_applied sciences_  
_Article_  
Transcriptome and Metabolome Analyses of Glucosinolate Biosynthesis-Related Genes in Different Organs of Broccoli (_Brassica oleracea_ L. var. _italica_)  
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studies have reported that sulforaphane could effectively reduce the development and recurrence of cancer, thereby improving patient survival [15; 16]. Furthermore, sulforaphane can protect against heart disease [17]. The GSLs constitute a well-defined group of secondary metabolites with many effects on plant defense, taste and health benefits [18; 19; 20; 21]. Although high numbers of natural GSLs have been listed in older papers, a recent critical revision concluded that the number of scientifically validated GSLs is less than 100 [18]. GSLs can be divided into three types according to their variable side chain structure, i.e., aliphatic GSLs derived from alanine, leucine, isoleucine, valine or methionine, benzenic GSLs derived from phenylalanine or tyrosine, and indolic GSLs derived from tryptophan [18; 19; 20; 21]. GSLs biosynthesis proceeds in three stages; firstly, the side chains of respective precursor amino acids were elongated; secondly, the formation of core structures of GSLs; and thirdly, secondary modifications of amino acid side chains by methoxylation, desaturation, hydroxylation, oxidation or benzoylation [5; 22]. GSLs levels in broccoli are determined by genotypes, as well as by genotype-environment interactions [23]. Moreover, many factors also significantly affect GSLs content in broccoli during growing seasons, including organ, developmental phase, cultivation and climate conditions [24; 25]. The genes related to the biosynthesis of GSLs mainly involve three biosynthetic steps and some regulatory genes. Most of them have been discovered, identified and functionally validated in _Arabidopsis thaliana_[22; 26; 27]. The aliphatic GSLs biosynthesis pathway depends upon _BCAT_ and _MAM_ for deamination and the process of chain elongation [28]. The formation of the core structure involves multiple biochemical reaction processes, in which cytochrome the P450 _CYP9_ and _CYP83_ gene family, C-S lyase _SUR1_, the _UGT74_ gene family, and sulfotransferases _SOT16/17/18_ play essential roles in these processes [5; 29]. Secondary modifications of the side chain have been regulated by _FMOGS-OX1-5_, _APO2_, _APO3_ and _GS-OH_[5]. Moreover, the transcription factor _MYB_ gene family plays a crucial role in regulating the above GSLs biosynthesis genes [30]. Previous studies have primarily focused on the effect of external conditions on GSLs content, while there is little evidence of the effects of genotype and developmental organs in broccoli. The objective of this study was to explore the differences in GSLs biosynthesis-related genes in different organs. Here, we formed contrasting bulk segregant populations of leaf, stalk and floret based on the glucoraphanin content from an F\({}_{2}\) broccoli population.