Abstract
LncRNAs (long noncoding RNAs) are 200 bp length crucial RNA molecules, lacking coding potential and having important roles in regulating gene expression, particularly in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in chickpea roots and predicted their intricate regulatory roles. A total of 3452 novel lncRNAs were identified to be distributed across all 08 chickpea chromosomes. On comparing salt-tolerant (ICCV 10, JG 11) and salt-sensitive cultivars (DCP 92–3, Pusa 256), 4446 differentially expressed lncRNAs were detected under various salt treatments. We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as eTMs (endogenous target mimic) targets of miRNAs and implicated them in the regulatory network of salt stress response. Functional analysis of these lncRNA revealed their association in targeting salt stress response-related genes like potassium transporter, transporter family genes, serine/threonine-protein kinase, aquaporins like TIP1-2, PIP2-5 and transcription factors like, AP2, NAC, bZIP, ERF, MYB and WRKY. Furthermore, about 614 lncRNA-SSRs (simple sequence repeats) were identified as a new generation of molecular markers with higher efficiency and specificity in chickpea. Overall, these findings will pave the understanding of comprehensive functional role of potential lncRNAs, which can help in providing insight into the molecular mechanism of salt tolerance in chickpea.
Highlights
Increasing soil salinity is important environmental problem leading deleterious consequences on agricultural productivity worldwide
We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as endogenous target mimic (eTM) targets of miRNAs and implicated them in the regulatory network of salt stress response
High-throughput RNA-seq data of chickpea under salt stress/control conditions have facilitated comprehensive identification of lncRNAs involved in salt stress response
Summary
Increasing soil salinity is important environmental problem leading deleterious consequences on agricultural productivity worldwide. More than 6% of global arable soil is directly affected by salinity (Yuan et al 2016). Loss of about 1.5 Mha arable land along with amount worth $27.5 billion incurred annually attributing to salinity stress (FAO 2015; Qadir et al 2014). Chickpea (Cicer arietinum L.) is most widely cultivated legume which is considered as important source of dietary proteins and fibers (Jukanti et al 2012). It is grown on over 17.8 million hectares area with a production of 17.2 million metric tons worldwide and India is the leading producer with a total production of 11.4 million metric tons, approximately 66% of the total global production (FAO 2018). Earlier considered as orphan crop, chickpea is enriched with availability of modern genomic resources
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