10.1021/acs.jafc.9b07107.s001 Juan Zhao Juan Zhao Pengkun Quan Pengkun Quan Hangkong Liu Hangkong Liu Lei Li Lei Li Siyan Qi Siyan Qi Mengsheng Zhang Mengsheng Zhang Bo Zhang Bo Zhang Hao Li Hao Li Yanru Zhao Yanru Zhao Baiquan Ma Baiquan Ma Mingyu Han Mingyu Han Haihui Zhang Haihui Zhang Libo Xing Libo Xing Transcriptomic and Metabolic Analyses Provide New Insights into the Apple Fruit Quality Decline during Long-Term Cold Storage American Chemical Society 2020 NAC Apple Fruit Quality Decline JA MYB AHA ALMT 35 organic-acid-related metabolites apple fruit deterioration DEG malic acid pathway GBSS ET Long-Term Cold Storage decreases apple fruit quality CS AATP LT-LTC transcription factor genes expression levels SBE apple fruit sucrose-metabolism-related gene expression levels ERF III ABA II malic acid 2020-04-13 13:40:05 Journal contribution https://acs.figshare.com/articles/journal_contribution/Transcriptomic_and_Metabolic_Analyses_Provide_New_Insights_into_the_Apple_Fruit_Quality_Decline_during_Long-Term_Cold_Storage/12118191 Long-term low-temperature conditioning (LT-LTC) decreases apple fruit quality, but the underlying physiological and molecular basis is relatively uncharacterized. We identified 12 clusters of differentially expressed genes (DEGs) involved in multiple biological processes (i.e., sugar, malic acid, fatty acid, lipid, complex phytohormone, and stress-response pathways). The expression levels of genes in sugar pathways were correlated with decreasing starch levels during LT-LTC. Specifically, starch-synthesis-related genes (e.g., <i>BE</i>, <i>SBE</i>, and <i>GBSS</i> genes) exhibited downregulated expression, whereas sucrose-metabolism-related gene expression levels were up- or downregulated. The expression levels of genes in the malic acid pathway (<i>ALMT9</i>, <i>AATP1</i>, and <i>AHA2</i>) were upregulated, as well as the content of malic acid in apple fruit during LT-LTC. A total of 151 metabolites, mainly related to amino acids and their isoforms, amines, organic acids, fatty acids, sugars, and polyols, were identified during LT-LTC. Additionally, 35 organic-acid-related metabolites grouped into three clusters, I (3), II (22), and III (10), increased in abundance during LT-LTC. Multiple phytohormones regulated the apple fruit chilling injury response. The ethylene (ET) and abscisic acid (ABA) levels increased at CS2 and CS3, and jasmonate (JA) levels also increased during LT-LTC. Furthermore, the expression levels of genes involved in ET, ABA, and JA synthesis and response pathways were upregulated. Finally, some key transcription factor genes (<i>MYB</i>, <i>bHLH</i>, <i>ERF</i>, <i>NAC</i>, and <i>bZIP</i> genes) related to the apple fruit cold acclimation response were differentially expressed. Our results suggest that the multilayered mechanism underlying apple fruit deterioration during LT-LTC is a complex, transcriptionally regulated process involving cell structures, sugars, lipids, hormones, and transcription factors.