Genome-Wide Identification and Characterization of the Lateral Organ Boundaries Domain (LBD) Gene Family in nine Rosaceae Species and Expression Pattern in <i>Prunus mume</i>

Transcription factors (TFs) encoded by the lateral organ boundaries domain (LBD) gene family are known to control many plant-specific developmental processes. However, the comparative analysis of the LBD gene family in Rosaceae species and its expression pattern in mei remains unclear. Here, we identified a total of 406 LBDs in nine Rosaceae species, including 39 in black raspberry (Rubus occidentalis), 34 in strawberry (Fragaria vesca), 39 in Chinese rose (Rosa chinensis), 42 in peach (Prunus persica), 41 in apricot (Prunus armeniaca), 41 in mei (Prunus mume var. tortuosa), 60 in pear (Pyrus communis), 41 in hawthorn (Crataegus pinnatifida) and 69 in apple (Malus domenstica), respectively. The LBDs of nine Rosaceae species were classified into seven major subclasses. The chromosome localization, collinearity analysis, and gene duplication relationship revealed that segment duplication was the main driving force for the amplification of LBDs in the Rosoideae and Amygdaloideae. Ka/Ks analysis suggested most of the LBD gene pairs might be under purification selection. GO and cis-acting elements analysis showed that LBDs may play important roles in many biological processes and could respond to hormones and stresses. RNA-seq data showed that PmLBD17/19/41 genes contained both low-temperature and MeJA response elements and played a significant variation across different geographic locations and periods. PmLBD30, the ortholog of EgLBD29, exhibited an up-regulation followed by a decrease, which is hypothesized to possibly play a role in the formation of a weeping trait in mei. Our research offers important data about the development of the LBD family in Rosaceae and the subsequent validation of LBDs' functional genes in P. mume.