Plants repeatedly combat abiotic stresses such as drought, high salinity, extreme temperatures, nutrient deficiency and toxicity
in their natural environment. Often plants are exposed to a combination of stresses such as drought and high temperature
attributable to excessive irradiation and low water availability. In comparison to the normal growth conditions abiotic stresses
reduce the overall yield significantly amidst the varieties of crops cultivated worldwide [1]. Different abiotic stresses affect the
plant growth and responses at various stages eventually leading to cessation of growth. Following stress perception activation in
the transcription of key enzymes, perturbation in metabolic flux, changes in biomolecules activity invoke tolerance response
against adverse environmental conditions [2].Plants possess an astonishing ability to sense change in the environmental conditions. The knowledge of molecular signaling
of stress tolerance mechanism would help in developing strategies for the survival of plants under adverse conditions. Any
external environmental stimulus when sensed by the plants activates downstream signaling cascades that amplify the signal as
well as alert analogues pathways. Several methodologies have been used to identify the genes that are involved in the stress
tolerance [3-5]. Isolation of these stress responsive genes will allow recognition of their associating cellular functions. However,
functional integration of large number of stress responsive genes is a big challenge that can potentially create a complete
understanding of the stress response pathways [6].In the post genomic era, development of a range of tools such as proteomics, metabolomics, transcriptomics, phenomics
have empowered the functional elucidation of proteins governing vital processes in plants. The practice of various omics based
tools for the functional characterization of a gene/s is termed as ‘functional genomics’ [3-5]. The broad genetic studies in various
crops have revealed the extensive variation in abiotic stress responsive genes among them. However, exploitation of this
knowledge to generate stress tolerant crops is difficult due to existence of relatively limited information about molecular response
pathway in these plants. Previous studies on complex and interconnected signal transduction pathways have been arduous
and challenging using traditional approaches. The advent of functional genomics approaches has simplified the analysis of
large number of genes and gene products involved in several defense and developmental processes in plants. Functional genomics
is now considered as a viable tool to examine abiotic stress response in crops such as rice and wheat, through which process
of stress perception, signaling cascade and tolerance responses can be analyzed from gene expression to protein complements
of cells, to comparative metabolite profiling of stressed tissue versus controlled tissue [7-9]. Using this background, plant biologists
are working to transfer the knowledge gained from model plants to the field crops to enhance their tolerance ability and
productivity.In volume II of our special issue, we have attempted to cover the latest, methodical, practical and successful use of functional
genomics approaches to divulge the molecular details of tolerance response. Volume II of this special issue comprises of
6 articles and the first research article by Kim et al. describes the whole transcriptome analysis of rice root and shoot under
ABA and JA. This article enlightens us about the phytohormones ABA and JA and suggests that they might have common gene
expression regulation system. Their study also aims to shed light on the conundrum why JA could respond for both abiotic and
biotic stress tolerance?The second research article by Lee et al. elaborate the results of genome-wide analysis of alternate splicing on inbred lines
of cabbage under heat stress. This study primarily identify that number of alternate splicing events markedly increased under
heat stress and among these are heat shock transcription factor (Hsf) and heat shock protein (Hsp) genes. The third article of
this volume identifies the possible role of microRNA (miRNA) in glyoxylase overexpressing transgenic plants of rice under salt
stress. Based on the Next Generation Sequencing (NGS) analysis, the role of miRNAs and their involvement in the glyoxalaseregulated
metabolism pathway during salt stress response is explored by Tripathi and co-workers.Followed by this is an interesting report describing the affects of widely used herbicide glyphosate. Lu et al. describes the
impact of glyphosate on the rhizosphere microbial communities of an EPSPS-transgenic soybean line by metagenome sequencing.
From this study, authors concluded that glyphosate did not significantly affect the alpha and beta diversity of the rhizobacterial
community of the soybean line ZUTS31, whereas it significantly influenced some functional genes involved in plant
growth-promoting traits in the rhizosphere.The next research article by Kumar et al. covers a detailed analysis of one of the CBS domain containing protein widely
known as sensors of cellular energy. The functional characterization of rice cystathionine-β-synthase domain-containing protein,
OsCBSCBSPB4 suggest that it impart abiotic stress tolerance.Previously, genetic basis of salt tolerance has been well defined in model plant Arabidopsis by identification of Salt-Overly
Sensitive pathway (SOS). After the discovery of this SOS pathway in Arabidopsis, several researchers investigated the presence
of SOS pathway components in crop plants as well. The abiotic stress signals trigger the change in cellular calcium (Ca+2) levels,
which is then perceived by various calcium sensors such as CBLs to regulate the downstream signaling cascades. The last
research article by Nutan et al. studied the role of BjSOS3 (also known as calcineurin B-like 4, CBL4) from Brassica juncea in
salt stress tolerance by complementation of Arabidopsis sos3 mutant.Henceforth, this volume of our special issue comprising of several research articles will aware readers about the potential
areas of abiotic stress signaling with genomics and functional genomics perspectives. In this post-genomic era, huge amount of
data and information is generated. This required unified attention of plant biologists to make holistic and successful efforts in
order to develop new technologies, to enhance the crop yield under these prevailing stressful conditions.The articles in this special issue put forward several potential problems, which need to be addressed using the tools of
multidisciplinary fields of genomics and functional genomics. We hope that this special issue will provide a practical update on
our knowledge of plant’s abiotic stress response and will prompt contemplation and promotion of superior approaches for sustainable
crop production.