Construction of drought stress regulation networks in potato based on SMRT and RNA sequencing data

Jian H. Sun H. Liu R. Zhang W. Shang L. Wang J. Khassanov V. Lyu D.
December 2022 BioMed Central Ltd

BMC Plant Biology
2022 #22 Issue 1

Background: Potato (Solanum tuberosum) is the fourth most important food crop in the world and plays an important role in food security. Drought stress has a significantly negative impact on potato growth and production. There are several publications involved drought stress in potato, this research contributes to enrich the knowledge. Results: In this study, next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technology were used to study the transcription profiles in potato in response to 20%PEG6000 simulates drought stress. The leaves of the variety “Désirée” from in vitro plantlets after drought stress at six time points from 0 to 48 hours were used to perform NGS and SMRT sequencing. According to the sequencing data, a total of 12,798 differentially expressed genes (DEGs) were identified in six time points. The real-time (RT)-PCR results are significantly correlated with the sequencing data, confirming the accuracy of the sequencing data. Gene ontology and KEGG analysis show that these DEGs participate in response to drought stress through galactose metabolism, fatty acid metabolism, plant-pathogen interaction, glutathione metabolism and other pathways. Through the analysis of alternative splicing of 66,888 transcripts, the functional pathways of these transcripts were enriched, and 51,098 transcripts were newly discovered from alternative splicing events and 47,994 transcripts were functionally annotated. Moreover, 3445 lncRNAs were predicted and enrichment analysis of corresponding target genes was also performed. Additionally, Alternative polyadenylation was analyzed by TADIS, and 26,153 poly (A) sites from 13,010 genes were detected in the Iso-Seq data. Conclusion: Our research greatly enhanced potato drought-induced gene annotations and provides transcriptome-wide insights into the molecular basis of potato drought resistance.

Alternative polyadenylation , Alternative splicing , Drought stress , LncRNAs , SMRT , Solanum tuberosum

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College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715, China
Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, 400715, China
S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue, Astana, 010011, Kazakhstan

College of Agronomy and Biotechnology
State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University
Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops
S. Seifullin Kazakh Agrotechnical University

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