Objective Fasciclin-like arabinogalactan proteins (FLAs) were a subclass of arabinogalactan- proteins (AGPs). The FLAs were widely involved in biological processes such as plant growth and development, sexual reproduction, and abiotic stress response. Identifying and analyzing the FLA gene family in Rosa plants (R. chinensis and R. rugosa) could help to understand the role of the FLA gene family in the biological processes of Rosa plants.

Method This study employed bioinformatics to conduct a genome-wide identification of the FLA gene family in R. chinensis and R. rugosa. The FLA gene families of the two species were compared, and the expression patterns of FLA genes in the stamens and pistils of R. chinensis and R. rugosa were analyzed.

Result Twenty-five FLA genes were identified in both R. chinensis and R. rugosa, unevenly distributed across their respective seven chromosomes. Analysis of the structure of FLA genes in R. chinensis and R. rugosa revealed that 18 RcFLA in R. chinensis and 21 RrFLA in R. rugosa did not contain introns. Analysis of cis-regulatory elements found that light response elements, MeJA response elements, and auxin-related cis-elements were widely distributed. Among all 50 FLA proteins, 33 had signal peptides at their N-termini, 30 were transmembrane protein, and all 44 were likely localized on the cell membrane. The closely related FLA proteins showed strong similarity in their two-dimensional and three-dimensional structures and motif distribution. Phylogenetic analysis divided all FLAs into six groups, with Group Ⅰ having the most members and branches, and other groups containing FLAs from both R. chinensis and R. rugosa. Analysis of the expression patterns of FLA genes in the stamens and pistils of R. chinensis and R. rugosa revealed that some FLA were specifically highly expressed in the stamens or pistils.

Conclusion A total of 25 FLA genes were identified in both R. chinensis and R. rugosa, indicating that these FLA genes are conserved and also species-specific. Additionally, some FLA genes were specifically highly expressed in the pistil or stamen, and were potentially involved in the fertility regulation of R. chinensis and R. rugosa,  providing a reference for further research on the regulation of reproductive development in Rosa plants.