Datasets contained in MaizeDomesticationTraitsSupplementaryFiles.zip: File S1. Realized additive relationship matrix for 2480 inbred lines NCRPIS panel based on a subset of 111,282 SNPs selected from Romay et al (2013) data. SNPs were chosen based on minimum imputation accuracy of 0.995 and having at least 20 observed minor allele homozygotes. Each element of the matrix estimates two times the realized coancestry of a pair of lines. File S2. Best linear unbiased estimates (BLUEs) for shank length of NCRPIS lines. File S3. Best linear unbiased estimates (BLUEs) for cob length of NCRPIS lines. File S4. Best linear unbiased estimates (BLUEs) for kernel row number of NCRPIS lines. File S5. Best linear unbiased estimates (BLUEs) for shank length of NAM lines. File S6. Best linear unbiased estimates (BLUEs) for cob length of NAM lines. File S7. Best linear unbiased estimates (BLUEs) for kernel row number of NAM lines. File S8. Chromosome-specific residuals for shank length of NAM lines, adjusted for the effects of QTL off the target chromosome, used for genome-wide association study. File S9. Chromosome-specific residuals for cob length of NAM lines, adjusted for the effects of QTL off the target chromosome, used for genome-wide association study. File S10. Chromosome-specific residuals for kernel row number of NAM lines, adjusted for the effects of QTL off the target chromosome, used for genome-wide association study.