G., and Nopsa, J. (2014). "Climate change and plant pathogen invasions," in Invasive Species and Global Climate Change, eds. L. Ziska & J. Dukes. CABI).
Garrett, K.A., Dendy, S.P., Frank, E.E., Rouse, M.N., and Travers, S.E. (2006). Climate change effects on plant disease: genomes to ecosystems. Annual Review of Phytopathology 44, 489-509.
Gillis, J., Mistry, M., and Pavlidis, P. (2010). Gene function analysis in complex data sets using ErmineJ Nature Protocols 5(6), 1148-1159.
Glazebrook, J. (2005). Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annual Review of Phytopathology 43, 205 - 227.
Guo, Y., Samans, B., Chen, S., Kibret, K., Hatzig, S., Turner, N., et al. (2017). Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress. Plant Molecular Biology Reporter 35, 416-430. doi: 10.1007/s11105-017-1032-4.
Hartl, D.L., and Clark, A. (2007). Principles of Population Genetics.
Hoffmann, A., and Sgro, C. (2011). Climate change and evolutionary adaptation. Nature 470, 479 - 485.
Hoth, S., Morgante, M., Sanchez, J., Hanafey, M., Tingey, S., and Chua, N. (2002). Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant. Journal of Cell Science 115(24), 4891 - 4900.
Huang, D., Wu, W., Abrams, S., and Cutler, A. (2008). The relationship of drought-related gene expression in Arabidopsis thaliana to hormonal and environmental factors. Journal of Experimental Botany 59(11), 2991 - 3007.
Jorgensen, T., and Emerson, B. (2008). Functional variation in disease resistance gene in populations of Arabidopsis thaliana. Molecular Ecology 17(22), 4912 - 4923.
Journot-Catalino, N., Somssich, I., Roby, D., and Kroj, T. (2006). The Transcription Factors WRKY11 and WRKY17 Act as Negative Regulators of Basal Resistance in Arabidopsis thaliana. The Plant Cell 18, 3289 - 3302.
Karlsson, E., Baranowska, I., Wade, C., Hillbertz, N., Zody, M., Anderson, N., et al. (2007). Efficient mapping of mendelian traits in dogs through genome-wide association. Nature Genetics 39, 1321-1328.
Kofler, R., Orozco-terWengel, P., De Maio, N., and et al. (2011). PoPoolation: A toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One 6, e15925.
Koike, S., Gladders, P., and Paulus, A. (2006). Vegetable Diseases: a Color Handbook. USA: Academic Press.
Laine, A., Burdon, J., Dodds, P., and Thrall, P. (2011). Spatial variation in disease resistance: from molecules to metapopulations. Journal of Ecology 99(1), 96-112.
Lamesch, P., Berardini, T., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., et al. (2011). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research. doi: 10.1093/nar/gkr1090.
Lawrence, C., Mitchell, T., Craven, K., Cho, Y., Cramer, R., and Kim, K. (2008). At death's door: Alternaria pathogenecity mechanisms. Plant Pathology 24(2), 101-111.
Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatcs 25, 589 - 595.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatcs 25, 2078 - 2079.
Liu, H., Yang, W., Dongcheng, L., Han, Y., Zhang, A., and Shaohua, L. (2011). Ectopic expression of a grapevine transcription factor VvWRKY11 contributes to osmotic stress tolerance in Arabidopsis. Molecular Biology Reports 38, 417 - 427.
Marra, J., Eo, S., Hale, M., Waser, P., and DeWoody, J. (2012). A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: Osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 7(4), 328 - 339.
Mauch-Mani, B., and Mauch, F. (2005). The role of abscisic acid in plant-pathogen interactions. Current Opinion in Plant Biology 8, 409 - 414.
McDowell, J., and Dangl, J. (2000). Signal transduction in the plant immune response. Trends in Biochemical Sciences 25, 79 - 82.
McGrath, K., Dombrecht, B., Manners, J., PM, S., Edgar, C., Maclean, D., et al. (2005). Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiology 139, 949 - 959.
McKay, J., Rchards, J., and Mitchell-Olds, T. (2003). Genetics of drought adaptation in Arabidopsis thaliana: I. Pleiotropy contributes to genetic correlations among ecological traits. Molecular Ecology 12, 1137-1151.
Meena, P.D., Awasthi, R.P., Chattopadhyay, C., Kolte, S.J., and Kumar, A. (2010). Alternaria blight: a chronic disease in rapeseed-mustard. Journal of Oilseed Brassica 1(1), 1-11.
Mengiste, T. (2012). Plant immunity to necrotrophs. Annual Review of Phytopathology 50, 267-294.
Metcalf, C., and Mitchell-Olds, T. (2009). Life history in a model system: opening the black box with Arabidopsis thaliana. Ecology Letters 12, 593-600.
Mitchell-Olds, T., and Schmitt, J. (2006). Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 441, 947-952.
Mohr, P., and Cahill, D. (2007). Suppression by ABA of salicylic acid and lignin accumulation and the expression of multiple genes, in Arabidopsis infected with Pseudomonas syringae pv. tomato. Functional Integrative Genomics 7, 181 - 191.
Mole, S. (1994). Trade-offs and constraints in plant-herbivore defense theory: a life-history perspective. Oikos 71, 3 - 12.
Mukherjee, A., Lev, S., Gepstein, S., and Horwitz, B. (2009). A compatible interaction of Alternaria brassicicola with Arabidopsis thaliana ecotype DiG: evidence for a specific transcriptional signature. BMC Plant Biology 9.
Nemhauser, J., Hong, F., and Chory, J. (2006). Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell 126, 467 - 475.
Nowicki, M., Nowakowska, M., Niezgoda, A., and Kozik, E. (2012). Alternaria black spot of crucifers: symptoms, importance of disease, and perspectives of resistance breeding. Vegetable Crops Research Bulletin 76, 5 - 19.
O'Hara, N., Rest, J., and Franks, S. (2016a). Factors affecting the disease severity of Alternaria blackspot in natural Brassica rapa populations on the California and Oregon coasts. Madrono 63, 249-257.
O'Hara, N., Rest, J., and Franks, S. (2016b). Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa. Evolution 70(1), 241-248.
Pandey, R., Kofler, R., Orozco-terWengel, P., Nolte, V., and Schlotterer, C. (2011). PoPoolation DB: a user- friendly web-based database for the retrieval of natural polymorphisms in Drosophila. Bmc Genetics 12(27).
Pautasso, M., Doring, T., Garbelotto, M., Lorenzo, P., and Jeger, M. (2012). Impacts of climate change on plant disease - opinions and trends. European Journal of Plant Pathology 133, 295 - 313.
Penuelas, J., and Filella, I. (2001). Responses to a warming world. Science 294, 793 - 795.
Qi, J., Yu, S., Zhang, F., Shen, X., Zhao, X., Yu, Y., et al. (2010). Reference Gene Selection for Real-Time Quantitative Polymerase Chain Reaction of mRNA Transcript Levels in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). Plant Molecular Biology Reporter 28, 597-604.
R Core Team (2013). "R: A language and environment for statistical computing". (Vienna, Austria: R Foundation for Statistical Computing).
Rosas, U., Mei, Y., Xie, Q., Banta, J., Zhou, R., Seufferheld, G., et al. (2014). Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS. Nature Communications 5. doi: 10.1038/ncomms4651.
Rotem, J. (1994). The Genus Alternaria: Biology, Epidemiology, and Pathogenicity. St. Paul: APS Press.
Shinozaki, K., Yamaguchi-Shinozaki, K., and Seki, M. (2003). Regulatory network of gene expression in the drought and cold stress responses. Current Opinion in Plant Biology 6, 410-417.
Simms, E.L., and Rausher, M.D. (1987). Costs and benefits of plant resistance to herbivory. The American Naturalist 130(4), 570 - 581.
Storey, J., and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences 100, 9440.
Strimmer, K. (2008). fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatcs 24, 1461 - 1462.
Taiz, L., and Zeiger, E. (2006). Plant Physiology. Sunderland, Mass.: Sinauer.
Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
Thrall, P.H., and Burdon, J.J. (2003). Evolution of virulence in a plant host-pathogen metapopulation. Science 299, 1735 - 1737.
Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Guerts, R., and Leunissen, J. (2007). Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Research 35(W71- 4).
van Wees, S., Chang, H., Zhu, T., and Glazebrook, J. (2003). Characterization of the early response of Arabidopsis to Alternaria brassicicola infection using expression profiling. Plant Physiology 132, 606 - 617.
Vance, C., Kirk, T., and Sherwood, R. (1980). Lignification as a mechanism of disease resistance. Annual Review of Phytopathology 18, 259 - 288.
Walsh, B. (2009). Quantitative genetics, version 3.0: where have we gone since 1987 and where are we headed? Genetica 136, 213-223.
Wang, X. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics.
Williams, G. (1957). Pleiotropy, natural selection, and the evolution of senescence. Evolution 11(4), 398 - 411.
Wu, K., Zhang, L., Zhou, C., Yu, C., and Chaikam, V. (2008). HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. Journal of Experimental Botany 59(2), 225-234.
Xie, D., Feys, B., James, S., Nieto-Rostro, M., and Turner, J. (1998). COI1: an Arabidopsis gene required for jasmonate-regulated defense and fertility. Science 280, 1091 -1094.
Zhou, C., Zhang, L., Duan, J., Miki, B., and Wu, K. (2005). HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant cell 17, 1196-1204.