Transcriptome and Metabolome Analyses of ‘Bartlett’ and ‘Xiang Shuomi’ Pears (Pyrus communis L.) Unveil the Candidate Pathways and Genes Regulating Leaf and Fruit Size

The size of leaves and fruits is a crucial agronomic and economic trait for fruit trees. The ‘Bartlett’ pear is a famous cultivar with succulent and delicious fruit and is cultivated globally. ‘Xiang shuomi’ is a bud sport of the ‘Bartlett’ pear, discovered in our breeding work, and exhibits enlarged leaves and fruits. However, the specific regulatory mechanism of this superior agronomic trait is still elusive. In this study, comprehensive transcriptome and metabolome analyses were performed to explore the differences in gene expression and metabolite accumulation between these two pear cultivars. The transcriptome analysis showed a total of 1279 differentially expressed genes (DEGs), with the flavonoid biosynthetic process being the most significant enriched biological process. Metabolome data indicated the detection of 412 differentially abundant metabolites (DAMs), with the metabolites of flavonoid biosynthesis being enriched significantly. The integrative transcriptomic and metabolomics analysis further confirmed the pivotal role of the flavonoid biosynthetic process in distinguishing the two cultivars. Importantly, the genes that encoded enzymes related to flavonoid biosynthesis, including CHS, CHI, HCT, LAR and CYP75B1, increased their expressions in the ‘Xiang shuomi’ pear. Correspondingly, the metabolites galangin, chlorogenic acid, luteolin and catechin were found to accumulate in the ‘Xiang shuomi’ pear. Overall, this research identified key pathways and genes influencing the fruit and leaf size of pears, providing fundamental information for the high-yield breeding of fruit trees.