The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development

Abstract

Chickpea is one of the world's largest cultivated food legumes and is an excellent source of high-quality protein to the human diet. Plant growth and development are controlled by programmed expression of a suite of genes at the given time, stage, and tissue. Understanding how the underlying genome sequence translates into specific plant phenotypes at key developmental stages, information on gene expression patterns is crucial. Here, we present a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across different plant developmental stages and organs covering the entire life cycle of chickpea. One of the widely used drought tolerant cultivars, ICC 4958 has been used to generate RNA-Seq data from 27 samples at 5 major developmental stages of the plant. A total of 816 million raw reads were generated and of these, 794 million filtered reads after quality control (QC) were subjected to downstream analysis. A total of 15,947 unique number of differentially expressed genes across different pairwise tissue combinations were identified. Significant differences in gene expression patterns contributing in the process of flowering, nodulation, and seed and root development were inferred in this study. Furthermore, differentially expressed candidate genes from "QTL-hotspot" region associated with drought stress response in chickpea were validated.

Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea

“…This study identified 3190 novel genes, thus exhibiting the potential of RNA‐seq in the discovery of novel genes in the sequenced genomes as well. Similar results were also observed in other studies in chickpea (Garg et al ., ; Kudapa et al ., ). A total of 6767 genes showed differential expression pattern in different genotypes under different conditions at different time points.…”

Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses

“…Current advances in high throughput transcriptome sequencing technologies, especially RNA sequencing (RNA-seq), have provided novel insights into the molecular basis of drought tolerance by revealing the comprehensive landscape of divergent gene expression and their complex regulatory networks at various developmental stages at the transcriptional level (Garg et al, 2016;Kudapa et al, 2018). Before the advent of RNA-seq, microarray-based technologies and expressed sequenced tags (ESTs) were exclusively devoted to elucidating the preliminary function of various drought-stress-responsive genes/differentially expressed genes (DEGs) in chickpea (Mantri et al, 2007;Varshney et al, 2009;Deokar et al, 2011).…”

“…Furthermore, to identify the precise role of various candidate genes identified in the "hotspot QTL" region pinpointed by Kale et al (2015) at the gene expression level, RNA-seq based global gene expression analysis revealed differential expression of nine candidate genes under water stress (Kudapa et al, 2018). Four genes namely E3 ubiquitin-protein ligase, LRX 2, kinase i n t e r a c t i n g ( K I P 1l i k e ) f a m i l y , a n d h o m o c y s t e i n e S-methyltransferase, displayed induced expression under drought stress (Kudapa et al, 2018). Likewise, RNA-seq analysis of various vegetative and reproductive tissues subjected to heat stress identified several important candidate genes, viz.…”

“…However, the precise role of these lncRNAs in the drought stress response in chickpea and their functional annotation need further investigation. Further, availability of reference genome sequences, "C. arietinum gene expression atlas (CaGEA)" (Kudapa et al, 2018) and further refinement of transcriptome analysis could further increase our understanding of the complex drought and temperature stress responsive pathways, tracing the regulatory gene networks, and the underlying candidate gene(s), and their precise role in controlling drought and extreme temperature stress tolerances in chickpea. Moreover, transcriptome analysis could provide us great opportunity for revealing the genetic basis of higher adaptation of crop wild relatives (CWRs) and landraces to the counterpart of the cultivated species under various abiotic stresses (Srivastava et al, 2016).…”

Translational genomics and molecular breeding for enhancing precision and efficiency in crop improvement programs: Some examples in legumes

“…Thousands of differentially expressed genes (DEGs) emanating from gene expression experiments still remain inadequate to explain translation of genome sequence information into plant phenotypes (Kudapa et al 2018). To bridge this gap, Cicer arietinum gene expression atlas (CaGEA) was constructed from deep sequencing of 27 samples from five developmental stages (germination and seedling, vegetative, reproductive, and senescence) of the drought tolerant chickpea ICC 4958.…”