*4.6. Di*ff*erential Expression and Enrichment Analysis*

The read count was normalized and EdgeR Bioconductor package [93] was used to determine the differential expressed genes (DEGs) between the two cultivars with the fold change of > 2 [94] and false discovery rate correction (FDR) set at *p* < 0.01. GO enrichment analysis was performed using the topGO method [95] based on the wallenius non-central hypergeometric distribution with *p* < 0.05. KEGG pathway enrichment analysis of the DEGs was done using KOBAS2.0 [89]. The FDR correction was employed (*p* < 0.05) to reduce false positive prediction of enriched KEGG pathways.
