The seasonal timing of developmental transitions (phenology) constitutes the life history of individuals and is under intense natural selection. In the annual plant Arabidopsis thaliana, naturally variable environmental-sensing genes involved in dormancy and flowering pathways are hypothesized to determine life history variation. These pathways interact with each other and with the seasonal environment to produce life-history variation. This dissertation examined genes in these pathways, and the manner in which their function is contingent upon seasonal environmental factors and the genetic context. I examined natural allelic variation in these genes, context-dependent gene expression and phenotypic expression, and natural selection.

I first revealed a novel function for the well characterized flowering time gene, FLC by showing that FLC regulates seed germination under low temperature and that it does so through components of the flowering time pathway. The FLC effect on germination is maternally mediated, and FLC expression regulates hormonal pathways prior to germination.

Natural variation in gene expression of the major dormancy gene DOG1 exhibited a geographic pattern that reflects geographic variation in germination. DOG1 expression level also changed with seed-maturation temperature in a manner that predicts maternal effects on germination.

Field experiments examining the effects of allelic variation in dormancy and flowering time genes showed that DOG1 influenced germination timing and fitness in the field, but its effect depended on simulated flowering time. Surprisingly, flowering-time genes had no effect on flowering time, but DOG1 had strong effects on flowering through its effects on germination.

The results suggest that the genes in germination and flowering time pathways interact both at the molecular and organismal levels. Moreover, natural selection on genes in either flowering or germination pathways likely will affect the evolution of both life-history transitions.