| Summary: | Pear (<i>Pyrus</i> spp.) is one of the most commonly consumed temperate fruits, having considerable economic and health importance. Fresh-cut or processed pear fruits are prone to browning because of the abundant phenolic compounds; however, little is known about the molecular mechanisms underlying enzymatic browning of fresh-cut sand pear fruit. In this study, fruits of two sand pear genotypes (low browning cultivar ‘Eli No.2′ and high browning cultivar ‘Weiningdahuangli’) were used to analyze the molecular mechanism of enzymatic browning by SMRT-seq and RNA-seq. The results generated 69,122 consensus isoforms, 21,336 new transcripts, 7105 alternative splicing events, and 254 long non-coding RNAs (lncRNAs). Furthermore, five genes related to enzymatic browning were predicted to be targets of six lncRNAs, and 9930 differentially expressed genes (DEGs) were identified between two different flesh browning cultivars. Meanwhile, most DEGs (e.g., <i>PAL</i>, <i>4CL</i>, <i>CAD</i>, <i>CCR</i>, <i>CHS</i>, and <i>LAR</i>) involved in the phenylpropanoid biosynthesis pathway were up-regulated, and the expression of <i>PPO</i> and <i>POD</i> were highly expressed in the high-browning cultivar. Interestingly, the transcript level of <i>PbrPPO4</i> (Pbr000321.4) was significantly higher than other PPO and POD genes, and a high level of total polyphenol and PPO activity were observed in the high browning cultivar. We found that the expression of lncRNA PB.156.1 was significantly positively correlated with the target gene <i>PbrPPO4</i> (Pbr000321.4). The results suggest that <i>PbrPPO4</i> might act as a major contributor and a key enzyme encoding gene in regulating fresh-cut sand pear fruit enzymatic browning; the expression of <i>PbrPPO4</i> was probably regulated by lncRNA PB.156.1. Altogether, the transcriptomic and physiological analyses expand the knowledge of sand pear flesh enzymatic browning at the molecular level and provide a foundation for germplasm resources for molecular breeding of high polyphenol and low browning cultivars in sand pears.
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