Grafted plant is a chimeric organism formed by the connection of scion and rootstock through stems, so stem growth and development become one of the important factors to affect grafted plant state. However, information regarding the molecular responses of stems secondary growth after grafting is limited. A grafted Rosa plant, with R. rugosa ‘Rosea’ as the scion (Rr_scion) grafted onto R. multiflora ‘Innermis’ as the stock (Rm_stock), has been shown to significantly improve stem thickness. To elucidate the molecular mechanisms of stem secondary growth in grafted plant, a genome-wide transcription analysis was performed using an RNA sequence (RNA-seq) method between the scion and rootstock. Comparing ungrafted R. rugosa ‘Rosea’ (Rr) and R. multiflora ‘Innermis’ (Rm) plants, there were much more differentially expressed genes (DEGs) identified in Rr_scion (6887) than Rm_stock (229). Functional annotations revealed that DEGs in Rr_scion are involved in two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: the phenylpropanoid biosynthesis metabolism and plant hormone signal transduction, whereas DEGs in Rm_stock were associated with starch and sucrose metabolism pathway. Moreover, different kinds of signal transduction-related DEGs, e.g., receptor-like serine/threonine protein kinases (RLKs), transcription factor (TF), and transporters, were identified and could affect the stem secondary growth of both the scion and rootstock. This work provided new information regarding the underlying molecular mechanism between scion and rootstock after grafting.

Catalpa bungei C.A.Mey is an economically significant deciduous tree valued for timber production and landscaping applications. An efficient regeneration system is crucial for clonal propagation and serves as a foundation for future molecular breeding in C. bungei. This study established two in vitro regeneration pathways—indirect somatic embryogenesis and shoot organogenesis utilizing mature zygotic embryos as explants. Primary callus was induced from cotyledon, hypocotyl, and plumule explants. A high frequency (45.73%) of yellow-green compact callus was achieved on De-Klerk and Walton (DKW) medium supplemented with 2.0 mg/L 6-BA, 1.0 mg/L zeatin (ZT), and 0.1 mg/L NAA. Subsequent transfer to 1.5× Murashige and Skoog (MS) medium containing 1.5 mg/L 6-BA, 0.2 mg/L ZT, and 0.1 mg/L NAA yielded the highest embryogenic callus induction rate (16.67%). Embryogenic callus demonstrated bipotent potential, generating both adventitious shoots and somatic embryos under specific hormonal conditions. Histological analyses confirmed the typical developmental stages of somatic embryos, from globular to cotyledonary forms, validating the embryogenic origin of regenerated structures. Furthermore, hormone or osmotic additives such as abscisic acid (ABA), Phytagel, and polyethylene glycol 4000 (PEG4000) significantly enhanced somatic embryo induction, with Phytagel at 5.0 g/L achieving the highest rate (76.31%). For shoot organogenesis, the optimal hormonal combination of the 0.6 mg/L 6-BA, 0.4 mg/L KT, and 0.15 mg/L NAA achieved the highest bud induction rate (88.89%) and produced an average of 4.07 adventitious buds per explant. This study presents an efficient regeneration system for C. bungei, providing a practical platform for large-scale propagation and basis for biotechnological applications in woody plants.

To overcome the seasonal constraints of explant availability and facilitate genetic improvement in Catalpa ovata, this study established a dual-pathway in vitro regeneration system (encompassing adventitious shoot organogenesis and somatic embryogenesis) using mature zygotic embryos. We systematically evaluated the synergistic effects of maternal genotypes, plant growth regulators (PGRs), basal media, and the histone deacetylase inhibitor Trichostatin A (TSA). Genotype screening revealed significant divergence in regenerative potential, with the half-sib family 32F17 exhibiting superior responsiveness (84.7% callus induction). A high cytokinin-to-auxin ratio (ZA3 medium) optimally drove direct shoot organogenesis. For adventitious shoot proliferation, the addition of TDZ significantly improved the multiplication coefficient (up to 2.99 on ZB4 medium), although a physiological trade-off with shoot elongation was observed. In parallel, the application of 10 µM TSA significantly enhanced somatic embryogenesis from embryogenic calli, effectively alleviating the inhibitory constraints of exogenous PGRs. For rhizogenesis, the DKW basal medium proved superior to half-strength MS, with the ZE3 treatment (0.1 mg·L⁻¹ NAA + 0.1 mg·L⁻¹ IBA) yielding the highest rooting frequency (69.6%) and robust root architecture. Notably, while somatic embryo conversion remained recalcitrant, plantlets derived exclusively from the adventitious shoot organogenesis pathway were successfully acclimatized ex vitro. These transplanted plantlets exhibited consistently high survival rates (83.1–84.4%) across all tested genotypes, effectively overcoming the initial genotype-dependent recalcitrance. Collectively, this optimized protocol provides a reliable technical platform for the large-scale clonal propagation and biotechnological breeding of C. ovata.

Somatic embryogenesis (SE) is an indispensable biotechnological platform for plant regeneration, micropropagation and genetic modification. Members of WUSCHEL-related homeobox (WOX) transcription factor family are key regulators in SE, yet their roles in Catalpa bungei remain largely unexplored. C. bungei is a high-quality ornamental tree species endemic to China with prominent horticultural ornamental value. Here, we present the first genome-wide identification and expression profiling of the CbWOX gene family during SE in C. bungei. Fourteen CbWOX genes were identified and phylogenetically classified into three major clades. These genes are distributed across the 11 chromosomes of C. bungei, and their promoter regions are enriched with cis-regulatory elements associated with phytohormone response, stress adaptation, and growth/development. Integrated transcriptome and quantitative real-time PCR (qPCR) data indicated that CbWOX2, CbWOX5, CbWOX8, and CbWOX9 were highly expressed in embryogenic callus (EC), while CbWOX1.1 and CbWOX13 were predominantly expressed in non-embryogenic callus (NEC). Notably, only eight of the fourteen CbWOX genes were significantly expressed during SE, with distinct expression profiles across developmental stages. CbWOX4.1 and CbWOX4.2 were specifically associated with yellow-green hypocotyl callus development, while CbWOX2 and CbWOX8 were highly expressed at the EC stage. During later SE stages, CbWOX1.2, CbWUS, CbWOX5, and CbWOX13 showed significant expression at the globular embryo (GE) stage, while CbWOX1.3 was specifically upregulated at the cotyledon embryo (CE) stage. Our study provides a comprehensive genomic and transcriptomic foundation for the CbWOX family in C. bungei and reveals candidate genes with stage-specific expression during SE. These findings lay a solid basis for subsequent functional research to boost SE efficiency and advance the large-scale propagation of this precious ornamental tree.