Transcriptome Analysis of European Pears (Pyrus communis cv. Bartlett) Reveals Significant Gene Families and Co-expressed Genes Associated with Development of Ripening Capacity by Temperature Conditioning

Freshly harvested early-season European (Pyrus communis) pears often fail to achieve acceptable quality and need conditioning treatments including ethylene and/or cold temperature to develop ripening capacity. Our objective is to understand the influence of temperature on ripening capacity development, focusing on temperature conditioning and to identify genes closely associated with the onset of ripening capacity. Tissue samples collected from ‘Bartlett’ pears exposed to treatments that induce subsequent ripening within six days at room temperature (0 °C - 14 days and 10 °C - 5 days), together with the control (fruit at harvest) were submitted for RNA sequencing. Through Trinity assembler and RNA-Seq by Expectation-Maximization, 101,229 contigs (mean length = 911.7) and 68,067 unigenes were generated. Of these unigenes, more than 30.2 % were annotated to public databases.  By utilizing EBSeq, 8536 and 7938 unigenes were identified as differentially (DE) expressed sequences between the 0 °C treated and control fruit, and between the 10 °C treated and control fruit, respectively. The fold changes of these DE unigenes from the two comparisons were highly correlated in the regression analysis. Mercator–Mapman annotation classification showed that the 0 °C treatment induced more stress-related unigenes than the 10 °C treatment, the largest number of DE unigenes in the hormone group were auxin- and ethylene- related (30% and 33%, respectively), and the most abundant transcription factor families were bHLH, AP2/EREBP, and MYB. According to the protein interaction network analysis in Cytoscape using the IntAct database, some temperature-regulated genes appeared to be involved in the signaling network for ripening capacity development. Additionally, weighted gene co-expression network analysis determined five clusters of co-expressed genes correlated with fruit characteristics during ripening, such as firmness and ethylene production. The unigenes that were highly correlated to the firmness at day six are likely candidates for future research to determine biomarkers for detecting pear ripening capacity.