Loquat (Eriobotrya japonica) fruit accumulates lignin during postharvest storage under chilling conditions (0 °C), while low-temperature conditioning (LTC; 5 °C for 6 days followed by transfer to 0 °C) or heat treatment (HT; 40 °C for 4 h followed by transfer to 0 °C) can alleviate lignification. Here we compared transcriptome profiles of loquat fruit samples under LTC or HT to those stored at 0 °C at five time points from day 1 to day 8 after treatment. High-throughput transcriptome sequences were de novo assembled into 53,319 unique transcripts with an N50 length of 1306 bp. A total of 2235 differentially expressed genes were identified in LTC, and 1020 were identified in HT compared to 0 °C. Key genes in the lignin biosynthetic pathway, including EjPAL2, EjCAD1, EjCAD3, 4CL, COMT, and HCT, were responsive to LTC or HT treatment, but they showed different expression patterns during the treatments, indicating that different structural genes could regulate lignification at different treatment stages. Coexpression network analysis showed that these candidate biosynthetic genes were associated with a number of transcription factors, including those belonging to the AP2, MYB, and NAC families. Gene ontology (GO) enrichment analysis of differentially expressed genes indicated that biological processes such as stress responses, cell wall and lignin metabolism, hormone metabolism, and metal ion transport were significantly affected under LTC or HT treatment when compared to 0 °C. Our analyses provide insights into transcriptome responses to postharvest treatments in loquat fruit.

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