Structural variation haplotype frequencies in subpopulations of maize. Each of the genotypes was assigned to a subpopulation based on pedigree information or structure analysis. The subpopulations are nonstiff stalk (NSS, n = 4), ex-plant varietal protection varieties (exPVP, n = 6), inbred teosinte (TeoI, n = 4), wild teosinte (TeoW, n = 10), or tropical (Trop, n = 5). The frequency of the structural variant within this subpopulation was used to perform hierarchical clustering of both the structural variants and the subpopulations. The color indicates the type and frequency of each structural variant, with blue indicating DownCNV/PAV and red indicating UpCNV. The brighter colors represent higher allele frequencies.
