In this thesis, whole-genome and transcriptome sequencing data are used to analyze the genetic basis of polygenic adaptation in Solanum chilense. We correlate the demographic history, allele frequencies in space and time, the selection events and the ecological niche spanning 150,000 years. We then identified gene networks responding to drought stress and estimated the evolution of gene networks. Our results provide an insight into polygenic adaptation to stressful environments in S. chilense.