Analysis of transcriptome profiles of two Pyrus pyrifolia cultivars reveals genes associated with stone cell development

Abstract

Pyrus pyrifolia, which is famous for its delicate flesh, is the most widely cultivated oriental pear. Stone cell content is an important factor affecting P. pyrifolia fruit quality. However, the mechanism underlying stone cell development remains to be fully elucidated. In this study, the content and distribution of stone cells of two cultivars of P. pyrifolia, namely, ‘Twentieth Century’ (TC) and its bud variety ‘Golden Twentieth Century’ (GTC), were compared. Results showed that the contents of stone cells and lignin in TC were significantly higher than those in GTC during the entire fruit development process. Moreover, fruits that developed 60 days after flowering had the highest stone cell content. By transcriptome sequencing, 1558 differentially expressed genes (DEGs), including 530 upregulated genes and 1028 downregulated genes, were identified. Gene Ontology (GO) enrichment analysis indicated hemicellulose metabolic process (GO: 0010410), lignin metabolic process (GO:0009808) and lignin catabolic process (GO: 0046274) were highly active in stone cell development. Kyoto Encyclopedia of Genes and Genomes metabolic pathway enrichment analysis suggested that in phenylpropanoid biosynthesis (ko00940) pathway, two enzymes (glucosyltransferase [EC:2.4.1.111] and peroxidase [EC:1.11.1.7]) could be important factors of lower lignin content in GTC than TC. The quantitative real-time polymerase chain reaction was used to screen out several genes and TFs, such as peroxidase 42-like gene, vinorine synthase-like gene, and Myb4-like TFs, are likely associated with stone cell development. Our study would provide a basis for the molecular mechanisms of stone cell development in P. pyrifolia cultivars and would aid in improving quality of pear fruits by breeding.