Construction of heat stress regulation networks based on Illumina and SMRT sequencing data in potato

Lina Shang; Yonghong Zhou; Shiqi Wen; Ke Wang; Yang Li; Meihua Zhang; Hongju Jian; Dianqiu Lyu

doi:10.3389/fpls.2023.1271084

Construction of heat stress regulation networks based on Illumina and SMRT sequencing data in potato

Front Plant Sci. 2023 Nov 2:14:1271084. doi: 10.3389/fpls.2023.1271084. eCollection 2023.

Authors

Lina Shang^#^{1

2}, Yonghong Zhou^#^{1

2

3

4}, Shiqi Wen^{1

2}, Ke Wang^{1

2}, Yang Li^{1

2}, Meihua Zhang^{1

2}, Hongju Jian^{1

2

3

4}, Dianqiu Lyu^{1

2

3

4}

Affiliations

¹ Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China.
² College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
³ State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China.
⁴ Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China.

^# Contributed equally.

Abstract

Potato (Solanum tuberosum L.) is one of the most important tuber food crops in the world; however, the cultivated potatoes are susceptible to high temperature, by which potato production is adversely affected. Understanding the coping mechanism of potato to heat stress is essential to secure yield and expand adaptability under environmental conditions with rising temperature. However, the lack of heat-related information has significantly limited the identification and application of core genes. To gain deeper insights into heat tolerance genes, next-generation sequencing and single-molecule real-time sequencing were used to learn the transcriptional response of potato to heat stress and 13,159 differentially expressed genes (DEGs) were identified in this study. All DEGs were grouped into 12 clusters using the K-means clustering algorithm. Gene Ontology enrichment analysis revealed that they were involved in temperature signaling, phytohormone, and protein modification. Among them, there were 950 differentially expressed transcription factors (DETFs). According to the network analysis of DETFs at the sixth hour under heat stress, we found some genes that were previously reported to be associated with photoperiodic tuberization, StCO (CONSTANS), tuber formation, StBEL11 (BEL1-LIKE 11), and earliness in potato, StCDF1 (CYCLING DOF FACTOR 1) responding to temperature. Furthermore, we verified the relative expression levels using quantitative real-time polymerase chain reaction, and the results were consistent with the inferences from transcriptomes. In addition, there were 22,125 alternative splicing events and 2,048 long non-coding RNAs. The database and network established in this study will extend our understanding of potato response to heat stress. It ultimately provided valuable resources for molecular analysis of heat stress response in potato and cultivation of potato varieties with heat tolerance.

Keywords: NGS sequencing; SMRT sequencing; alternative splicing; heat stress; lncRNAs; potato.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by the National Key Research and Development Program of China (2018YFE0127900), the National Natural Science Foundation of China (32101659), Chongqing Technical Innovation and Application Development Special Project (CSTB2022TIAD-CUX0012), and the Talent Introduction Program of Southwest University Project (SWU019008).