Evolutionary Analysis and Functional Identification of Clock-Associated PSEUDO-RESPONSE REGULATOR ( PRRs ) Genes in the Flowering Regulation of Roses.

Pseudo-response regulators ( PRRs ) are the important genes for flowering in roses. In this work, clock PRRs were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw a comparative network and flow of clock PRRs in roses, a co-expression network of flowering pathway genes was drawn using a string database, and their functional analysis was studied by silencing using VIGS and protein-to-protein interaction. We revealed that the clock PRRs were significantly expanded in Rosaceae and were divided into three major clades, i.e., PRR5/9 (clade 1), PRR3/7 (clade 2), and TOC1/PRR1 (clade 3), based on their phylogeny. Within the clades, five clock PRRs were identified in Rosa chinensis . Clock PRRs had conserved RR domain and shared similar features, suggesting the duplication occurred during evolution. Divergence analysis indicated the role of duplication events in the expansion of clock PRRs . The diverse cis elements and interaction of clock PRRs with miRNAs suggested their role in plant development. Co-expression network analysis showed that the clock PRRs from Rosa chinensis had a strong association with flowering controlling genes. Further silencing of RcPRR1b and RcPRR5 in Rosa chinensis using VIGS led to earlier flowering, confirming them as negative flowering regulators. The protein-to-protein interactions between RcPRR1a / RcPRR5 and RcCO suggested that RcPRR1a / RcPRR5 may suppress flowering by interfering with the binding of RcCO to the promoter of RcFT . Collectively, these results provided an understanding of the evolutionary profiles as well as the functional role of clock PRRs in controlling flowering in roses.