Comparative transcriptome profiling of high and low grain-iron containing Indian barnyard millet (Echinochloa frumentacea L.) genotypes during different stages of grain development

Abstract In the era of food nutritional security, the development of minerals-rich grains is an essence for fighting malnutrition. In the present study, we tried to identify the transcripts responsible for the higher accumulation of grain-Fe in Indian barnyard millet through transcriptome sequencing of genotype BAR-1433 (high Fe content) and BAR-1423 (low Fe content) during two stages of spike development i.e., spike emergence and milking stage. During the spike emergence stage, a set of 895 up-regulated and 126 down-regulated transcripts were identified between the high and low grain-Fe containing genotype, while during the milking stage, the number of up-regulated and down-regulated transcripts were 436 and 285. The transcripts which were commonly up-regulated during both the stages were having roles in nucleolar protein, metal-nicotianamine transporter, ribonucleoprotein complex, Vinorine synthase, Cellulose synthase, Auxin response factor, embryogenesis abundant protein, Cytochrome c oxidase, and Zinc finger BED domain-containing protein. Transcripts with significant differences in induction or repression between the two genotypes included genes related to ABC Transporter family proteins, Calcium dependent kinase family, Ferritin, Metal ion binding, Iron-sulfurculster binding, Cytochrome family, Zinc finger transcription factor family, Ferredoxin–NADP reductase type 1 family, Putative laccase, Multicopper oxidase family and Terpene synthase family. Six contigs representing their probable function for metal transporter, iron sulfur, metal ion binding, auxin-responsive GH3-like protein 2, and cytochrome P450 71B16 were used for designing primers to be used for validation. The result of qRT-PCR coincided with the result of the transcriptome. Thus, this study reports a repertoire of genes associated with high iron content in barnyard millet and a proof concept for deployment of transcriptome information for validation in mapping population and its use in marker-assisted selection for bio fortification of barnyard millet with iron. This is first report on a detailed transcriptome analysis to identify transcripts associated with high and low grain-iron content during panicle developmental stages in barnyard millet.