Expression analysis of some long non-coding RNAs in sugarcane variety cp73-21 in response to cold stress

Document Type : Research Paper

Authors

1 MSc degree of Plant Breeding, Plant Production and Genetics Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

2 Assistant Professor, Plant Production and Genetics Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran. Iran.

3 Associate Professor, Plant Production and Genetics Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

Abstract

Objective
Sugarcane is one of the most important industrial plants used in sugar production, as well as in the generation of biofuels such as bioethanol and electricity. This plant is native to tropical regions, and cold stress is considered the most significant environmental factor limiting sugarcane growth. According to available information, some long non-coding RNAs (lncRNAs) play a significant role in adapting to environmental stresses, including cold stress.
Materials and Methods
In this research, after obtaining the sugarcane reference genome from the NCBI database and aligning the sequences, gene frequency was estimated using RSEM software. Differentially expressed genes (DEGs) were identified using the edgeR software package. Subsequently, BLAST2GO was employed to perform gene ontology analysis and classify genes into cellular, molecular, and biological categories.
Results
Based on bioinformatics analysis, 170 genes showed differential expression under stress conditions, and 64 lncRNAs were identified using four parameters: sequence length, CNCI, CPC2, and ORF. Since their target genes are linked to cold stress, the expression changes of five lncRNAs were evaluated for the CP73-21 variety. For this purpose, leaves from 8-week-old sugarcane seedlings treated at 4°C for 0, 12, 24, and 48 hours in three biological replicates were used. To confirm the effect of cold stress on the seedlings, the physiological damage indices ELI and MDA were measured. Both ELI and MDA indices increased over time. According to bioinformatics analysis conducted with edgeR, the expression of lncRNAs coded as numbers 1, 3, and 5 increased during cold stress, whereas the expression of lncRNAs coded as numbers 2 and 4 decreased. Examining the relative expression levels of the target genes coding for Cpn60, Zipper family gene, WRKY, SAT1, and CBF revealed an increase in expression for all five genes, generally following an upward trend over time.
Conclusions
Based on the present study, the increased expression of these genes and their associated lncRNAs compared to the control plant suggests enhanced plant tolerance to temperature stresses, including cold stress.

Keywords

References

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Agricultural Biotechnology Journal
Volume 17, Issue 1
March 2025
Pages 97-120

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