Advances in Transcriptomics of Plants

Abstract

The current global population of 7.3 billion is estimated to reach 9.7 billion in the year 2050. Rapid population growth is driving up global food demand. Additionally, global climate change, environmental degradation, drought, emerging diseases, and salty soils are the current threats to global food security. In order to mitigate the adverse effects of these diverse agricultural productivity constraints and enhance crop yield and stress-tolerance in plants, we need to go beyond traditional and molecular plant breeding. The powerful new tools for genome editing, Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR)/Cas systems (CRISPR-Cas9), have been hailed as a quantum leap forward in the development of stress-resistant plants. Plant breeding techniques, however, have several drawbacks. Hence, identification of transcriptional regulatory elements and deciphering mechanisms underlying transcriptional regulation are crucial to avoiding unintended consequences in modified crop plants, which could ultimately have negative impacts on human health. RNA splicing as an essential regulated post-transcriptional process, alternative polyadenylation as an RNA-processing mechanism, along with non-coding RNAs (microRNAs, small interfering RNAs and long non-coding RNAs) have been identified as major players in gene regulation. In this chapter, we highlight new findings on the essential roles of alternative splicing and alternative polyadenylation in plant development and response to biotic and abiotic stresses. We also discuss biogenesis and the functions of microRNAs (miRNAs) and small interfering RNAs (siRNAs) in plants and recent advances in our knowledge of the roles of miRNAs and siRNAs in plant stress response. Graphical Abstract.

Transcriptome Analysis Reveals Potential Roles of Abscisic Acid and Polyphenols in Adaptation of Onobrychis viciifolia to Extreme Environmental Conditions in the Qinghai-Tibetan Plateau

“…In the past 10 to 15 years, the application of transcriptomics has substantially facilitated a deep understanding of responsiveness or resistance mechanisms of plants in the face of various specific stresses at a molecular level, especially with regard to unravelling differentially expressed genes (DEGs), signaling pathways and regulation of metabolic networks involved in responses to diverse stresses [ 14 , 15 ]. For example, an increasing number of TFs involved in plant responses to abiotic stresses have been discovered in many plant species, such as C-repeat binding factor/dehydration responsive element-binding (CBF/DREB), myeloblastosis (MYB), WRKY, nam-ataf1,2-cuc2 (NAC) and basic region/leucine zipper motif (bZIP) TFs, the biological functions of which have been confirmed by transgenic studies [ 16 , 17 , 18 , 19 , 20 ].…”

Potential of genomics for the improvement of underutilized legumes in sub‐Saharan Africa

“…Another recently developed powerful approach aiding precision breeding is genome‐editing, through TALENs (transcription activator‐like effector nucleases), or CRISPR‐Cas9 (clustered regulatory interspaced short palindromic repeats‐CAS systems). These have been adapted as a significant drive forward in improved stress‐resistant plants (Nejat, Ramalingam, & Mantri, 2018; Zhang et al, 2016). Genome‐editing offers to look beyond traditional and molecular plant breeding and can play a significant role in mitigating the adverse effects of yield constraints of crops, especially under climate change scenarios.…”

Genetic Improvement in Sunflower Breeding—Integrated Omics Approach

“…Transcriptomic study in plants is usually performed for analyzing diverse effects of stresses in order to explain dynamic and complex processes on molecular level, which lead to modifications in plant tissues [60][61][62][63]. Identifying complex transcriptional changes in tissues is possible through identification of transcription regulatory elements and deciphering the mechanisms on which transcription regulation is based [64,65]. Considering that plants are often exposed to various external pressures, comparative transcriptome analyses for plants exposed to different stresses is useful for understanding the role of commonly regulated genes under combined and individual stresses and utilization of such genes in breeding process for combined stress tolerance [66,67].…”