Table 4. Summary statistics of number of differentially expressed contigs as determined by GLM analysis.

Transcript isoform-level expected counts matrices for each genotype were obtained from RSEM and passed to R v3.1.1⁵² with the edgeR (version v3.8.6) package used for differential expression analysis. Only matrix rows containing four or more samples with counts per million (CPM) greater than three were retained for the analysis. A Benjamini-Hochberg false discovery rate (FDR) of 0.05 or less and an absolute log₂-fold change greater than 1 was required to define a gene as differentially expressed (DE). GLM, generalized linear model; Z1, meristematic zone; Z2, elongation zone; Z3, maturation zone. The full data sets are provided in Supplemental Data Sets S1 (cv. Clipper) and S2 (LR Sahara).