Transcriptome analysis of chickpea during heat stress unveils the signatures of long intergenic non-coding RNAs (lincRNAs) and mRNAs in the heat-QTL region

In plants, besides the role of messenger RNAs (mRNAs) in gene expression, long intergenic non-coding RNAs (lincRNAs) play a key role in regulating various biological processes. Chickpea (Cicer arietinum L.), an important legume crop, is sensitive to extreme temperature regimes. Here, we identified the lincRNAs and mRNAs in three chickpea genotypes contrasting for heat stress response (two tolerant- ICC 1356, ICC 15614; one sensitive- ICC 4567) and investigated their role in heat stress. A total of 894 putative lincRNAs and 61,110 mRNAs were identified from leaf and root tissues at the vegetative and reproductive stages of the plant under control and heat stress conditions. Co-expression studies revealed the significant association of lincRNAs with mRNAs which are attributed to heat stress leaf samples at the reproductive stage. Further, mRNAs encoding heat shock transcription factors (HSFs), heat shock proteins (HSPs), starch, and sucrose metabolism pathway genes played an essential role in mitigating heat stress. Furthermore, three key lincRNAs underlying chickpea's heat-quantitative trait locus (QTL) region were identified. This study provided new insights into the regulation of heat stress tolerance in chickpea by identifying candidate lincRNAs and mRNAs.