Kaashyap, M and Kaur, S and Ford, R and Edwards, D and Siddique, K H M and Varshney, R K and Mantri, N (2022) Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea. Plant Biotechnology Journal (TSI), 20 (7). pp. 1402-1416. ISSN 1467-7644
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Salinity severely affects the yield of chickpea. Understanding the role of lncRNAs can shed light on chickpea salt tolerance mechanisms. However, because lncRNAs are encoded by multiple sites within the genome, their classification to reveal functional versatility at the transcriptional and the post-transcriptional levels is challenging. To address this, we deep sequenced 24 salt-challenged flower transcriptomes from two parental genotypes of a RIL population that significantly differ in salt tolerance ability. The transcriptomes for the first time included 12polyadenylated and 12 non-polyadenylated RNA libraries to a sequencing depth of~50 million reads. The ab initio transcriptome assembly comprised ~34082 transcripts from three biological replicates of salt-tolerant (JG11) and salt-sensitive (ICCV2) flowers. A total of 9419 lncRNAs responding to salt stress were identified, 2345 of which were novel lncRNAs specific to chickpea.The expression of poly(A+) lncRNAs and naturally antisense transcribed RNAs suggest their role in post-transcriptional modification and gene silencing. Notably, 178 differentially expressed lncRNAs were induced in the tolerant genotype but repressed in the sensitive genotype. Co-expression network analysis revealed that the induced lncRNAs interacted with the FLOWERING LOCUS(FLC), chromatin remodelling and DNA methylation genes, thus inducing flowering during salt stress. Furthermore, 26 lncRNAs showed homology with reported lncRNAs such as COOLAIR, IPS1 and AT4, thus confirming the role of chickpea lncRNAs in controlling flowering time as a crucial salt tolerance mechanism in tolerant chickpea genotype. These robust set of differentially expressed lncRNAs provide a deeper insight into the regulatory mechanisms controlled by lncRNAs under salt stress.
| Item Type: | Article |
|---|---|
| Divisions: | Center of Excellence in Genomics and Systems Biology |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | antisense transcribed, coding potential, flowering locus, intergenic, long noncoding RNA, salinity |
| Subjects: | Mandate crops > Chickpea Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 16 Jan 2024 05:44 |
| Last Modified: | 16 Jan 2024 05:50 |
| URI: | http://oar.icrisat.org/id/eprint/12363 |
| Official URL: | https://onlinelibrary.wiley.com/doi/full/10.1111/p... |
| Projects: | Australia–India Strategic Research Fund (AISRF) Grant number GCF01001 |
| Funders: | Commonwealth of Australia |
| Acknowledgement: | The authors are grateful to VLSCI (Melbourne Bioinformatics) for providing some of the bioinformatics tools used for analysis. |
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