SMXL genes constitute a conserved gene family that is ubiquitous in angiosperms and involved in regulating various plant processes, including branching, leaf elongation, and anthocyanin biosynthesis, but little is known about their molecular functions in pear branching. Here, we performed genome-wide identification and investigation of the SMXL genes in 16 angiosperms and analyzed their phylogenetics, structural features, conserved motifs, and expression patterns. In total, 121 SMXLs genes were identified and were classified into four groups. The number of non-redundant SMXL genes in each species varied from 3 (Amborella trichopoda Baill.) to 18 (Glycine max Merr.) and revealed clear gene expansion events over evolutionary history. All the SMXL genes showed conserved structures, containing no more than two introns. Three-dimensional protein structure prediction revealed distinct structures between but similar structures within groups. A quantitative real-time PCR analysis revealed different expressions of 10 SMXL genes from pear branching induced by fruit-thinning treatment. Overall, our study provides a comprehensive investigation of SMXL genes in the Rosaceae family, especially pear. The results offer a reference for understanding the evolutionary history of SMXL genes and provide excellent candidates for studying fruit tree branching regulation, and in facilitating pear pruning and planting strategies.

Soil salinization severely restricts the sustainable development of the pear industry. Pyrus betulifolia, a vital native salt-tolerant rootstock in China, holds great significance for investigating stress resistance mechanisms. Plant-specific DNA-binding One Zinc Finger (Dof) transcription factors act as pivotal regulators in stress adaptation. However, their functions in P. betulifolia remain largely unexplored. In this study, we identified 43 PbeDof members within the P. betulifolia genome and classified them into eight subfamilies via phylogenetic analysis. Gene structure and conserved motif analyses revealed that PbeDof members within the same subfamily share similar exon-intron organizations and protein architecture, suggesting evolutionary conservation. Promoter analysis indicated that PbeDof genes are rich in cis-acting elements related to light, phytohormones (especially ABA and MeJA), and stress responses, implying their potential roles in diverse biological processes. Chromosomal localization and collinearity analyses revealed that segmental duplication was the primary driver of this family’s expansion. Combined transcriptomic profiling and qRT-PCR assays demonstrated that PbeDof9.1 is predominantly expressed in roots and is strongly induced by salt stress. Subcellular localization confirmed that PbeDof9.1 targets the nucleus. Functional characterization indicated that heterologous overexpression of PbeDof9.1 in Arabidopsis thaliana significantly enhances salt tolerance at germination and seedling stages. Notably, under 175 mM NaCl stress, the transgenic lines exhibited a superior root system architecture, with primary root length and lateral root numbers being approximately 1.5-fold higher than those of the wild type. Furthermore, homologous overexpression in pear calli confirmed that PbeDof9.1 mitigates oxidative damage by boosting the activities of peroxidase (POD) and catalase (CAT) to scavenge reactive oxygen species (ROS), thereby reducing malondialdehyde (MDA) accumulation. Collectively, this study characterizes the PbeDof family and establishes PbeDof9.1 as a key candidate gene for the genetic improvement of salt tolerance in pear rootstocks.

Salt stress severely restricts the growth and development of pear trees, and DNA methylation may potentially modulate the salt tolerance of Pyrus betulaefolia by regulating ion transporter genes. Cyclic nucleotide-gated channel (CNGC) family genes are essential for plant ion transport and salt stress adaptation; however, the epigenetic regulatory relationship between DNA methylation and CNGC genes underlying pear salt tolerance remains unclear. In this study, 26 PbCNGC genes were systematically identified from P. betulaefolia, which possess the conserved motifs characteristic of the CNGC family and can be classified into five subclades. PbCNGC members exhibit distinct spatiotemporal expression patterns in ordinary and salt-tolerant genotypes. Under salt stress, core members PbCNGC3, PbCNGC4, PbCNGC10, and PbCNGC14 displayed typical fluctuating up-and-down expression patterns across roots, stems, and leaves, with distinct spatiotemporal specificity in their expression peaks. In contrast, PbCNGC19 and PbCNGC20;1 were exclusively induced in roots under salt stress. Quantitative results showed marked genotypic differences in salt responsiveness. At 4 h of salt treatment, the root transcript levels of PbCNGC4 and PbCNGC14 were upregulated by 8.27-fold and 6.76-fold in the salt-tolerant genotype, respectively, which were considerably higher than those in the ordinary genotype (2.08-fold and 4.50-fold). Obvious genotypic differences in mCHH methylation modifications of PbCNGC4 and PbCNGC14 were detected after salt treatment, and pharmacological experiments confirmed that DNA methylation negatively modulates the transcription of these two genes. Yeast functional complementation assays further demonstrated that PbCNGC4 and PbCNGC14 act as functional Na⁺ and K⁺ permeable cation influx channels. Combined with methylation analysis results, this study reveals a potential regulatory cascade in which DNA methylation may inhibit the transcription of PbCNGC4 and PbCNGC14, modulating their ion-transport capacity, effectively reduces Na⁺ overaccumulation, sustains cellular K⁺ retention to alleviate salt-induced ionic toxicity, and may ultimately shape the salt tolerance of P. betulaefolia. These findings enrich the understanding of epigenetic regulation of plant salt tolerance and provide valuable candidate genes and theoretical references for salt-tolerant molecular breeding in pear trees.