Global analysis of the AP2/ERF gene family in rose (Rosa chinensis) genome unveils the role of RcERF099 in Botrytis resistance

Abstract

Background The AP2/ERFs belong to a large family of transcription factors in plants. The AP2/ERF gene family has been identified as a key player involved in both biotic and abiotic stress responses in plants, however, no comprehensive study has yet been carried out on the AP2/ERF gene family in rose (Rosa sp.), the most important ornamental crop worldwide. Results The present study comprises a genome-wide analysis of the AP2/ERF family genes (RcERFs) in the rose, involving their identification, gene structure, phylogenetic relationship, chromosome localization, collinearity analysis, as well as their expression patterns. Throughout the phylogenetic analysis, a total of 131 AP2/ERF genes in the rose genome were divided into 5 subgroups. The RcERFs are distributed over all the seven chromosomes of the rose, and genome duplication may have played a key role in their duplication. Furthermore, Ka/Ks analysis indicated that the duplicated RcERF genes often undergo purification selection with limited functional differentiation. Gene expression analysis revealed that 23 RcERFs were induced by infection of the necrotrophic fungal pathogen Botrytis cinerea. Presumably, these RcERFs are candidate genes which can react to the rose’s resistance against Botrytis cinerea infection. By using virus-induced gene silencing, we confirmed that RcERF099 is an important regulator involved in the B.cinerea resistance in the rose petal. Conclusion Overall, our results conclude the necessity for further study of the AP2/ERF gene family in rose, and promote their potential application in improving the rose when subjected to biological stress.

Recent Progress in Enhancing Fungal Disease Resistance in Ornamental Plants

“…Despite its economic importance as a predominant pathogen, studies examining B. cinerea infections in roses are limited to the comparisons of pathogen behavior in model plants such as Arabidopsis [94]. Recently, transcriptomic analyses of rose petals infected by B. cinerea determined that RcERF099, a gene that encodes member of the AP2/ERF transcription factor family, is involved in the regulation of resistance against B. cinerea in rose flowers, and this finding can provide a stepping stone for further studies aiming to improve gray mold disease resistance in roses [95].…”

Genome-Wide Analysis of BURP Genes and Identification of a BURP-V Gene RcBURP4 in Rosa Chienesis

“…Total RNAs were extracted using FastPure Plant Total RNA Isolation Kit (Vazyme, Nanjing, China) and then used for the HiScript II One Step RT-PCR Kit (Vazyme, Nanjing, China), according to the manufactory instructions. qRT-PCR was conducted using as previously described (Li et al, 2020). The stress-responsive genes were selected and AtACTIN2 (AT3G18780) was used as the reference gene.…”

“…To investigate the phylogenetic relationship of BURPs, we constructed an unrooted phylogenetic tree with other 166 predicted BURP proteins from three monocot plants: O. sativa (14), S. biocolor (11), and Z. mays (10); and eight dicot plants: A. thaliana (5), G. max (21), G. arboretum (17), G. hirsutum (30), G. raimondii (18), P. trichocarpa (18), R. chinensis (9), and R. multi ora (13), using MEGA-X with the NJ method (Fig. 1 and Supplementary Table 3).…”

“…To gain insight into the expression pattern of RcBURPs under drought stress, we searched the gene expression data from our previous transcriptomic study (Li et al, 2020). Six treatments included normal conditions (ND) in leaves (NL) and roots (NR), mild drought stress (MD) in leaves (ML) and roots (MR), and severe drought stress (SD) in leaves (SL) and roots (SR).…”

Genome-wide Characterization of GRAS Transcription Factors and Their Potential Roles in Development and Drought Resilience in Rose (Rosa chinensis)

“…After the release of whole genome sequences (Nakamura et al, 2018;Raymond et al, 2018;Saint-Oyant et al, 2018), a genome-wide study for identifying important gene families have been taken place in rose in the last two years. Some important examples include the identi cation of AP2/ERF (Li et al, 2020), WRKY (X. , Rdr1 (Menz et al, 2020), R2R3-MYB (Han et al, 2019) gene families and their potential role in different biological process i.e., growth and development, phenylpropanoid pathway, abiotic stress tolerance, and tolerance against biotic stresses like Botrytis, gray mold and black spot. However, a comprehensive study of rose GRAS genes is still lacking.…”