Spatiotemporal and subgenome expression dynamics and regulatory divergence of the glucosinolate gene homologs in the allopolyploid Brassica juncea

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Plant glucosinolates (GSLs) have attracted considerable attention due to their significant roles in plant defense mechanisms and cancer prevention. However, the gene expression characteristics and mechanisms underlying phenotypic variations in Brassica juncea , particularly in key vegetable and oilseed varieties, remain largely unexplored. This study examined the retention and the spatiotemporal expression and subgenome expression dynamics of duplicated genes predicted to regulate GSL metabolism in the allopolyploid B. juncea . Our findings reveal that homologs of Arabidopsis GSL genes (HAGG) are preferentially retained in the B. juncea genome compared to other genes. Most HAGG genes (76.5%) were expressed across all tissues, while the remainders exhibited tissue-specific expression patterns. A majority of homoeologous pairs (54.09%) demonstrated balanced expression levels, whereas the rest showed a pronounced A-genome dominance in leaves and stems. Notably, two GRT2 homologs, Bju.GTR2.A03 and Bju.GTR2.B06 , which exhibit regulatory divergence in GSL accumulation, were identified. Co-dominant allele-specific markers developed for Bju.GTR2.A03 and Bju.GTR2.B06 colocalized with their respective quantitative trait loci (QTLs) and co-segregated with GSL content, corroborating the results of QTL mapping. Furthermore, GSL content was significantly correlated with resistance to Sclerotinia sclerotiorum . Predictions regarding the functions of HAGG genes further validated their functional divergence. This study provides a foundation for enhancing GSL content in whole plants or specific tissues, facilitating future applications in agriculture and cancer prevention in B. juncea .