Interactive studies of small RNAs and RNAs identified using RNA-Seq analyses uncovers a complex regulatory network of seed storage proteins in chickpea (C. arietinum L.) cultivars

Chickpea seeds are especially valued for their high protein and carbohydrate content. A major proportion of the seed proteins is constituted by the seed storage proteins (SSPs). Their importance during seed development has been previously established through various studies. This study aims at deciphering the molecular basis for the observed differences in seed protein content between two contrasting chickpea cultivars (ICC8397, high protein content and FG212, low protein content) with respect to storage protein content (SPC) using two different sequencing approaches i.e., RNA-seq and small RNA sequencing analysis (smRNA-Seq). The RNA-Seq analysis of mature seeds of these cultivars generated about 44 million reads which were assembled based on reference genome. The small RNA-Seq analysis resulted in identification of 23 and 26 conserved miRNAs in FG212 and ICC8397, respectively. The novel miRNAs identified in both the cultivars viz. FG212 and ICC8397 were 258 and 512, respectively. The RNA-Seq data was also used for miRNA target prediction. Such interactome studies provide a base for investigating the complex transcriptional and post-transcriptional regulation of genes governing the SPC in chickpea. This information will be helpful in breeding new chickpea cultivars with enhanced seed protein content and higher nutritional values.