Structural variation (SV) is defined as rearrangements, gain or loss of genomic DNA sequences including deletion, insertion, inversion, and translocation. Copy number variant commonly refers to deletions and insertions. SV has been shaping the genetic diversity and genome complexity and is essential for plant phenotypes such as copy number variation in GL7 contributing to grain size diversity in rice and retrotransposon insertion upstream an MYB transcription factor controlling the color of blood orange. Besides contributing to the phenotypes, SV plays an important role related to adaptation in the new environment, disease resistant and recently more evidence suggest structural variation is a primary driver of metabolite diversity. Currently I am using whole genome sequence from a single natural population of the maize wild relative teosinte to investigate evolutionary consequence and function of copy number variant.