Characterizing The Maize Transcriptome Using RNAseq

Maize has extensive genetic variation, including single nucleotide polymorphisms (SNPs), indels, presence-absence variants, and copy-number variants. We conducted RNA-seq on whole-seedling RNA from 503 maize inbreds, primarily of Midwestern origin, for the purposes of SNP discovery and genotyping, and to expand our knowledge of the expressed pan-genome. A set of high confidence SNPs with unprecedented completeness and coverage were identified from the 503 lines and used for multiple genetic analyses. Inbreds cluster into expected heterotic groups and pedigrees, but the knowledge of recombination breakpoints and haplotype composition has been dramatically enhanced. Initial eQTL analysis using association analysis indicates extensive cis and trans control of gene expression. Association analysis of seedling and adult plant phenotypes exemplifies the value of this data set for gene discovery. In addition to genetic variants characterized relative to the B73 reference, we identified a large number of genes not present in the reference genome and these pan-genes are being mapped to an approximate position relative to the reference genome. Based on this Midwest Dent-enriched subset of inbred lines and using only RNA from seedlings, we have been able to expand the maize pan-genome relative to the reference accession, B73. Extrapolating our observations to maize diversity across races and diverse germplasm collections containing landraces and other open-pollinated populations, it is reasonable to predict that many more expressed pan-genes remain to be discovered.