Multi-omics analysis of green- and russet skin pear cultivars identify key regulators of skin russeting.

• The skin dynamics development of two pear cultivars and their mutants were analyzed. • The key genes and metabolites involved in russet skin formation were identified. • A set of TFs was predicted as putative regulators of russet skin formation. • We emphasis on exploring the underlying mechanisms of russet pear skin formation. Different periderm development makes the partial and full russet skin of pear fruit, which negatively influence pear fruit appearance quality. The switch gene for russet skin formation and the functional conservation of the homologs among different species showed to have multiple significance to clarify the transcriptional network underlying russet skin formation. In this study, two pear cultivars coupled with their mutants were used to explore the underlying molecular regulatory network of russet skin formation. RNA-sequencing and metabolomics were used to identify the key pathways and switch genes involved in russet skin formation, and identified genes involved in lignin biosynthesis, suberin biosynthesis, and suberin transporters. Additionally, a set of transcription factors was identified via coexpression network analysis and differential expression analysis, including PbMYB308, PbbHLH49, PbWRKY24 , and PbNAC40 , which had a high correlation with russet skin-related genes. These genes were predicted as putative regulators involved in russet pear skin formation. qRT–PCR was performed to validate the transcriptome data. Two varieties and their mutants were used for the first time to explore the switch genes and underlying mechanisms of russet formation. We concentrated on the russet skin development in pear fruit, with an emphasis on exploring the underlying regulatory mechanisms. [ABSTRACT FROM AUTHOR]