Comparative physiology and transcriptome response patterns in cold-tolerant and cold-sensitive varieties of Solanum melongena
Authors: cai Peng , lan Yanhong , Gong Fangyi , Li Chun , Xia Feng , Li Yifan , Fang Chao 
Published: November 2023

Abstract
Background
Climate change has caused severe cold, affecting global crop production. Eggplant (Solanum melongena L.) is an important economic crop, whose yield and quality are easily severely affected by cold damage. Identifying key genes and comprehensive transcriptional regulation molecular mechanisms for cold resistance is essential to grow new varieties with stronger tolerance.
Results
To explore the response mechanism of eggplants to cold stress, this study compared the leaf physiological indexes and transcriptome sequencing results of cold-tolerant "A" and cold-sensitive "B" treated at 5 ℃ for 0, 1, 2, 4, and 7 d, respectively. The late physiological cold response of cultivar B was similar to the early physiological cold response of cultivar A through the analysis of chemical stoichiometry. The VIP values of peroxidase (POD) activity and soluble protein content are 1.09 and 1.12, respectively, using orthogonal partial least squares discriminant analysis (OPLS-DA), which are identified as important physiological indicators for the two varieties. RNA seq data analysis under low-temperature stress showed that 7024 differentially expressed genes (DEGs) were identified in A, and 6209 DEGs were identified in B. GO analysis showed that protein modification transport, membrane components, plant hormone signal transduction, photosynthesis, calcium and mitogen-activated protein kinase (MAPK) signal pathways, active oxygen scavenging, energy metabolism, and carbohydrate metabolism were closely related to the cold stress response of eggplant. The KEGG pathway enrichment of DEGs showed that starch and sucrose metabolism, GSH metabolism, terpenoid synthesis, and energy metabolism (TCA and HMP cycling) were promoted by low-temperature stress, improving antioxidant activity and stress resistance. Weighted gene co-expression network analysis (WGCNA) showed that many cold response genes, pathways, and soluble proteins were enriched in the MEgrep60 modules. The core hub genes of the co-expression network were POD, membrane transporter-related gene MDR1, abscisic acid-related genes (PP2C and SnRK2), growth factor enrichment gene DELLA, core components of biological clock PRR7 and five transcription factors (MYB, AP2/ERF, bZIP, bHLH, C2H2), respectively. The core transcription factor MYB was co-expressed with signal transduction, plant hormone, biosynthesis, and metabolism-related genes, indicating that this transcription factor played a key role in the cold response network.
Conclusion
This study integrates physiological indicators and transcriptomics to reveal the molecular mechanisms underlying the differences in cold tolerance between eggplant cold tolerant variety “A” and cold sensitive variety “B”, including ROS modulation (glutathione), increase in the content of osmotic carbohydrate and free proline, and the expression of terpenoids synthesis genes, which will help to reveal how key cold responsive transcription factors or other related genes are involved in through network. It also provides new insights into the molecular mechanisms underlying cold stress tolerance and helping to improve crop cold tolerance.