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Background  Seed coat color is an important horticultural trait in  Brassica  crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a desirable trait in hybrid breeding of  Brassica rapa, Brassica juncea  and  Brassica napus .    Methods  Comprehensive analysis of the abundance transcripts for seed coat color at three development stages by RNA-sequencing (RNA-seq) and corresponding flavonoids compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out in  B. rapa .    Results  We identified 41,286 unigenes with 4,989 differentially expressed genes between brown seeds (B147) and yellow seeds (B80) at the same development stage. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 19 unigenes associated with the phenylpropanoid, flavonoid, flavone and flavonol biosynthetic pathways as involved in seed coat color formation. Interestingly, expression levels of early biosynthetic genes ( BrCHS ,  BrCHI ,  BrF3H ,  BrF3’H  and  BrFLS ) in the flavonoid biosynthetic pathway were down-regulated while late biosynthetic genes ( BrDFR ,  BrLDOX  and  BrBAN ) were hardly or not expressed in seeds of B80. At the same time,  BrTT8  and  BrMYB5  were down-regulated in B80. Results of LC-MS also showed that epicatechin was not detected in seeds of B80. We validated the accuracy of our RNA-seq data by RT-qPCR of nine critical genes. Epicatechin was not detected in seeds of B80 by LC-MS/MS.    Conclusions  The expression levels of flavonoid biosynthetic pathway genes and the relative content of flavonoid biosynthetic pathway metabolites clearly explained yellow seed color formation in  B. rapa . This study provides a foundation for further research on the molecular mechanism of seed coat color formation.

peerj

Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of <i>Brassica rapa</i> L.

Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.