Document Type : Research Articles
Authors
1
Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
2
Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
10.22067/jcmr.2026.97970.1131
Abstract
Chickpea (Cicer arietinum L.), a highly nutritious and economically important legume crop, is widely cultivated in over 50 countries around the world and currently ranks as the third most produced legume globally, following common bean and soybean. Cold stress, as a major abiotic stress factor, severely limits plant growth, development, survival, and overall productivity, particularly during early growth stages. This study aimed to identify and characterize genes and long non-coding RNAs (lncRNAs) associated with cold tolerance in two contrasting chickpea cultivars, namely ILC533 (cold-sensitive) and Saral (cold-tolerant), through comprehensive transcriptomic data analysis. Using RNA-seq data, comprising approximately 200 million high-quality reads obtained from leaf samples, a total of 14,956 lncRNAs were identified, including 14,078 novel and 878 previously known lncRNAs. Expression analysis further revealed that, in the Saral cultivar, 427 lncRNAs were significantly up-regulated and 556 were down-regulated, whereas in ILC533, 494 lncRNAs were up-regulated and 454 were down-regulated under cold stress conditions. The majority of the differentially expressed lncRNAs were found to be located on chromosomes 4 and 6, and their predicted target genes, including Dehydration-responsive element-binding protein 1A, Abscisic acid and environmental stress-inducible protein-like, Glycine-rich cell wall structural protein, Calcium-dependent protein kinase 1-like, and Late embryogenesis abundant protein 7, were shown to play important and functional roles in cold tolerance. Gene Ontology analysis further indicated that these genes are actively involved in various biological processes, cellular components, and molecular functions. Additionally, most lncRNAs were predicted to be primarily localized in the cytoplasm, thereby influencing and regulating cytoplasmic functions. Overall, this study confirms the critical regulatory role of lncRNAs in the cold stress response of chickpea and provides valuable insights for future breeding of cold-tolerant varieties.
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