Next generation sequencing based transcriptomic studies for crop improvement in pigeonpea

Abstract

Transcriptomic studies are rapidly evolving as a powerful tool with next-generation sequencing technology to understand gene functions and molecular mechanisms. RNA sequencing (RNAseq) provides a dynamic range for transcript detection and a better quantification of expression levels.With the availability of genome sequence in pigeonpea, RNA-seq was used to link the sequence information to phenotypic traits resulting from specific developmental processes. In pigeonpea, three-line hybrid breeding system is well-established; however, it is technically demanding and cumbersome. In order to explore the possibility of a two-line hybrid breeding system, a coherent transcriptomic approach supported by physiological and cytological data has led to the identification of a temperature-sensitive male sterile (TSMS) line. This line has been characterized for critical (tetrad) stage and temperature (23°C), and the identification of candidate genes involved in abscisic acid signaling for fertility reversion. Furthermore, a gene expression atlas (CcGEA) has been developed and transcriptomic profiles generated for studying pod and seed development with a dataset of 590.84 and 342 million paired-end reads, respectively in pigeonpea. These data have been analyzed for genes with differential, specific, spatio-temporal and constitutive expression. In addition, CcGEA identified a gene network of 28 co-expressed genes, including two regulatory genes, a pollen specific SF3 and a sucrose-proton symporter to be involved in pollen fertility, which has potential implication in seed yield improvement. In summary, this study, especially identification of TSMS and development of CcGEA, will accelerate on-going efforts to enhance genetic gains in pigeonpea