Identification and expression analysis of R2R3-MYB transcription factors in Docynia delavayi

The R2R3-MYB genes, as one of the largest transcription factors (TFs) families in the plant kingdom, play a significant role in the regulation of pigment accumulation. The aim of this study was to screen the candidate R2R3-MYB genes involved in peel coloration, as there are remarkable variations in the pericarp's color of Docynia delavayi (Franch.) Schneid.

The pericarp of three D. delavayi types was used as the material, the R2R3-MYB genes were identified based on the transcriptomic data and subsequently analyzed for their physicochemical properties, phylogeny, conserved domains, conserved motifs and expression patterns.

A total of 99 R2R3-MYB genes were identified, and most of them were hydrophilic proteins with an amino acid sequence varying from 86 to 881aa, molecular weight between 10.21 and 99.63 kDa, an isoelectric point between 5.01 and 11.44, and an aliphatic index between 55.77 and 91.78. The phylogenetic tree showed that 4 R2R3-MYBs of D. delavayi (DdR2R3-MYB) and MdMYB10 were co-clustered in the subgroup 6, suggesting a possible association with anthocyanin biosynthesis. Additionally, 8 DdR2R3-MYBs were clustered in subgroup 22, indicating that they might be related to carotenoid biosynthesis. Each DdR2R3-MYB contained 2 R domains, which displayed high conservation in the evolutionary process. Conserved motif analysis showed that motif 1 ～ motif 4 were located at the N terminus of most members, which was similar to the R2 and R3 conserved domains. Expression pattern analysis showed that the 48 differentially expressed DdR2R3-MYB genes exhibited 5 expression patterns, indicating diverse functions of DdR2R3-MYBs. RT-qPCR analysis showed that DdR2R3-MYB2/16/18 was significantly up-regulated in the red pericarp, and DdR2R3-MYB47/48 was accumulated in the yellow pericarp.

Based on the phylogenetic and expression pattern analyses, three candidate genes have been screened for anthocyanin biosynthesis regulation and two candidate genes were obtained for carotenoid biosynthesis regulation, which laid a theoretical foundation for the mining of the genes related to peel coloration in D. delavayi.