Transcriptome reveals the role of ELONGATED HYPOCOTYL 5 in the regulation of glucosinolate metabolism in broccoli

To investigate role of <i>ELONGATED HYPOCOTYL 5</i> (<i>HY5</i>) in the regulation of glucosinolate (GSL) metabolism, we conducted RNA-seq on <i>BoHY5</i> overexpression line B42OE, knockout line B42CR, wild-type B42WT. <i>BoHY5</i> plays a negative regulatory role in the transcription of <i>MYB</i> transcription factors (TFs) and GSL pathway genes. Furthermore, <i>BoHY5</i> overexpression reduces the content of aliphatic GSLs (especially glucoraphanin), but increases the content of indolic GSLs (especially glucobrassicin). Knocking out <i>BoHY5</i> can increase the content of aliphatic and aromatic GSLs and raise the total GSL content, but it can decrease the content of indolic GSLs. These results suggest that <i>BoHY5</i> is a key regulatory factor in balancing the metabolic levels between aliphatic and indolic GSLs, which provides a theoretical basis for efficient biosynthesis of GSL in broccoli.