Expression analysis in IBM maize roots

Roots of young plants undergo highly regulated gene expression changes that pattern root architecture and physiology, with lifelong effects on the structural integrity, water-use efficiency, and nutrient flow of the plant. To understand gene regulatory networks in maize roots, we measured transcript levels in two-week-old roots of 218 greenhouse-grown lines belonging to the maize Intermated B73 x Mo17 (IBM) recombinant inbred population. After performing quality control on the root RNA-seq data, we retained an average of 19.6 million reads per sample. Sample identity was verified by calling SNPs on the RNA-seq data to compare with SNPs used in previous work with this population (Asaro et al. 2016). Samples were considered validated if the new SNPs matched previous SNPs with an accuracy above 90% once low accuracy SNPs (<85% accuracy) were removed. 146 IBM RILs were validated as the correct RIL or parent, and samples that could not be validated or re-assigned with the correct name were labeled as "unknown cultivar".