Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering

Stone cell content is an important factor affecting pear fruit flavor. Lignin, a major component of pear stone cells, hinders the quality and value of commercial fruit. The completion of the Chinese white pear (<i>Pyrus bretschneideri</i>) genome sequence provides an opportunity to perform integrative analysis of the genes encoding the eleven protein families (i.e., <i>PAL</i>, <i>C4H</i>, <i>4CL</i>, <i>HCT</i>, <i>C3H</i>, <i>CSE</i>, <i>CCoAOMT</i>, <i>CCR</i>, <i>F5H</i>, <i>COMT,</i> and <i>CAD</i>) in the phenylpropanoid pathway. Here, a systematic study based on expression patterns and phylogenetic analyses was performed to identify the members of each gene family potentially involved in the lignification in the Chinese white pear. The phylogenetic analysis suggested that 35 <i>P. bretschneideri</i> genes belong to bona fide lignification clade members. Compared to other plants, some multigene families are expanded by tandem gene duplication, such as <i>HCT</i>, <i>C3H</i>, <i>COMT</i>, and <i>CCR</i>. RNA sequencing was used to study the expression patterns of the genes in different tissues, including leaf, petal, bud, sepal, ovary, stem, and fruit. Eighteen genes presented a high expression in fruit, indicating that these genes may be involved in the biosynthesis of lignin in pear fruit. Similarly to what has been observed for <i>Populus trichocarpa</i>, a bimolecular fluorescence complementation (BiFC) experiment indicated that <i>P. bretschneideri C3H</i> and <i>C4H</i> might also interact with each other to regulate monolignol biosynthesis in <i>P. bretschneideri</i>, ultimately affecting the stone cell content in pear fruits. The identification of the major genes involved in lignin biosynthesis in pear fruits provides the basis for the development of strategies to improve fruit quality.