Transcriptomic data of developing siliques of three Brassica juncea (L.) with contrasting seed glucosinolate abundance and composition

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Though glucosinolate (GSL) accumulation is a key determinant of the economic value of Brassica juncea, the underlying mechanisms remain poorly understood, limiting the ability to realize the full potential of this versatile crop. Low GSL levels in seeds are a key breeding target to develop B. juncea into an oil crop, while high levels of beneficial GSL (i.e. sinigrin) are desirable in cultivars for condiment industries. Comparative transcriptomics of two high GSL lines with different predominant aliphatic GSLs (i.e. sinigrin and gluconapin) against a low GSL line was used to identify key drivers of GSL accumulation in B. juncea seeds. RNA sequencing data from developing siliques at seed filling stage revealed an overall higher GSL metabolic activity in the low GSL line. Though known key genes of GSL biosynthesis and transport, including a copy of MAM1 and GTR2 were expressed stronger in the high GSL backgrounds, many candidates of GSL biosynthesis, regulation and degradation were found to be expressed at higher rates in the low GSL line. Collectively, differential activity of GSL catabolism, rather than anabolism was found the main driver behind the observed seed GSL phenotypes. Finally, a copy of CYP79F1 was identified as a strong candidate for preferential accumulation of sinigrin.