Read mapping, expression, and single nucleotide polymorphism (SNP) summary for 21 diverse maize lines.

Reads were mapped requiring a unique hit for the SNPs and multiple hits for fragments per kilobase of exon model per million fragments mapped (FPKM) and mapping to the pseudomolecules plus the Velvet and Oases [45] assembled transcripts. FPKM values were calculated using Cufflinks [56]. Genes with a FPKM 95% confidence interval lower boundary greater than zero were considered expressed. For each inbred line, a gene was considered to have SNP coverage if there was at least one polymorphic locus with coverage in the gene. SSS = Stiff Stalk Synthetic, NSS = Non-Stiff Stalk Synthetic, NA = Not applicable.