Identification of genic SSRs in jute (Corchorus capsularis, Malvaceae) and development of markers for phenylpropanoid biosynthesis genes and regulatory genes

In jute (Corchorus spp.), phenylpropanoid biosynthesis pathway is associated with lignocellulosic bast fibre development and production of various phytochemicals. Development of phenylpropanoid-related genic markers is thus a key component of gene-specific precision molecular breeding in jute. We identified a total of 12,772 SSRs in 10,041 unigenes and designed genic SSR markers associated with phenylpropanoid biosynthesis from bast transcriptome of Corchorus capsularis cv. ‘JRC-212’. A total of 39 and 14 SSR markers were developed from key genes of phenylpropanoid biosynthesis and bast fibre formation, respectively. Further, we developed 457 SSR markers associated with different regulatory gene sequences. Of these, 137 markers were for transcription factors such as WRKY, MYB, MYB-related, bHLH and zinc finger, which are key regulators and/or modulators of the biosynthesis of phenylpropanoids. Additionally, 600 SSR primer pairs were also designed for other unigenes containing SSR. Diversity analysis based on a set of 41 genic SSR markers in 35 genotypes revealed high polymorphism. The genic SSRs described here are expected to be useful for molecular breeding targeting fibre quality, phytochemical-related and stress tolerance traits in jute.