Plant development is highly plastic, as many traits change in response to environmental cues. But when plasticity evolves, what types of genes and mutations contribute? Does gene regulatory network architecture foster or constrain a gene's ability to respond appropriately to selection on plasticity and how often are parallel changes in genotype responsible for parallel changes in phenotypic plasticity?;I addressed these questions by studying the genetic basis of variation in the response of flowering time to photoperiod in the common sunflower, Helianthus annuus. Long-day, short-day, and aphotoperiodic flowering responses are found in both domesticated and wild H. annuus. Taking advantage of this remarkable diversity, I have examined the molecular basis of changes in flowering that occurred during two important evolutionary processes: (1) domestication; and (2) clinal adaptation in wild populations.;To identify domestication genes, genetic mapping, sequence and expression comparison, and molecular evolution studies were conducted on sunflower genes similar to genes that function as flowering regulators in other plants. This led to identification and functional characterization of a dominant-negative frameshift mutation in one of several recently duplicated FT/TFL1 gene family members. The mutation alters flowering behavior and experienced selection during early domestication. These findings suggest that this copy of FT is the first functionally identified sunflower "domestication gene." Notably, variants in other FT copies experienced selection during modern breeding.;Phenotypic analyses of North American wild populations found that flowering time decreases with latitude, and photoperiod response transitions occur along this cline. Northern populations are day-neutral; mid-latitude populations are short-day; and southern populations are long-day. Gene expression analyses demonstrated that genes at multiple hierarchical levels of multiple pathways factor into the overall cline. Paralog-specific changes in FT expression and tissue-specific changes in SOC1 expression contribute to transitions to day neutrality and long-day sensitivity respectively. Thus, functional redundancy and modular control of gene expression are sources of evolutionary lability often exploited by natural selection. Finally, gene expression comparisons between domesticated and wild H. annuus revealed that both parallel and convergent mechanisms have participated in repeated evolution of similar photoperiod responses in independent lineages.
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