De novo assembly and comparative transcriptome analysis of contrasting pearl millet (Pennisetum glaucum L.) genotypes under terminal drought stress using illumina sequencing

Pearl millet (Pennisetum glaucum L.) is one of the most important small-grained annual cereal crops grown in the arid and semi-arid regions of India and Africa, where terminal drought is a major constraint for its productivity. Terminal drought stress is more damaging to pearl millet than drought at vegetative stage as 50% or more reduction in yield may incur. However, a pearl millet genotype, PRLT2/89-33, parent of a mapping population is tolerant to terminal drought stress. With the aim to understand the molecular mechanism underlying terminal drought tolerance in this naturally drought tolerant crop, we examined the leaf transcriptome of contrasting pearl millet genotypes namely, PRLT2/89-33 and H77/833-2 differing for terminal drought tolerance using illumina Miseq sequencing platform. In this study, 40,880 genes were found to be differentially expressed and 8273 unigenes showed significant similarities to known sequences in NCBI non-redundant (nr) database and were classified into 189 Gene Ontology and 24 Clusters of Orthologous Group terms for both the genotypes. Expression profiling of 13 randomly selected transcripts was done to validate the RNA-Seq data. The study revealed that the genes for phytohormones biosynthesis, secondary metabolites and abiotic stress related transcription factors were more expressed in PRLT2/89-33, throwing insights into the molecular basis of its terminal drought tolerance. The study also supported that Illumina Miseq Platform is a powerful tool for transcriptome analysis and molecular-marker development in economically important non-model crop species, particularly those with large and complex genomes.