Gene Expression Atlas of Pigeonpea, an Important Resilient Food Legume Crop for the Semi-Arid Tropics

Pigeonpea (Cajanus cajan) is an important grain legume of the semi-arid tropics, mainly used for its protein rich seeds. The genome sequence of pigeonpea has been decoded and it has provided a set of potential genes that played important role in its adaptability to marginal environment. In order to link genes with functions in native biological system, it is highly imperative to have detailed expression profiling. With an objective to have a global overview of the gene expression, a gene expression atlas (GEA) has been developed in pigeonpea variety “ICPL 87119 (Asha)”. RNA sequencing was performed using llumina sequencing platform. As a result, a total of 590.84 million paired-end reads were generated from 30 samples representing aerial and underground tissues from different developmental stages from germination to senescence. Detailed analysis has provided a compendium of 28,793 genes that showed abundance with ≥ 1 FPKM value. The RNA-seq data was analyzed by pair-wise comparisons, in addition to gene co-expression analysis, gene clustering and network construction. The GEA deciphers genes which exhibited differential, specific, spatio-temporal, constitutive expression during the various phase of development, including master regulators involved during various metabolic pathways. This would be useful for studying the basal expression of genes when investigating mutant lines, candidate genes for specific trait and towards understanding the well-orchestrated growth and development process in this resilient crop.