{"paper_id":"31648fd5-e90f-4c67-9413-e1329f3d9e05","body_text":"Comparative transcriptome analysis provides insights into the dwarfing mechanism of pear trees | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Comparative transcriptome analysis provides insights into the dwarfing mechanism of pear trees Yi Xiao, Qionghou Li, Shuo Li, Kaijie Qi, Yuan Gao, Hongxiang Li, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9020477/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 14 You are reading this latest preprint version Abstract Background Dwarfism is crucial for intensive cultivation and labor-saving management in modern orchard. However, the molecular mechanisms underlying pear tree dwarfing remain largely unclear. Here, we performed comparative transcriptome analysis between dwarf pear germplasm and pear cultivar ‘Cuiguan’. Result The dwarf pear germplasm presents significantly shorter internode and branch length compared to ‘Cuiguan’. Histological analysis revealed that cortical cells in the dwarf pear germplasm are disordered and irregular, and longer than those of ‘Cuiguan’. Comparative transcriptome analysis of shoot apex from young shoots of the dwarf germplasm and ‘Cuiguan’ was conducted and a total of 13,169 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that function terms related to plant hormone biosynthesis and signal transduction were overrepresented in DEGs. Genes involved in brassinosteroid (BR) and gibberellin (GA) inactivation and degradation were upregulated in the dwarf germplasm. DEGs involved in transcription regulation and cell wall formation were also identified, which play potential roles in tree dwarfing. In addition, expression level of genes within the chromosomal region containing PcDw locus, which has been reported as the dominant gene controlling dwarf trait, was investigated in both the dwarf pear germplasm and ‘Cuiguan’. Based on comparative analysis, 9 genes in this region are considered to be closely associated with dwarf traits. Conclusions Overall, the results of this study provide insights for understanding the genetic and molecular mechanisms underlying pear tree dwarfing. pear dwarf germplasm ‘Cuiguan’ comparative transcriptome dwarfing mechanism Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 1 Background Dwarfing traits are critical for high-density planting and mechanical management in modern pear orchard system. However, dwarfing pear rootstocks and dwarf pear cultivars are limited in pear production, and the molecular mechanisms governing pear tree dwarfing remain poorly understood. Several pear rootstocks have been selected for dwarfing cultivation, including quince rootstocks (e.g., Quince A, Quince C, BA 29) OHxF rootstocks (e.g., OHxF 87, OHxF 333), ‘Zhongai’ rootstocks (NO. 1 – NO. 5), and ‘Qingzhen D1’ rootstocks [ 1 ][ 2 ][ 3 ][ 4 ][ 5 ] . In addition, a French pear cultivar ‘Le Nain Vert’ (LNV, Pyrus communis ) characterized as shortened internodes and dwarfed growth was selected, and its seed-derived dwarf offspring was crossed by a Chinese white pear cultivar ‘Chili’ ( Pyrus bretschneideri Rehd.) to breed the rootstock ‘Qingzhen D1’ (QZD1, Pyrus communis × bretschneideri ) [ 3 ][ 8 ] . Previous studies have shown that the dwarf phenotype of LNV is controlled by a dominant single gene PcDw , which was initially mapped it to linkage group 16 (LG16) of pear linkage map based on SSR markers [ 6 ] . Further, the PcDw was localized to scaffold00074 in European pear genome [ 7 ] . Based on a hybrid population produced from crossing ‘Aihuali’ (seed-derived dwarf offspring of LNV) and ‘Chili’, comparative transcriptome analysis of young apical stems from dwarf and standard offspring was conducted and 2,170 differentially expressed genes (DEGs) were identified. Among all DEGs, 88 were identified as transcription factors (TFs), belong to 22 TF families [ 8 ] . The most abundant TF families included AP2 (9 genes), NAC (9), C2H2-type (8), C3H-type (8), and MYB (8). Expression patterns of all genes located on scaffold00074 were subsequently analyzed, and four differentially expressed genes (DEGs) were identified after excluding genes located far from the SSR markers that are closely linked to PcDw . Among these four DEGs, PCP021014_v1.0 and PCP021015_v1.0 , annotated as a classical arabinogalactan protein 7–like gene [ 9 ] and a WVD2-like 7 gene [ 10 ] respectively, were considered as the candidates of PcDw locus. Next, the molecular function of PCP021014_v1.0 ( PcAGP7-1 ) was validated [ 11 ] . Transgenic pear lines overexpressing PcAGP7-1 exhibited a pronounced dwarf phenotype, whereas RNA interference (RNAi) lines of PcAGP7-1 were taller than the wild type. Furthermore, a regulatory module BL– BZR/BES – AGP –BL responsible for the dwarf phenotype was revealed, in which BL repress expression of PcAGP7-1 through binding of PcBZR1/2 to three E-box motifs in the PcAGP7-1 promoter, but the deficient mutation in the third E-box (–100 bp) in dwarf lines alleviate the repression imposed by PcBZR1/2 thus resulted in higher expression of PcAGP7-1 , increased cell wall thickness, and decreased BL content. In a more recent study, comparative transcriptome analysis was performed on dwarf and standard offspring in a hybrid population produced from crossing between a dwarf pear cultivar ‘Aiyuxiang’ which inherited the dwarf phenotype of LNV and ‘Cuiguan’ (CG, Pyrus pyrifolia ) [ 12 ] . A total of 1,401 DEGs were identified, including 101 TFs belong to 38 TF families. The most abundant TF families included AP2/ERF (14), MYBs (9), bZIPs (7), and bHLHs (7). In addition, 45 genes involved in plant hormone metabolism and signal transduction pathways were identified. In the gibberellin (GA) pathway, genes associated with GA degradation and inactivation showed higher expression levels in the dwarf offspring. In the brassinosteroid (BR) pathway, key BR signaling regulators BZR1/BES1 ( Pbr022869.1 , Pbr000539.1 , and Pbr016089.1 ) were downregulated in the dwarf offspring. Furthermore, 26 DEGs associated with the cell cycle and cell wall metabolism were identified, and cyclins that promote cell cycle progression were downregulated in the dwarf offspring. Among 17 DEGs related to cell wall biosynthesis and degradation, genes involved in cell wall biogenesis exhibited lower expression levels in the dwarf offspring. Based on syntenic blocks identification in genome of Chinese white pear (cv. ‘Dangshansuli’) for European pear genome segment scaffold00074 which harbors PcDw locus [ 13 ] and expression profiles analysis, four genes were identified as candidates of PcDw locus. Among them, Pbr012085.1, predicted to encode a DELLA protein, was considered to be the key gene responsible for the dwarf phenotype. In this study, the dwarf germplasm was obtained from a hybrid population constructed by our research group through crossing CG with the seedling progeny of LNV. Comparative transcriptome analysis was conducted between the dwarf germplasm and CG. Differentially expressed genes were identified and their functional involvement were investigated. In addition, expression patterns of genes located in the chromosomal region harboring the PcDw gene locus were analyzed. The results of this study provide new addition to our understanding about the molecular mechanisms of pear tree dwarfing. 2 Materials and methods 2.1 Collection of plant materials The materials used in this study including pear cultivar ‘Cuiguan’ (CG) and the hybrid population derived from crossing CG with the seedling progeny of ‘Le Nain Vert’ (LNV) were planted in the Baima Farming and Research Base of Nanjing Agricultural University. Shoot apices were collected from CG and dwarf lines in the hybrid population in late May 2024, during the rapid shoot growth stage. For each group, shoot apices were sampled from three independent trees as biological replicates. Samples were immediately frozen in liquid nitrogen after collection and stored at − 80 ° C for subsequent analysis. 2.2 Preparation and analysis of paraffin sections The collected shoot tips of CG and the dwarf germplasm combinations were used as paraffin section materials. It was immersed in formalin-acetic acid-alcohol (FAA) fixative and sent to Servicebio (Wuhan, China) for paraffin sectioning, scanning and photographing. 2.3 RNA extraction and reverse transcription Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, catalog number 15596018) following the manufacturer's protocol. The quantity and purity of the total RNA were assessed using the Bioanalyzer 2100 and RNA 6000 Nano LabChip kits (Agilent Technologies, California, USA, catalog number 5067 − 1511). High-quality RNA samples with an RNA Integrity Number (RIN) greater than 7.0 were selected for sequencing library construction. After extraction, 5 µg of total RNA was subjected to two rounds of purification using Dynabeads Oligo(dT) (Thermo Fisher Scientific, California, USA) to isolate mRNA. 2.4 Illumina short read library construction and sequencing After purification, the mRNA was fragmented into short fragments using divalent cations at elevated temperatures (Magnesium RNA Fragmentation Module (NEB, USA, cat.e 6150) 94 ° C for 5–7 min). Then the lysed RNA fragments were reverse transcribed into cDNA using SuperScriptTM II reverse transcriptase (Invitrogen, USA, cat. 1896649). Next, E.coli DNA polymerase I (NEB, USA, cat. M0209), RNase H (NEB, USA, cat. M0297) and dUTP solution (Thermo Fisher, USA, cat. R0133) were used to synthesize U-labeled second-strand DNA. Then, an A base is added to the flat end of each chain to prepare for connection with the index adapter. Each adapter has a T base protruding to connect the adapter to the fragmented DNA of the A tail. Connect the dual-index adapter to the fragment and use AMPureXP beads for size selection. After treatment of U-labeled second-strand DNA with thermally unstable uridine (NEB, USA, cat.m0280), the ligation product was amplified by PCR. The amplification conditions were as follows: Initial denaturation at 95 ° C for 3 min; eight cycles of denaturation at 98 ° C for 15 s, annealing at 60 ° C for 15 s, and extension at 72 ° C for 30 s; then the final extension of 72 ° C for 5 minutes. The average insert size of the final cDNA library was 300 ± 50 bp. Finally, 2 × 150 bp paired-end sequencing was performed on Illumina NovaseqTM 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) (PE150). 2.5 Data processing and quality control A cDNA library was constructed from pooled RNA extracted from the stem tip, as well as the upper, middle, and lower parts of one-year-old branches of CG and also selected the same parts of the dwarf offspring, and sequenced on the Illumina NovaSeqTM 6000 platform. Transcriptome sequencing was performed using the Illumina paired-end RNA-seq strategy, generating a total of millon 2 × 150 bp paired-end reads. Raw reads were filtered to remove adapter sequences and low-quality reads using Cutadapt (version 1.9; https://cutadapt.readthedocs.io/en/stable/ ). Reads containing poly-A or poly-G sequences, more than 5% unknown nucleotides (N), or more than 20% low-quality bases (Q ≤ 20) were discarded. The quality of the clean reads was assessed using FastQC (version 0.11.9; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ), including evaluation of Q20, Q30, and GC content. 2.6 Differential expression analysis Gene differential expression analysis was performed between two different groups using DESeq2 software (between two samples using edgeR). The expression abundance of the corresponding genes was represented by FPKM. Pearson 's correlation coefficient (r) was used to analyze the FPKM between biological replicates. The closer the r 2 value was to 1, the stronger the correlation between samples was. Genes with false discovery rate (FDR) < 0.05 and |fold change| ≥ 2 were considered to be differentially expressed genes. Then the differentially expressed genes were subjected to GO function and KEGG pathway enrichment analysis. 2.7 Functional annotation and enrichment analysis All the different expressed genes were annotated by gene ontology (GO; http://www.geneontology.org ) and Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/ ). GO annotation contains biological processes, cellular components and molecular functions of gene products. Each category is defined individually. KEGG is a major public pathway-related database that integrates genomic information, chemical information, and functional information of biological systems. Pathway enrichment analysis identified metabolic pathways or signal transduction pathways that were significantly enriched in differentially expressed genes compared to the entire genome background. Gene set enrichment analysis was performed using GSEA software (version 4.1.0) and MSigDB to determine whether there was a significant difference between the two groups in a specific GO term, a group of genes in the KEGG pathway. In short, we input the gene expression matrix and sort the genes by Signal2Noise normalization method. The enrichment fraction and p value were calculated under the default parameters. GO terms and KEGG pathways (DO terms, Reactome) that meet the conditions of | NES | > 1, NOM p-val < 0.05, FDR q-val < 0.25 were considered to be different between the two populations. 2.8 Synteny analysis Whole-genome protein sequences and gene annotation files for genomes of ‘Bartlett’ ( P. communis , v1.0 and v2.0) and CG ( P. pyrifolia ) were downloaded from the Rosaceae Genome Database ( https://www.rosaceae.org/ ) and Genome Warehouse ( https://ngdc.cncb.ac.cn/gwh/Assembly/18534/show ). Intra- and intergenomic homologous protein search was performed using DIAMOND software [ 14 ] with the E-value threshold of < 1E-10 and retaining the top five hits. Synteny analysis was performed using MCScanX software with default parameters [ 15 ] . 2.9 RT-qPCR validation of RNA-Seq data Specific primers for eight genes were designed using the NCBI website, with Pyrus UBQ as the internal reference gene. The 10 µL RT-qPCR reaction consisted of 5 µL qPCR SYBR Color Master Mix, 0.2 µL of each primer (10 µM), 1 µL of cDNA, and 3.6 µL of ddH₂O. All reactions were performed on the LightCycler 480 II (Roche, USA) with the following cycling conditions: 95°C pre-denaturation for 3 min; 95°C denaturation for 3 s, 60°C annealing for 10 s, and 72°C extension for 30 s for 40 cycles; followed by a final extension at 72°C for 5 min. After the program, the average threshold cycle (CT) was calculated, and relative expression levels were determined using the 2 –ΔΔCt method 3 Result 3.1 Phenotypic assessment Phenotype analysis revealed significant difference between the dwarf germplasm and CG (Fig. 1 ). Specifically, the dwarf germplasm has shorter internodes and branch length. The average length of one-year-old branches of the dwarf germplasm is 6.9 cm, which is significantly shorter than that of CG (40 cm) (Fig. 1 a). The average internode length of the dwarf germplasm is approximately 1 cm, which is significantly shorter than that of CG (6.7 cm) (Fig. 1 b). Cell division and expansion are responsible for stem elongation. Microscopic observations of paraffin sections were conducted to investigate cell arrangement and cell length in the shoot apex of the dwarf germplasm and CG. Compared to CG, the cortex of the dwarf germplasm was significantly thicker, and exhibited significantly longer cell length ( p < 0.0001, t -test), irregular cell shape and more cell number (Fig. c-f). This result suggested that the dwarf phenotype can be attributed to abnormal cell division and expansion. 3.2 Identification of differentially expressed genes An average of 39,756,612 RNA-seq raw reads were generated from shoot apex of the dwarf germplasm, and 38,308,318 raw reads were generated from CG (Table 1 ). The average mapping rate of clean reads for the dwarf germplasm is 83.22%, while for CG is 89.21%. Principal component analysis (PCA) revealed that the samples from the same accession were clustered together but showed a clear separation between two accessions, suggesting the large expression difference between them (Fig. 2 ). A total of 13,169 DEGs were identified between ZJ (hereafter the dwarf germplasm denoted as ‘Z’ and ‘J’ indicating apex) vs CGJ, including 6,024 up-regulated genes and 7,145 down-regulated genes. Table 1 The statistics of RNA-seq data. Sample Raw Reads Valid Reads Mapping reads Mapping rate Unique mapped reads Multi mapped reads CGJ1 36439028 35583126 31719912 89.14% 29052828(81.65%) 2667084(7.50%) CGJ2 42208412 41282584 36878440 89.33% 33886361(82.08%) 2992079(7.25%) CGJ3 36277514 35315818 31482926 89.15% 28474637(80.63%) 3008289(8.52%) ZJ1 43127498 42224278 35246090 83.47% 32397664(76.73%) 2848426(6.75%) ZJ2 38767914 38031004 31645703 83.21% 29185251(76.74%) 2460452(6.47%) ZJ3 37374424 36402972 30205808 82.98% 27846058(76.49%) 2359750(6.48%) 3.3 Functional enrichment analysis of DEGs GO enrichment analysis was performed on DEGs to explore their functional involvement (Fig. 3 a and Supplementary Table 1). For biological process (BP), the top three enriched terms were defense response, protein phosphorylation, and signal transduction. In addition, processes such as transmembrane receptor protein tyrosine kinase signaling pathway, response to wounding, and flavonoid biosynthetic process were also enriched. For cellular component (CC), the enriched terms were plasma membrane, membrane, and extracellular region. For molecular function (MF), the top enriched terms included protein serine/threonine kinase activity, ADP binding, and quercetin 3-O-glucosyltransferase activity. KEGG pathway enrichment analysis revealed a total of 137 enriched KEGG pathways (Fig. 3 b and Supplementary Table 2), of which the top enriched KEGG pathways included plant–pathogen interaction, plant hormone signal transduction, and indole alkaloid biosynthesis, flavonoid biosynthesis, MAPK signaling pathway-plant, and ABC transporters. KEGG enrichment analysis suggested that genes related to plant hormone response and signaling transduction potentially play important roles in regulating the dwarfing trait. 3.4 Differential expression of plant hormone-related genes A comprehensive set of Arabidopsis genes involved in plant hormones biosynthesis, signaling and transport was compiled based on literature search and used as reference to search for their homologous genes in pear genome (Supplementary Table 3). Combining with the results of GO and KEGG pathway enrichment analyses, a total of 49 differentially expressed genes related to plant hormone biosynthesis, signal transduction, and transport were identified between the dwarf offspring and CG. Five DEGs involved in auxin biosynthesis, signaling, and transport were identified (Fig. 4 ). Among them, EVM0020980 ( TAA1 ) and EVM0005496 ( YUCCA1 ), which encode two key enzymes in the auxin biosynthesis pathway, EVM0041437 ( ARF10 ), a key component of the auxin signaling pathway, and EVM0000187 ( ABCB1 ), which is involved in auxin transport, showed higher expression in CG. In contrast, EVM0034292 , annotated as PILS1 which is involved in auxin transport [ 16 ] , showed higher expression in the dwarf germplasm, consistent with previous reports that PILS overexpression shortens internode length [ 17 ] . Four DEGs associated with brassinosteroid (BR) biosynthesis and signaling were identified. Among them, EVM0042507 ( DWARF4 ) was involved in BR biosynthesis, showed higher expression in CG, whereas EVM0001604 ( BZR1 ), a key component of the BR signaling pathway, was upregulated in the dwarf germplasm. Three DEGs in the strigolactone (SL) signaling pathway were identified, including EVM0017280 ( MAX2 ), EVM0032611 ( D14 ), and EVM0041100 ( SMXL6 ). All three showed higher expression in the dwarf germplasm, which may contribute to suppressed axillary bud outgrowth and reduced branching in the dwarf germplasm [ 18 ][ 19 ][ 20 ] . Two DEGs involved in gibberellin (GA) biosynthesis were identified: EVM0011564 ( KO1 ) and EVM0009219 ( GA20ox3 ). Among them, EVM0009219 ( GA20ox3 ) showed higher expression in CG, which may result in elevated GA levels and thereby promote vigorous growth [ 21 ] . OPR3 is a key enzyme in the jasmonic acid (JA) biosynthesis pathway, and JAR1 is a crucial enzyme in the JA signaling pathway that converts JA into its bioactive form to initiate JA responses. Jasmonic acid and gibberellin exhibit antagonistic effects in regulating plant growth and development in response to environmental and endogenous cues [ 22 ] . Genes ( EVM0006505 and EVM0001797 ) encoding these two enzymes were expressed at higher level in the dwarf germplasm. 3.5 Differentially expressed TFs The iTAK software [ 23 ] was used to annotate transcription factors (TFs) from the whole set of DEGs. A total of 1,118 DEGs were identified as TFs (Supplementary Table 4). Among them, the five most enriched TF families were MYB , NAC , AP2/ERF-ERF , bHLH , and WRKY. In addition, 22 differentially expressed TCP genes were identified. Interestingly, among the differentially expressed TFs, five ARID genes, five C2C2-YABBY genes, and three CPP genes showed higher expression in CG, whereas three BES1 genes, five CAMTA genes, five Tifys genes, three GeBP genes, and seven KNOX genes exhibited higher expression in the dwarf germplasm. In YABBY deficient tissues, auxin distribution is disrupted, which is accompanied by a reduction in the abundance of the auxin efflux carrier PIN1 , indicating that YABBY genes are required for proper auxin transport during lateral organ development [ 24 ] . In apple, MdKNOX15 regulates plant height by promoting the transcription of MdGA2ox7 , which enhances gibberellin deactivation and consequently leads to a dwarf phenotype [ 25 ] . These differentially expressed TFs are likely to play key roles in regulating the dwarfing phenotype. 3.6 Differentially expressed genes related to cell wall A comprehensive set of genes involved in cell wall biosynthesis, modification and degradation was compiled based on literature search and used as reference to search for their homologous genes in pear genome (Supplementary Table 5) (Fig. 5 ). Combining with RNA-Seq data analysis, 28 genes involved in cell wall formation and degradation showed differential expression between the dwarf germplasm and CG. Within the cell wall biosynthetic pathway, EVM0021398 annotated as homologs of AT2G37090 ( IRX9 ) which is involved in xylan backbone elongation and promoting plant growth [ 26 ] , showed higher expression in CG. Arabinogalactan proteins ( AGPs ) are known to play essential roles in multiple cellular processes during plant development. EVM0016345 , a homolog of AT4G21060 which encodes a GalT enzyme that modifies hydroxyproline (Hyp) residues to promote AGP biosynthesis [ 27 ] , showed higher expression in CG. EVM0001088 and EVM0005604 were annotated as IRX7/F8H and showed higher expression in CG. Overexpression of F8H in FRA8 mutants, which exhibit thinner secondary cell walls, abnormal xylem morphology, and inhibited plant growth, fully rescues their phenotype, indicating that F8H shares similar function as FRA8 although single F8H mutants do not show any detectable cell wall defects [ 28 ] . EVM0012106 was annotated as GALT31A which belongs to the GT31 glycosyltransferase family and showed higher expression in CG. It has been reported that AtGALT31A can elongate the β-1,6-galactan side chains of AGPs and is one of the key enzymes in AGP glycan biosynthesis [ 29 ] . EVM0006210 was upregulated in CG and annotated as GlcAT14A which is involved in the modification of cell wall–associated glycoproteins, cell elongation, and organ growth regulation. In Arabidopsis, GlcAT14A mutants exhibit enhanced hypocotyl and root cell elongation, leading to altered seedling elongation growth [ 30 ] . EVM0020399 was upregulated in CG and annotated as GUX1 , one of the key genes involved in secondary cell wall formation. In Arabidopsis, a complete loss of GlcA and MeGlcA side chains in the gux1/2/3 triple mutant results in reduced secondary wall thickening, collapsed vessel morphology, and stunted plant growth [ 31 ] . Within the pathways of cell wall modification and degradation, EVM0034734 showed high expression in CG and was annotated as AGM1 which is involved in protein O-GlcNAcylation and is important for plant growth [ 32 ] . EVM0022278 was upregulated in CG and annotated as BGAL10 . In Arabidopsis, AtBGAL10 mutants exhibit abnormal xyloglucan structure, resulting in growth defects and notably shortened stems [ 33 ] . 3.7 Differential expression of genes within the chromosomal region containing PcDw In previous studies, a dominant gene ( PcDw ) controlling dwarf trait in pear cultivar ‘Le Nain Vert’ was mapped to scaffold00074 of P. communis genome v1.0 [ 8 ] , which harbors two SSR markers linked to the PcDw locus. Here, we identified syntenic homologous regions of scaffold00074 in chromosome-scale genome of P. communis (v2.0) and CG ( P. pyrifolia ), and investigated expression patterns of genes within this chromosomal region in shoot apex between the dwarf germplasm and CG. A total of 52 genes were identified in this region and their potential functions were predicted based on homolog search against Arabidopsis genes (Fig. 6 ). Among them, 19 genes showed differential expression, of which 9 genes have functional annotation information. Of these nine genes, seven showed higher expression in the dwarf germplasm, whereas two showed higher expression in CG. (Supplementary Table 6). Among the two DEGs upregulated in CG, EVM0015682 was annotated as a pectin methylesterase inhibitor (PEMI ) which can enhance brassinosteroid signaling, thereby promoting plant growth [ 34 ] . EVM0011700 was annotated as PUB10-like which suppresses MYC2 activity and defense responses and promotes growth, making the antagonistic interaction between jasmonic acid (JA) and gibberellin (GA) more pronounced [ 22 ] . Among the seven DEGs upregulated in the dwarf germplasm, EVM0008541 , EVM0027056 , EVM0004698 , EVM0022781 and EVM0038290 were annotated as a member of the pathogenesis-related protein Bet v 1 family [ 35 ] , which inhibit plant growth in rice [ 36 ] . EVM0021367 belongs to the serine carboxypeptidase family, of which BRS1 regulates plant growth and development through modulating BRI1 signaling [ 37 ] . Moreover, EVM0008593 , belongs to the DELLA proteins which are central suppressor of gibberellin signaling and restrict plant development, showed upregulated expression in the dwarf germplasm. 3.8 Validation of RNA-Seq data by RT-qPCR To validate the reliability of the RNA-Seq data, eight DEGs related to plant hormones, cell wall biosynthesis, and contained in chromosomal region harboring PcDw locus were randomly selected, and their expression levels were measured by quantitative real-time PCR (RT-qPCR) (Fig. 7 ). Pearson correlation coefficients (PCCs) between RT-qPCR and RNA-Seq expression profiles were calculated for each gene using the Pearson function in R. The results showed a high correlation between the RT-qPCR and RNA-Seq data for all selected genes, with an average PCC greater than 0.7, indicating the reliability of the RNA-Seq data. 4 Discussion Decreasing plant height and maintaining compact canopy are crucial for achieving high-density planting in fruit tree cultivation. Dwarfing rootstocks can reduce tree height and canopy size and are desirable for high-density planting. However, the molecular mechanisms governing dwarf phenotype of dwarfing pear rootstocks have not been well studied. In this study, we compared transcriptome of shoot apex between the dwarf germplasm which inherited dwarf traits from LNV and pear cultivar CG with standard tree height. GO and KEGG enrichment analyses revealed that DEGs are enriched in plant hormone biosynthesis, signaling and transport, indicating that phytohormones play important roles in regulating tree height. Therefore, we further identified plant hormone-related genes in pear genome and investigated their expression patterns between the dwarf germplasm and CG. Phytohormones play important roles in regulating plant growth and development. In this study, DEGs involved in phytohormone biosynthesis, transport, and signaling were identified. YUCCA -mediated auxin biosynthesis is crucial for floral organ formation, vascular development, and plant architecture. Here, we found EVM0005496 (YUCCA1) showed higher expression in CG. In addition, EVM0020980 (TAA1) and EVM0000187 (ABCB1) involved in auxin biosynthesis and transport also showed higher expression in CG, consistent with their important roles in promoting plant growth [ 38 ][ 39 ][ 40 ] . The BR biosynthesis gene DWARF4 (EVM0042507) was upregulated in CG, in agreement with prior report that BR promotes bud outgrowth and growth [ 41 ] . BZR1 is a positive regulator of BR signaling [ 42 ] , which has been reported to be downregulated in dwarf varieties. However, in our data, BZR1 is upregulated in the dwarf germplasm. As the key components of the strigolactone signaling pathway, EVM0017280 (MAX2) and EVM0032611 (D14) , showed higher expression in the dwarf germplasm, supporting the association between increased level of SL and reduced plant height and branching [ 43 ][ 44 ] . However, SMXL family genes were also upregulated in the dwarf germplasm, suggesting complex feedback or post-translational regulation of SL signaling. For gibberellin metabolism, EVM0011564 (KO1) and EVM0009219 (GA20ox3) showed higher expression in CG, consistent with their roles in GA biosynthesis and thus promoting stem elongation and plant growth [ 45 ][ 46 ] . Differentially expressed transcription factors were mainly enriched in the MYB , AP2/ERF, NAC, bHLH, and WRKY families. In previous studies, genes encoding growth-regulating factor (GRF) domain transcription factors and YABBY domain transcription factors were found to show downregulated expression in dwarf pear [ 8 ] . In our results, all YABBY genes were also downregulated in the dwarf germplasm, whereas most GRF genes were upregulated in the dwarf germplasm. NACs and Tifys have been revealed to be upregulated in the dwarf pear lines [ 12 ] , consistent with our results. Numerous DEGs related to cell wall biosynthesis, modification, and degradation were also identified. In CG, multiple cellulose synthases, xylan synthesis/modification genes (e.g., CESA , IRX , GUX , and ESK1 ), and AGP biosynthesis genes were highly expressed, which may promote cell wall biosynthesis and cell growth, thereby supporting normal plant height. This supported previous studies that genes involved in cell wall biosynthesis are expressed at lower levels in dwarf plants. The PcDw gene, which has been reported to control the dwarf phenotype of a French pear cultivar ‘Le Nain Vert’, was mapped between two SSR markers on scaffold00074 of P. communis v1.0 genome. In this study, we identified homologous regions of scaffold00074 in chromosome-scale P. communis v2.0 and CG genome and investigated their expression and functional involvement. Among them, EVM0015682 (PEMI) exhibited higher expression in CG, which may enhance brassinosteroid signaling and consequently promote plant growth. EVM0011700 (PUB10-like) was downregulated in the dwarf germplasm, which may enhance MYC2 activity, thereby promoting plant defense responses and inhibiting growth [ 34 ] . EVM0008541 , EVM0027056 , EVM0004698 , EVM0022781 , and EVM0038290 , members of the pathogenesis-related protein Bet v 1 family [ 35 ] , have been associated with reduced plant height, shorter panicles, and lower seed set when overexpressing [ 36 ] . Moreover, EVM0008593 , annotated as the DELLA protein, showed upregulated expression in the dwarf germplasm, consistent with previous report [ 12 ] In addition, EVM0021367 , a serine carboxypeptidase, may affect BR signaling, similar to BRS1 , whose regulation of BRI1 is critical for normal plant growth and development [ 37 ] . 5 Conclusion In this study, we conducted comparative transcriptome analysis of shoot apex between the dwarf germplasm and cultivar CG. The dwarf germplasm exhibits a thicker cortex, longer cells, and irregular and loosely arranged cell structure. Functional terms involved in plant hormones biosynthesis and signal transduction were enriched in DEGs, indicating important roles of phytohormones in controlling dwarf phenotype of the dwarf germplasm. A set of DEGs involved in TFs, biosynthesis and signaling, and cell wall biosynthesis and degradation were identified, and their roles were clarified. By integrating our transcriptome data with previously reported molecular markers linked to the dwarf locus PcDW, several candidate genes were identified. Taken together, the results of this study contribute to elucidate the molecular mechanisms underlying pear dwarfism. Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Availability of data and materials The raw RNA-seq data have been deposited in the National Genomics Data Center (NGDC, https://www.cncb.ac.cn/?lang=en) under BioProject accession PRJCA059134 with CRA accession CRA039345. Competing interests The authors declare that they have no competing interests. Funding This study was supported by the Seed Industry Promotion Project of Jiangsu (JBGS (2021)022) and Nanjing Agricultural University High-Level Talent Recruitment Start-up Fund. The bioinformatic analysis was supported by the Bioinformatics Center of Nanjing Agricultural University. Author s’ contributions YX, HHD and SL were responsible for data collection. YX conducted data analysis. QHL, HXL and KM participated in data analysis. SLZ, KJQ, and ZHX contributed to experimental materials collection and management. YX prepared the manuscript. XQ and QHL revised the manuscript. XQ conceived and supervised this study. All authors have read and approved the final manuscript. Acknowledgments : Not applicable References Ou C, Wang F, Wang J, Li S, Zhang Y, Fang M, Ma L, Zhao Y, Jiang S. A de novo genome assembly of the dwarfing pear rootstock Zhongai 1. Sci Data. 2019;6(1):281. 10.1038/s41597-019-0291-3 . Wertheim SJ. Rootstocks for European pear: a review[C]//VIII International Symposium on Pear 596. 2000: 299–309. Wang J, Zhang W, Han P, et al. Effect of salt stress tolerance of four pear rootstock clones on the salt resistance of their grafted and the involvement of possible mechanisms[J]. Sci Rep. 2026;16(1):1890. Webster T, Tobutt K, Evans K. 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Additional Declarations No competing interests reported. Supplementary Files SupplementaryTable1.xlsx SupplementaryTable2.xlsx SupplementaryTable3.xlsx SupplementaryTable4.xlsx SupplementaryTable5.xlsx SupplementaryTable6.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 31 Mar, 2026 Reviews received at journal 30 Mar, 2026 Reviews received at journal 28 Mar, 2026 Reviews received at journal 26 Mar, 2026 Reviews received at journal 24 Mar, 2026 Reviewers agreed at journal 19 Mar, 2026 Reviewers agreed at journal 18 Mar, 2026 Reviewers agreed at journal 18 Mar, 2026 Reviewers agreed at journal 17 Mar, 2026 Reviewers invited by journal 17 Mar, 2026 Editor invited by journal 12 Mar, 2026 Editor assigned by journal 12 Mar, 2026 Submission checks completed at journal 12 Mar, 2026 First submitted to journal 03 Mar, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Cell arrangement in the cortex of CG and the dwarf offspring (c), comparison of cell length (d), the number of cortical cells within a 0.5–0.6 mm² area (e) and under the 20× magnification (f). \\u003cem\\u003et\\u003c/em\\u003e-test, *\\u003cem\\u003ep\\u003c/em\\u003e\\u0026lt;0.05, **\\u003cem\\u003ep\\u003c/em\\u003e\\u0026lt;0.01, ***\\u003cem\\u003ep\\u003c/em\\u003e\\u0026lt;0.001, ****\\u003cem\\u003ep\\u003c/em\\u003e\\u0026lt;0.0001\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"image1.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/8c7bcc7023af2b76a07e92d7.jpg\"},{\"id\":105562843,\"identity\":\"7acbb2c6-4506-4b78-8d46-a8d69c052b92\",\"added_by\":\"auto\",\"created_at\":\"2026-03-27 12:44:55\",\"extension\":\"jpg\",\"order_by\":2,\"title\":\"Figure 2\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":26104,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003ePCA analysis. Scatter plot shows sample clustering from PCA analysis. ‘Z’ indicates the dwarf germplasm, while ‘CG’ indicates ‘Cuiguan’, ‘J’ indicates the shoot apex.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"image2.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/62b6d8ba9d9f943556ae84c8.jpg\"},{\"id\":105062792,\"identity\":\"42356c9c-f219-494d-ab7b-561164348b99\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"jpg\",\"order_by\":3,\"title\":\"Figure 3\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":87493,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eGO (a) and KEGG (b) enrichment of DEGs. The size of the dot represents the number of DEGs enriched in each GO term or pathway. Q value \\u0026lt; 0.01 was used as the threshold for determining enriched GO terms.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"image3.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/f1b1aa321d570f1d8c3127a3.jpg\"},{\"id\":105562686,\"identity\":\"7c3cdec4-0267-45c0-a393-2df389f5d8e2\",\"added_by\":\"auto\",\"created_at\":\"2026-03-27 12:44:04\",\"extension\":\"jpg\",\"order_by\":4,\"title\":\"Figure 4\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":178233,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eExpression patterns of DEGs related to plant hormones biosynthesis, signal transduction and transport\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"image4.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/d52cdc37188f01e41d2da306.jpg\"},{\"id\":105563094,\"identity\":\"7f8c4132-a2b3-490e-8b21-32433d1cacac\",\"added_by\":\"auto\",\"created_at\":\"2026-03-27 12:45:55\",\"extension\":\"jpg\",\"order_by\":5,\"title\":\"Figure 5\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":100272,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eDifferentially expressed genes associated with cell wall biosynthesis, degradation, and modification.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"image5.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/1391636928c9455e38d69c85.jpg\"},{\"id\":105062800,\"identity\":\"3a920b49-8608-480c-a4c1-1b4b72ecd047\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"jpg\",\"order_by\":6,\"title\":\"Figure 6\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":202012,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eExpression patterns of genes located in the chromosomal region containing the \\u003cem\\u003ePcDw\\u003c/em\\u003elocus. The horizontal tracks represent syntenic blocks among scaffold00074 of the \\u003cem\\u003eP. communis\\u003c/em\\u003e v1.0 genome, \\u003cem\\u003eP. communis\\u003c/em\\u003e v2.0, and the CG genome. Grey bands link syntenic gene pairs. Green boxes indicate genes in the forward orientation, whereas blue boxes indicate genes in the reverse orientation. Gene names highlighted in red denote differentially expressed genes with functional annotation.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"image6.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/94676a3189d480bfbc7ba12c.jpg\"},{\"id\":105062802,\"identity\":\"fe7c6105-6adf-4854-9a6d-55931f1bc847\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"jpg\",\"order_by\":7,\"title\":\"Figure 7\",\"display\":\"\",\"copyAsset\":false,\"role\":\"figure\",\"size\":92941,\"visible\":true,\"origin\":\"\",\"legend\":\"\\u003cp\\u003eValidation of RNA-seq data by RT-qPCR.\\u003c/p\\u003e\",\"description\":\"\",\"filename\":\"image7.jpg\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/ebf83a824c411e9a9bcd3bde.jpg\"},{\"id\":105729721,\"identity\":\"c1dd6f13-33d0-42f1-bee8-89b7d814fca9\",\"added_by\":\"auto\",\"created_at\":\"2026-03-30 11:19:03\",\"extension\":\"pdf\",\"order_by\":0,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"manuscript-pdf\",\"size\":1962683,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"manuscript.pdf\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/199c616e-e33c-496e-aeca-66c2b177e070.pdf\"},{\"id\":105062794,\"identity\":\"7a690d56-a36d-41dc-8896-4b61fab96353\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"xlsx\",\"order_by\":1,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":111885,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryTable1.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/71153ec177057242bdf74c7b.xlsx\"},{\"id\":105062796,\"identity\":\"4be4660b-85ef-4b1e-ae5c-383ca5ee09ee\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"xlsx\",\"order_by\":2,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":69129,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryTable2.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/e76fc16d878d48c7c35e1695.xlsx\"},{\"id\":105062799,\"identity\":\"4ed16300-e173-4e34-9841-6e92f576bb0f\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"xlsx\",\"order_by\":3,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":19045,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryTable3.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/9e37d1f9b3948769faf77775.xlsx\"},{\"id\":105727735,\"identity\":\"5d2b98bf-ef56-4fec-a847-a3c36179314a\",\"added_by\":\"auto\",\"created_at\":\"2026-03-30 11:02:27\",\"extension\":\"xlsx\",\"order_by\":4,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":254347,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryTable4.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/37ff3285e8e39d698e50e001.xlsx\"},{\"id\":105062797,\"identity\":\"536e85f3-3632-40dc-89d5-ef22f90a59e1\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"xlsx\",\"order_by\":5,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":15172,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryTable5.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/d49a8e21fa826d75ba76c074.xlsx\"},{\"id\":105062801,\"identity\":\"fb466355-d0da-433f-9ca7-397390e4d608\",\"added_by\":\"auto\",\"created_at\":\"2026-03-20 13:14:57\",\"extension\":\"xlsx\",\"order_by\":6,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":16393,\"visible\":true,\"origin\":\"\",\"legend\":\"\",\"description\":\"\",\"filename\":\"SupplementaryTable6.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-9020477/v1/1044b7d2f7dde0de4d9463ef.xlsx\"}],\"financialInterests\":\"No competing interests reported.\",\"formattedTitle\":\"Comparative transcriptome analysis provides insights into the dwarfing mechanism of pear trees\",\"fulltext\":[{\"header\":\"1 Background\",\"content\":\"\\u003cp\\u003eDwarfing traits are critical for high-density planting and mechanical management in modern pear orchard system. However, dwarfing pear rootstocks and dwarf pear cultivars are limited in pear production, and the molecular mechanisms governing pear tree dwarfing remain poorly understood. Several pear rootstocks have been selected for dwarfing cultivation, including quince rootstocks (e.g., Quince A, Quince C, BA 29) OHxF rootstocks (e.g., OHxF 87, OHxF 333), \\u0026lsquo;Zhongai\\u0026rsquo; rootstocks (NO. 1 \\u0026ndash; NO. 5), and \\u0026lsquo;Qingzhen D1\\u0026rsquo; rootstocks\\u003csup\\u003e[\\u003cspan citationid=\\\"CR1\\\" class=\\\"CitationRef\\\"\\u003e1\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR2\\\" class=\\\"CitationRef\\\"\\u003e2\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR3\\\" class=\\\"CitationRef\\\"\\u003e3\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR4\\\" class=\\\"CitationRef\\\"\\u003e4\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR5\\\" class=\\\"CitationRef\\\"\\u003e5\\u003c/span\\u003e]\\u003c/sup\\u003e. In addition, a French pear cultivar \\u0026lsquo;Le Nain Vert\\u0026rsquo; (LNV, \\u003cem\\u003ePyrus communis\\u003c/em\\u003e) characterized as shortened internodes and dwarfed growth was selected, and its seed-derived dwarf offspring was crossed by a Chinese white pear cultivar \\u0026lsquo;Chili\\u0026rsquo; (\\u003cem\\u003ePyrus bretschneideri\\u003c/em\\u003e Rehd.) to breed the rootstock \\u0026lsquo;Qingzhen D1\\u0026rsquo; (QZD1, \\u003cem\\u003ePyrus communis \\u0026times; bretschneideri\\u003c/em\\u003e)\\u003csup\\u003e[\\u003cspan citationid=\\\"CR3\\\" class=\\\"CitationRef\\\"\\u003e3\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR8\\\" class=\\\"CitationRef\\\"\\u003e8\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003ePrevious studies have shown that the dwarf phenotype of LNV is controlled by a dominant single gene \\u003cem\\u003ePcDw\\u003c/em\\u003e, which was initially mapped it to linkage group 16 (LG16) of pear linkage map based on SSR markers\\u003csup\\u003e[\\u003cspan citationid=\\\"CR6\\\" class=\\\"CitationRef\\\"\\u003e6\\u003c/span\\u003e]\\u003c/sup\\u003e. Further, the \\u003cem\\u003ePcDw\\u003c/em\\u003e was localized to scaffold00074 in European pear genome \\u003csup\\u003e[\\u003cspan citationid=\\\"CR7\\\" class=\\\"CitationRef\\\"\\u003e7\\u003c/span\\u003e]\\u003c/sup\\u003e. Based on a hybrid population produced from crossing \\u0026lsquo;Aihuali\\u0026rsquo; (seed-derived dwarf offspring of LNV) and \\u0026lsquo;Chili\\u0026rsquo;, comparative transcriptome analysis of young apical stems from dwarf and standard offspring was conducted and 2,170 differentially expressed genes (DEGs) were identified. Among all DEGs, 88 were identified as transcription factors (TFs), belong to 22 TF families\\u003csup\\u003e[\\u003cspan citationid=\\\"CR8\\\" class=\\\"CitationRef\\\"\\u003e8\\u003c/span\\u003e]\\u003c/sup\\u003e. The most abundant TF families included \\u003cem\\u003eAP2\\u003c/em\\u003e (9 genes), \\u003cem\\u003eNAC\\u003c/em\\u003e (9), \\u003cem\\u003eC2H2-type\\u003c/em\\u003e (8), \\u003cem\\u003eC3H-type\\u003c/em\\u003e (8), and \\u003cem\\u003eMYB\\u003c/em\\u003e (8). Expression patterns of all genes located on scaffold00074 were subsequently analyzed, and four differentially expressed genes (DEGs) were identified after excluding genes located far from the SSR markers that are closely linked to \\u003cem\\u003ePcDw\\u003c/em\\u003e. Among these four DEGs, \\u003cem\\u003ePCP021014_v1.0\\u003c/em\\u003e and \\u003cem\\u003ePCP021015_v1.0\\u003c/em\\u003e, annotated as a classical arabinogalactan protein 7\\u0026ndash;like gene\\u003csup\\u003e[\\u003cspan citationid=\\\"CR9\\\" class=\\\"CitationRef\\\"\\u003e9\\u003c/span\\u003e]\\u003c/sup\\u003e and a WVD2-like 7 gene\\u003csup\\u003e[\\u003cspan citationid=\\\"CR10\\\" class=\\\"CitationRef\\\"\\u003e10\\u003c/span\\u003e]\\u003c/sup\\u003e respectively, were considered as the candidates of \\u003cem\\u003ePcDw\\u003c/em\\u003e locus. Next, the molecular function of \\u003cem\\u003ePCP021014_v1.0\\u003c/em\\u003e (\\u003cem\\u003ePcAGP7-1\\u003c/em\\u003e) was validated \\u003csup\\u003e[\\u003cspan citationid=\\\"CR11\\\" class=\\\"CitationRef\\\"\\u003e11\\u003c/span\\u003e]\\u003c/sup\\u003e. Transgenic pear lines overexpressing \\u003cem\\u003ePcAGP7-1\\u003c/em\\u003e exhibited a pronounced dwarf phenotype, whereas RNA interference (RNAi) lines of \\u003cem\\u003ePcAGP7-1\\u003c/em\\u003e were taller than the wild type. Furthermore, a regulatory module BL\\u0026ndash;\\u003cem\\u003eBZR/BES\\u003c/em\\u003e\\u0026ndash;\\u003cem\\u003eAGP\\u003c/em\\u003e\\u0026ndash;BL responsible for the dwarf phenotype was revealed, in which BL repress expression of \\u003cem\\u003ePcAGP7-1\\u003c/em\\u003e through binding of \\u003cem\\u003ePcBZR1/2\\u003c/em\\u003e to three E-box motifs in the \\u003cem\\u003ePcAGP7-1\\u003c/em\\u003e promoter, but the deficient mutation in the third E-box (\\u0026ndash;100 bp) in dwarf lines alleviate the repression imposed by \\u003cem\\u003ePcBZR1/2\\u003c/em\\u003e thus resulted in higher expression of \\u003cem\\u003ePcAGP7-1\\u003c/em\\u003e, increased cell wall thickness, and decreased BL content.\\u003c/p\\u003e \\u003cp\\u003eIn a more recent study, comparative transcriptome analysis was performed on dwarf and standard offspring in a hybrid population produced from crossing between a dwarf pear cultivar \\u0026lsquo;Aiyuxiang\\u0026rsquo; which inherited the dwarf phenotype of LNV and \\u0026lsquo;Cuiguan\\u0026rsquo; (CG, \\u003cem\\u003ePyrus pyrifolia\\u003c/em\\u003e)\\u003csup\\u003e[\\u003cspan citationid=\\\"CR12\\\" class=\\\"CitationRef\\\"\\u003e12\\u003c/span\\u003e]\\u003c/sup\\u003e. A total of 1,401 DEGs were identified, including 101 TFs belong to 38 TF families. The most abundant TF families included \\u003cem\\u003eAP2/ERF\\u003c/em\\u003e (14), \\u003cem\\u003eMYBs\\u003c/em\\u003e (9), \\u003cem\\u003ebZIPs\\u003c/em\\u003e (7), and \\u003cem\\u003ebHLHs\\u003c/em\\u003e (7). In addition, 45 genes involved in plant hormone metabolism and signal transduction pathways were identified. In the gibberellin (GA) pathway, genes associated with GA degradation and inactivation showed higher expression levels in the dwarf offspring. In the brassinosteroid (BR) pathway, key BR signaling regulators \\u003cem\\u003eBZR1/BES1\\u003c/em\\u003e (\\u003cem\\u003ePbr022869.1\\u003c/em\\u003e, \\u003cem\\u003ePbr000539.1\\u003c/em\\u003e, and \\u003cem\\u003ePbr016089.1\\u003c/em\\u003e) were downregulated in the dwarf offspring. Furthermore, 26 DEGs associated with the cell cycle and cell wall metabolism were identified, and cyclins that promote cell cycle progression were downregulated in the dwarf offspring. Among 17 DEGs related to cell wall biosynthesis and degradation, genes involved in cell wall biogenesis exhibited lower expression levels in the dwarf offspring. Based on syntenic blocks identification in genome of Chinese white pear (cv. \\u0026lsquo;Dangshansuli\\u0026rsquo;) for European pear genome segment scaffold00074 which harbors \\u003cem\\u003ePcDw\\u003c/em\\u003e locus\\u003csup\\u003e[\\u003cspan citationid=\\\"CR13\\\" class=\\\"CitationRef\\\"\\u003e13\\u003c/span\\u003e]\\u003c/sup\\u003e and expression profiles analysis, four genes were identified as candidates of \\u003cem\\u003ePcDw\\u003c/em\\u003e locus. Among them, Pbr012085.1, predicted to encode a DELLA protein, was considered to be the key gene responsible for the dwarf phenotype.\\u003c/p\\u003e \\u003cp\\u003eIn this study, the dwarf germplasm was obtained from a hybrid population constructed by our research group through crossing CG with the seedling progeny of LNV. Comparative transcriptome analysis was conducted between the dwarf germplasm and CG. Differentially expressed genes were identified and their functional involvement were investigated. In addition, expression patterns of genes located in the chromosomal region harboring the \\u003cem\\u003ePcDw\\u003c/em\\u003e gene locus were analyzed. The results of this study provide new addition to our understanding about the molecular mechanisms of pear tree dwarfing.\\u003c/p\\u003e\"},{\"header\":\"2 Materials and methods\",\"content\":\"\\u003cdiv id=\\\"Sec3\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.1 Collection of plant materials\\u003c/h2\\u003e \\u003cp\\u003eThe materials used in this study including pear cultivar \\u0026lsquo;Cuiguan\\u0026rsquo; (CG) and the hybrid population derived from crossing CG with the seedling progeny of \\u0026lsquo;Le Nain Vert\\u0026rsquo; (LNV) were planted in the Baima Farming and Research Base of Nanjing Agricultural University. Shoot apices were collected from CG and dwarf lines in the hybrid population in late May 2024, during the rapid shoot growth stage. For each group, shoot apices were sampled from three independent trees as biological replicates. Samples were immediately frozen in liquid nitrogen after collection and stored at \\u0026minus;\\u0026thinsp;80 \\u0026deg; C for subsequent analysis.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec4\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.2 Preparation and analysis of paraffin sections\\u003c/h2\\u003e \\u003cp\\u003eThe collected shoot tips of CG and the dwarf germplasm combinations were used as paraffin section materials. It was immersed in formalin-acetic acid-alcohol (FAA) fixative and sent to Servicebio (Wuhan, China) for paraffin sectioning, scanning and photographing.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec5\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.3 RNA extraction and reverse transcription\\u003c/h2\\u003e \\u003cp\\u003eTotal RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, catalog number 15596018) following the manufacturer's protocol. The quantity and purity of the total RNA were assessed using the Bioanalyzer 2100 and RNA 6000 Nano LabChip kits (Agilent Technologies, California, USA, catalog number 5067\\u0026thinsp;\\u0026minus;\\u0026thinsp;1511). High-quality RNA samples with an RNA Integrity Number (RIN) greater than 7.0 were selected for sequencing library construction. After extraction, 5 \\u0026micro;g of total RNA was subjected to two rounds of purification using Dynabeads Oligo(dT) (Thermo Fisher Scientific, California, USA) to isolate mRNA.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec6\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.4 Illumina short read library construction and sequencing\\u003c/h2\\u003e \\u003cp\\u003eAfter purification, the mRNA was fragmented into short fragments using divalent cations at elevated temperatures (Magnesium RNA Fragmentation Module (NEB, USA, cat.e 6150) 94 \\u0026deg; C for 5\\u0026ndash;7 min). Then the lysed RNA fragments were reverse transcribed into cDNA using SuperScriptTM II reverse transcriptase (Invitrogen, USA, cat. 1896649). Next, \\u003cem\\u003eE.coli\\u003c/em\\u003e DNA polymerase I (NEB, USA, cat. M0209), RNase H (NEB, USA, cat. M0297) and dUTP solution (Thermo Fisher, USA, cat. R0133) were used to synthesize U-labeled second-strand DNA. Then, an A base is added to the flat end of each chain to prepare for connection with the index adapter. Each adapter has a T base protruding to connect the adapter to the fragmented DNA of the A tail. Connect the dual-index adapter to the fragment and use AMPureXP beads for size selection. After treatment of U-labeled second-strand DNA with thermally unstable uridine (NEB, USA, cat.m0280), the ligation product was amplified by PCR. The amplification conditions were as follows: Initial denaturation at 95 \\u0026deg; C for 3 min; eight cycles of denaturation at 98 \\u0026deg; C for 15 s, annealing at 60 \\u0026deg; C for 15 s, and extension at 72 \\u0026deg; C for 30 s; then the final extension of 72 \\u0026deg; C for 5 minutes. The average insert size of the final cDNA library was 300\\u0026thinsp;\\u0026plusmn;\\u0026thinsp;50 bp. Finally, 2 \\u0026times; 150 bp paired-end sequencing was performed on Illumina NovaseqTM 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) (PE150).\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec7\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.5 Data processing and quality control\\u003c/h2\\u003e \\u003cp\\u003eA cDNA library was constructed from pooled RNA extracted from the stem tip, as well as the upper, middle, and lower parts of one-year-old branches of CG and also selected the same parts of the dwarf offspring, and sequenced on the Illumina NovaSeqTM 6000 platform. Transcriptome sequencing was performed using the Illumina paired-end RNA-seq strategy, generating a total of millon 2 \\u0026times; 150 bp paired-end reads. Raw reads were filtered to remove adapter sequences and low-quality reads using Cutadapt (version 1.9; \\u003cspan class=\\\"ExternalRef\\\"\\u003e\\u003cspan class=\\\"RefSource\\\"\\u003ehttps://cutadapt.readthedocs.io/en/stable/\\u003c/span\\u003e\\u003cspan address=\\\"https://cutadapt.readthedocs.io/en/stable/\\\" targettype=\\\"URL\\\" class=\\\"RefTarget\\\"\\u003e\\u003c/span\\u003e\\u003c/span\\u003e). Reads containing poly-A or poly-G sequences, more than 5% unknown nucleotides (N), or more than 20% low-quality bases (Q\\u0026thinsp;\\u0026le;\\u0026thinsp;20) were discarded. The quality of the clean reads was assessed using FastQC (version 0.11.9; \\u003cspan class=\\\"ExternalRef\\\"\\u003e\\u003cspan class=\\\"RefSource\\\"\\u003ehttp://www.bioinformatics.babraham.ac.uk/projects/fastqc/\\u003c/span\\u003e\\u003cspan address=\\\"http://www.bioinformatics.babraham.ac.uk/projects/fastqc/\\\" targettype=\\\"URL\\\" class=\\\"RefTarget\\\"\\u003e\\u003c/span\\u003e\\u003c/span\\u003e), including evaluation of Q20, Q30, and GC content.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec8\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.6 Differential expression analysis\\u003c/h2\\u003e \\u003cp\\u003eGene differential expression analysis was performed between two different groups using DESeq2 software (between two samples using edgeR). The expression abundance of the corresponding genes was represented by FPKM. Pearson 's correlation coefficient (r) was used to analyze the FPKM between biological replicates. The closer the r\\u003csup\\u003e2\\u003c/sup\\u003e value was to 1, the stronger the correlation between samples was. Genes with false discovery rate (FDR)\\u0026thinsp;\\u0026lt;\\u0026thinsp;0.05 and |fold change| \\u0026ge; 2 were considered to be differentially expressed genes. Then the differentially expressed genes were subjected to GO function and KEGG pathway enrichment analysis.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec9\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.7 Functional annotation and enrichment analysis\\u003c/h2\\u003e \\u003cp\\u003eAll the different expressed genes were annotated by gene ontology (GO; \\u003cspan class=\\\"ExternalRef\\\"\\u003e\\u003cspan class=\\\"RefSource\\\"\\u003ehttp://www.geneontology.org\\u003c/span\\u003e\\u003cspan address=\\\"http://www.geneontology.org\\\" targettype=\\\"URL\\\" class=\\\"RefTarget\\\"\\u003e\\u003c/span\\u003e\\u003c/span\\u003e) and Kyoto Encyclopedia of Genes and Genomes (KEGG; \\u003cspan class=\\\"ExternalRef\\\"\\u003e\\u003cspan class=\\\"RefSource\\\"\\u003ehttp://www.genome.jp/kegg/\\u003c/span\\u003e\\u003cspan address=\\\"http://www.genome.jp/kegg/\\\" targettype=\\\"URL\\\" class=\\\"RefTarget\\\"\\u003e\\u003c/span\\u003e\\u003c/span\\u003e). GO annotation contains biological processes, cellular components and molecular functions of gene products. Each category is defined individually. KEGG is a major public pathway-related database that integrates genomic information, chemical information, and functional information of biological systems. Pathway enrichment analysis identified metabolic pathways or signal transduction pathways that were significantly enriched in differentially expressed genes compared to the entire genome background.\\u003c/p\\u003e \\u003cp\\u003eGene set enrichment analysis was performed using GSEA software (version 4.1.0) and MSigDB to determine whether there was a significant difference between the two groups in a specific GO term, a group of genes in the KEGG pathway. In short, we input the gene expression matrix and sort the genes by Signal2Noise normalization method. The enrichment fraction and p value were calculated under the default parameters. GO terms and KEGG pathways (DO terms, Reactome) that meet the conditions of | NES | \\u0026gt; 1, NOM p-val\\u0026thinsp;\\u0026lt;\\u0026thinsp;0.05, FDR q-val\\u0026thinsp;\\u0026lt;\\u0026thinsp;0.25 were considered to be different between the two populations.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec10\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.8 Synteny analysis\\u003c/h2\\u003e \\u003cp\\u003eWhole-genome protein sequences and gene annotation files for genomes of \\u0026lsquo;Bartlett\\u0026rsquo; (\\u003cem\\u003eP. communis\\u003c/em\\u003e, v1.0 and v2.0) and CG (\\u003cem\\u003eP. pyrifolia\\u003c/em\\u003e) were downloaded from the Rosaceae Genome Database (\\u003cspan class=\\\"ExternalRef\\\"\\u003e\\u003cspan class=\\\"RefSource\\\"\\u003ehttps://www.rosaceae.org/\\u003c/span\\u003e\\u003cspan address=\\\"https://www.rosaceae.org/\\\" targettype=\\\"URL\\\" class=\\\"RefTarget\\\"\\u003e\\u003c/span\\u003e\\u003c/span\\u003e) and Genome Warehouse (\\u003cspan class=\\\"ExternalRef\\\"\\u003e\\u003cspan class=\\\"RefSource\\\"\\u003ehttps://ngdc.cncb.ac.cn/gwh/Assembly/18534/show\\u003c/span\\u003e\\u003cspan address=\\\"https://ngdc.cncb.ac.cn/gwh/Assembly/18534/show\\\" targettype=\\\"URL\\\" class=\\\"RefTarget\\\"\\u003e\\u003c/span\\u003e\\u003c/span\\u003e). Intra- and intergenomic homologous protein search was performed using DIAMOND software\\u003csup\\u003e[\\u003cspan citationid=\\\"CR14\\\" class=\\\"CitationRef\\\"\\u003e14\\u003c/span\\u003e]\\u003c/sup\\u003e with the E-value threshold of \\u0026lt;\\u0026thinsp;1E-10 and retaining the top five hits. Synteny analysis was performed using MCScanX software with default parameters\\u003csup\\u003e[\\u003cspan citationid=\\\"CR15\\\" class=\\\"CitationRef\\\"\\u003e15\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec11\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e2.9 RT-qPCR validation of RNA-Seq data\\u003c/h2\\u003e \\u003cp\\u003eSpecific primers for eight genes were designed using the NCBI website, with Pyrus UBQ as the internal reference gene. The 10 \\u0026micro;L RT-qPCR reaction consisted of 5 \\u0026micro;L qPCR SYBR Color Master Mix, 0.2 \\u0026micro;L of each primer (10 \\u0026micro;M), 1 \\u0026micro;L of cDNA, and 3.6 \\u0026micro;L of ddH₂O. All reactions were performed on the LightCycler 480 II (Roche, USA) with the following cycling conditions: 95\\u0026deg;C pre-denaturation for 3 min; 95\\u0026deg;C denaturation for 3 s, 60\\u0026deg;C annealing for 10 s, and 72\\u0026deg;C extension for 30 s for 40 cycles; followed by a final extension at 72\\u0026deg;C for 5 min. After the program, the average threshold cycle (CT) was calculated, and relative expression levels were determined using the 2\\u003csup\\u003e\\u0026ndash;ΔΔCt\\u003c/sup\\u003e method\\u003c/p\\u003e \\u003c/div\\u003e\"},{\"header\":\"3 Result\",\"content\":\"\\u003cdiv id=\\\"Sec13\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.1 Phenotypic assessment\\u003c/h2\\u003e \\u003cp\\u003ePhenotype analysis revealed significant difference between the dwarf germplasm and CG (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003e). Specifically, the dwarf germplasm has shorter internodes and branch length. The average length of one-year-old branches of the dwarf germplasm is 6.9 cm, which is significantly shorter than that of CG (40 cm) (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003ea). The average internode length of the dwarf germplasm is approximately 1 cm, which is significantly shorter than that of CG (6.7 cm) (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003eb). Cell division and expansion are responsible for stem elongation. Microscopic observations of paraffin sections were conducted to investigate cell arrangement and cell length in the shoot apex of the dwarf germplasm and CG. Compared to CG, the cortex of the dwarf germplasm was significantly thicker, and exhibited significantly longer cell length (\\u003cem\\u003ep\\u003c/em\\u003e\\u0026thinsp;\\u0026lt;\\u0026thinsp;0.0001, \\u003cem\\u003et\\u003c/em\\u003e-test), irregular cell shape and more cell number (Fig. c-f). This result suggested that the dwarf phenotype can be attributed to abnormal cell division and expansion.\\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec14\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.2 Identification of differentially expressed genes\\u003c/h2\\u003e \\u003cp\\u003eAn average of 39,756,612 RNA-seq raw reads were generated from shoot apex of the dwarf germplasm, and 38,308,318 raw reads were generated from CG (Table\\u0026nbsp;\\u003cspan refid=\\\"Tab1\\\" class=\\\"InternalRef\\\"\\u003e1\\u003c/span\\u003e). The average mapping rate of clean reads for the dwarf germplasm is 83.22%, while for CG is 89.21%. Principal component analysis (PCA) revealed that the samples from the same accession were clustered together but showed a clear separation between two accessions, suggesting the large expression difference between them (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig2\\\" class=\\\"InternalRef\\\"\\u003e2\\u003c/span\\u003e). A total of 13,169 DEGs were identified between ZJ (hereafter the dwarf germplasm denoted as \\u0026lsquo;Z\\u0026rsquo; and \\u0026lsquo;J\\u0026rsquo; indicating apex) vs CGJ, including 6,024 up-regulated genes and 7,145 down-regulated genes.\\u003c/p\\u003e \\u003cp\\u003e \\u003cdiv class=\\\"gridtable\\\"\\u003e\\u003ctable float=\\\"Yes\\\" id=\\\"Tab1\\\" border=\\\"1\\\"\\u003e \\u003ccaption language=\\\"En\\\"\\u003e \\u003cdiv class=\\\"CaptionNumber\\\"\\u003eTable 1\\u003c/div\\u003e \\u003cdiv class=\\\"CaptionContent\\\"\\u003e \\u003cp\\u003eThe statistics of RNA-seq data.\\u003c/p\\u003e \\u003c/div\\u003e \\u003c/caption\\u003e \\u003ccolgroup cols=\\\"8\\\"\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c1\\\" colnum=\\\"1\\\"\\u003e\\u003c/div\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c2\\\" colnum=\\\"2\\\"\\u003e\\u003c/div\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c3\\\" colnum=\\\"3\\\"\\u003e\\u003c/div\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c4\\\" colnum=\\\"4\\\"\\u003e\\u003c/div\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c5\\\" colnum=\\\"5\\\"\\u003e\\u003c/div\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c6\\\" colnum=\\\"6\\\"\\u003e\\u003c/div\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c7\\\" colnum=\\\"7\\\"\\u003e\\u003c/div\\u003e \\u003cdiv align=\\\"left\\\" class=\\\"colspec\\\" colname=\\\"c8\\\" colnum=\\\"8\\\"\\u003e\\u003c/div\\u003e \\u003cthead\\u003e \\u003ctr\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eSample\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003eRaw Reads\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003eValid Reads\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c5\\\" namest=\\\"c4\\\"\\u003e \\u003cp\\u003eMapping reads\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c6\\\"\\u003e \\u003cp\\u003eMapping rate\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c7\\\"\\u003e \\u003cp\\u003eUnique mapped reads\\u003c/p\\u003e \\u003c/th\\u003e \\u003cth align=\\\"left\\\" colname=\\\"c8\\\"\\u003e \\u003cp\\u003eMulti mapped reads\\u003c/p\\u003e \\u003c/th\\u003e \\u003c/tr\\u003e \\u003c/thead\\u003e \\u003ctbody\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eCGJ1\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e36439028\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e35583126\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e31719912\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c6\\\" namest=\\\"c5\\\"\\u003e \\u003cp\\u003e89.14%\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e \\u003cp\\u003e29052828(81.65%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e \\u003cp\\u003e2667084(7.50%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eCGJ2\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e42208412\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e41282584\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e36878440\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c6\\\" namest=\\\"c5\\\"\\u003e \\u003cp\\u003e89.33%\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e \\u003cp\\u003e33886361(82.08%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e \\u003cp\\u003e2992079(7.25%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eCGJ3\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e36277514\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e35315818\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e31482926\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c6\\\" namest=\\\"c5\\\"\\u003e \\u003cp\\u003e89.15%\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e \\u003cp\\u003e28474637(80.63%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e \\u003cp\\u003e3008289(8.52%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eZJ1\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e43127498\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e42224278\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e35246090\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c6\\\" namest=\\\"c5\\\"\\u003e \\u003cp\\u003e83.47%\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e \\u003cp\\u003e32397664(76.73%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e \\u003cp\\u003e2848426(6.75%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eZJ2\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e38767914\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e38031004\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e31645703\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c6\\\" namest=\\\"c5\\\"\\u003e \\u003cp\\u003e83.21%\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e \\u003cp\\u003e29185251(76.74%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e \\u003cp\\u003e2460452(6.47%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003ctr\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c1\\\"\\u003e \\u003cp\\u003eZJ3\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c2\\\"\\u003e \\u003cp\\u003e37374424\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c3\\\"\\u003e \\u003cp\\u003e36402972\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c4\\\"\\u003e \\u003cp\\u003e30205808\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colspan=\\\"2\\\" nameend=\\\"c6\\\" namest=\\\"c5\\\"\\u003e \\u003cp\\u003e82.98%\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c7\\\"\\u003e \\u003cp\\u003e27846058(76.49%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003ctd align=\\\"left\\\" colname=\\\"c8\\\"\\u003e \\u003cp\\u003e2359750(6.48%)\\u003c/p\\u003e \\u003c/td\\u003e \\u003c/tr\\u003e \\u003c/tbody\\u003e \\u003c/colgroup\\u003e \\u003c/table\\u003e\\u003c/div\\u003e \\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec15\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.3 Functional enrichment analysis of DEGs\\u003c/h2\\u003e \\u003cp\\u003eGO enrichment analysis was performed on DEGs to explore their functional involvement (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003ea and Supplementary Table\\u0026nbsp;1). For biological process (BP), the top three enriched terms were defense response, protein phosphorylation, and signal transduction. In addition, processes such as transmembrane receptor protein tyrosine kinase signaling pathway, response to wounding, and flavonoid biosynthetic process were also enriched. For cellular component (CC), the enriched terms were plasma membrane, membrane, and extracellular region. For molecular function (MF), the top enriched terms included protein serine/threonine kinase activity, ADP binding, and quercetin 3-O-glucosyltransferase activity. KEGG pathway enrichment analysis revealed a total of 137 enriched KEGG pathways (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig3\\\" class=\\\"InternalRef\\\"\\u003e3\\u003c/span\\u003eb and Supplementary Table\\u0026nbsp;2), of which the top enriched KEGG pathways included plant\\u0026ndash;pathogen interaction, plant hormone signal transduction, and indole alkaloid biosynthesis, flavonoid biosynthesis, MAPK signaling pathway-plant, and ABC transporters. KEGG enrichment analysis suggested that genes related to plant hormone response and signaling transduction potentially play important roles in regulating the dwarfing trait.\\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec16\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.4 Differential expression of plant hormone-related genes\\u003c/h2\\u003e \\u003cp\\u003eA comprehensive set of Arabidopsis genes involved in plant hormones biosynthesis, signaling and transport was compiled based on literature search and used as reference to search for their homologous genes in pear genome (Supplementary Table\\u0026nbsp;3). Combining with the results of GO and KEGG pathway enrichment analyses, a total of 49 differentially expressed genes related to plant hormone biosynthesis, signal transduction, and transport were identified between the dwarf offspring and CG.\\u003c/p\\u003e \\u003cp\\u003eFive DEGs involved in auxin biosynthesis, signaling, and transport were identified (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig4\\\" class=\\\"InternalRef\\\"\\u003e4\\u003c/span\\u003e). Among them, \\u003cem\\u003eEVM0020980\\u003c/em\\u003e (\\u003cem\\u003eTAA1\\u003c/em\\u003e) and \\u003cem\\u003eEVM0005496\\u003c/em\\u003e (\\u003cem\\u003eYUCCA1\\u003c/em\\u003e), which encode two key enzymes in the auxin biosynthesis pathway, \\u003cem\\u003eEVM0041437\\u003c/em\\u003e (\\u003cem\\u003eARF10\\u003c/em\\u003e), a key component of the auxin signaling pathway, and \\u003cem\\u003eEVM0000187\\u003c/em\\u003e (\\u003cem\\u003eABCB1\\u003c/em\\u003e), which is involved in auxin transport, showed higher expression in CG. In contrast, \\u003cem\\u003eEVM0034292\\u003c/em\\u003e, annotated as PILS1 which is involved in auxin transport\\u003csup\\u003e[\\u003cspan citationid=\\\"CR16\\\" class=\\\"CitationRef\\\"\\u003e16\\u003c/span\\u003e]\\u003c/sup\\u003e, showed higher expression in the dwarf germplasm, consistent with previous reports that PILS overexpression shortens internode length\\u003csup\\u003e[\\u003cspan citationid=\\\"CR17\\\" class=\\\"CitationRef\\\"\\u003e17\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003eFour DEGs associated with brassinosteroid (BR) biosynthesis and signaling were identified. Among them, \\u003cem\\u003eEVM0042507\\u003c/em\\u003e (\\u003cem\\u003eDWARF4\\u003c/em\\u003e) was involved in BR biosynthesis, showed higher expression in CG, whereas \\u003cem\\u003eEVM0001604\\u003c/em\\u003e (\\u003cem\\u003eBZR1\\u003c/em\\u003e), a key component of the BR signaling pathway, was upregulated in the dwarf germplasm.\\u003c/p\\u003e \\u003cp\\u003eThree DEGs in the strigolactone (SL) signaling pathway were identified, including \\u003cem\\u003eEVM0017280\\u003c/em\\u003e (\\u003cem\\u003eMAX2\\u003c/em\\u003e), \\u003cem\\u003eEVM0032611\\u003c/em\\u003e (\\u003cem\\u003eD14\\u003c/em\\u003e), and \\u003cem\\u003eEVM0041100\\u003c/em\\u003e (\\u003cem\\u003eSMXL6\\u003c/em\\u003e). All three showed higher expression in the dwarf germplasm, which may contribute to suppressed axillary bud outgrowth and reduced branching in the dwarf germplasm \\u003csup\\u003e[\\u003cspan citationid=\\\"CR18\\\" class=\\\"CitationRef\\\"\\u003e18\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR19\\\" class=\\\"CitationRef\\\"\\u003e19\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR20\\\" class=\\\"CitationRef\\\"\\u003e20\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003eTwo DEGs involved in gibberellin (GA) biosynthesis were identified: \\u003cem\\u003eEVM0011564\\u003c/em\\u003e (\\u003cem\\u003eKO1\\u003c/em\\u003e) and \\u003cem\\u003eEVM0009219\\u003c/em\\u003e (\\u003cem\\u003eGA20ox3\\u003c/em\\u003e). Among them, \\u003cem\\u003eEVM0009219\\u003c/em\\u003e (\\u003cem\\u003eGA20ox3\\u003c/em\\u003e) showed higher expression in CG, which may result in elevated GA levels and thereby promote vigorous growth \\u003csup\\u003e[\\u003cspan citationid=\\\"CR21\\\" class=\\\"CitationRef\\\"\\u003e21\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003eOPR3 is a key enzyme in the jasmonic acid (JA) biosynthesis pathway, and JAR1 is a crucial enzyme in the JA signaling pathway that converts JA into its bioactive form to initiate JA responses. Jasmonic acid and gibberellin exhibit antagonistic effects in regulating plant growth and development in response to environmental and endogenous cues\\u003csup\\u003e[\\u003cspan citationid=\\\"CR22\\\" class=\\\"CitationRef\\\"\\u003e22\\u003c/span\\u003e]\\u003c/sup\\u003e. Genes (\\u003cem\\u003eEVM0006505\\u003c/em\\u003e and \\u003cem\\u003eEVM0001797\\u003c/em\\u003e) encoding these two enzymes were expressed at higher level in the dwarf germplasm.\\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec17\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.5 Differentially expressed TFs\\u003c/h2\\u003e \\u003cp\\u003eThe iTAK software \\u003csup\\u003e[\\u003cspan citationid=\\\"CR23\\\" class=\\\"CitationRef\\\"\\u003e23\\u003c/span\\u003e]\\u003c/sup\\u003e was used to annotate transcription factors (TFs) from the whole set of DEGs. A total of 1,118 DEGs were identified as TFs (Supplementary Table\\u0026nbsp;4). Among them, the five most enriched TF families were \\u003cem\\u003eMYB\\u003c/em\\u003e, \\u003cem\\u003eNAC\\u003c/em\\u003e, \\u003cem\\u003eAP2/ERF-ERF\\u003c/em\\u003e, \\u003cem\\u003ebHLH\\u003c/em\\u003e, and \\u003cem\\u003eWRKY.\\u003c/em\\u003e In addition, 22 differentially expressed \\u003cem\\u003eTCP\\u003c/em\\u003e genes were identified. Interestingly, among the differentially expressed TFs, five \\u003cem\\u003eARID\\u003c/em\\u003e genes, five \\u003cem\\u003eC2C2-YABBY\\u003c/em\\u003e genes, and three \\u003cem\\u003eCPP\\u003c/em\\u003e genes showed higher expression in CG, whereas three \\u003cem\\u003eBES1\\u003c/em\\u003e genes, five \\u003cem\\u003eCAMTA\\u003c/em\\u003e genes, five \\u003cem\\u003eTifys\\u003c/em\\u003e genes, three \\u003cem\\u003eGeBP\\u003c/em\\u003e genes, and seven \\u003cem\\u003eKNOX\\u003c/em\\u003e genes exhibited higher expression in the dwarf germplasm. In \\u003cem\\u003eYABBY\\u003c/em\\u003e deficient tissues, auxin distribution is disrupted, which is accompanied by a reduction in the abundance of the auxin efflux carrier \\u003cem\\u003ePIN1\\u003c/em\\u003e, indicating that \\u003cem\\u003eYABBY\\u003c/em\\u003e genes are required for proper auxin transport during lateral organ development\\u003csup\\u003e[\\u003cspan citationid=\\\"CR24\\\" class=\\\"CitationRef\\\"\\u003e24\\u003c/span\\u003e]\\u003c/sup\\u003e. In apple, \\u003cem\\u003eMdKNOX15\\u003c/em\\u003e regulates plant height by promoting the transcription of \\u003cem\\u003eMdGA2ox7\\u003c/em\\u003e, which enhances gibberellin deactivation and consequently leads to a dwarf phenotype\\u003csup\\u003e[\\u003cspan citationid=\\\"CR25\\\" class=\\\"CitationRef\\\"\\u003e25\\u003c/span\\u003e]\\u003c/sup\\u003e. These differentially expressed TFs are likely to play key roles in regulating the dwarfing phenotype.\\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec18\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.6 Differentially expressed genes related to cell wall\\u003c/h2\\u003e \\u003cp\\u003eA comprehensive set of genes involved in cell wall biosynthesis, modification and degradation was compiled based on literature search and used as reference to search for their homologous genes in pear genome (Supplementary Table\\u0026nbsp;5) (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig5\\\" class=\\\"InternalRef\\\"\\u003e5\\u003c/span\\u003e). Combining with RNA-Seq data analysis, 28 genes involved in cell wall formation and degradation showed differential expression between the dwarf germplasm and CG.\\u003c/p\\u003e \\u003cp\\u003eWithin the cell wall biosynthetic pathway, \\u003cem\\u003eEVM0021398\\u003c/em\\u003e annotated as homologs of AT2G37090 (\\u003cem\\u003eIRX9\\u003c/em\\u003e) which is involved in xylan backbone elongation and promoting plant growth \\u003csup\\u003e[\\u003cspan citationid=\\\"CR26\\\" class=\\\"CitationRef\\\"\\u003e26\\u003c/span\\u003e]\\u003c/sup\\u003e, showed higher expression in CG. Arabinogalactan proteins (\\u003cem\\u003eAGPs\\u003c/em\\u003e) are known to play essential roles in multiple cellular processes during plant development. \\u003cem\\u003eEVM0016345\\u003c/em\\u003e, a homolog of AT4G21060 which encodes a GalT enzyme that modifies hydroxyproline (Hyp) residues to promote AGP biosynthesis\\u003csup\\u003e[\\u003cspan citationid=\\\"CR27\\\" class=\\\"CitationRef\\\"\\u003e27\\u003c/span\\u003e]\\u003c/sup\\u003e, showed higher expression in CG. \\u003cem\\u003eEVM0001088\\u003c/em\\u003e and \\u003cem\\u003eEVM0005604\\u003c/em\\u003e were annotated as \\u003cem\\u003eIRX7/F8H\\u003c/em\\u003e and showed higher expression in CG. Overexpression of \\u003cem\\u003eF8H\\u003c/em\\u003e in \\u003cem\\u003eFRA8\\u003c/em\\u003e mutants, which exhibit thinner secondary cell walls, abnormal xylem morphology, and inhibited plant growth, fully rescues their phenotype, indicating that \\u003cem\\u003eF8H\\u003c/em\\u003e shares similar function as \\u003cem\\u003eFRA8\\u003c/em\\u003e although single \\u003cem\\u003eF8H\\u003c/em\\u003e mutants do not show any detectable cell wall defects\\u003csup\\u003e[\\u003cspan citationid=\\\"CR28\\\" class=\\\"CitationRef\\\"\\u003e28\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003e \\u003cem\\u003eEVM0012106\\u003c/em\\u003e was annotated as GALT31A which belongs to the GT31 glycosyltransferase family and showed higher expression in CG. It has been reported that \\u003cem\\u003eAtGALT31A\\u003c/em\\u003e can elongate the β-1,6-galactan side chains of \\u003cem\\u003eAGPs\\u003c/em\\u003e and is one of the key enzymes in \\u003cem\\u003eAGP\\u003c/em\\u003e glycan biosynthesis \\u003csup\\u003e[\\u003cspan citationid=\\\"CR29\\\" class=\\\"CitationRef\\\"\\u003e29\\u003c/span\\u003e]\\u003c/sup\\u003e. \\u003cem\\u003eEVM0006210\\u003c/em\\u003e was upregulated in CG and annotated as GlcAT14A which is involved in the modification of cell wall\\u0026ndash;associated glycoproteins, cell elongation, and organ growth regulation. In Arabidopsis, GlcAT14A mutants exhibit enhanced hypocotyl and root cell elongation, leading to altered seedling elongation growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR30\\\" class=\\\"CitationRef\\\"\\u003e30\\u003c/span\\u003e]\\u003c/sup\\u003e. \\u003cem\\u003eEVM0020399\\u003c/em\\u003e was upregulated in CG and annotated as \\u003cem\\u003eGUX1\\u003c/em\\u003e, one of the key genes involved in secondary cell wall formation. In Arabidopsis, a complete loss of GlcA and MeGlcA side chains in the gux1/2/3 triple mutant results in reduced secondary wall thickening, collapsed vessel morphology, and stunted plant growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR31\\\" class=\\\"CitationRef\\\"\\u003e31\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003eWithin the pathways of cell wall modification and degradation, \\u003cem\\u003eEVM0034734\\u003c/em\\u003e showed high expression in CG and was annotated as AGM1 which is involved in protein O-GlcNAcylation and is important for plant growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR32\\\" class=\\\"CitationRef\\\"\\u003e32\\u003c/span\\u003e]\\u003c/sup\\u003e. \\u003cem\\u003eEVM0022278\\u003c/em\\u003e was upregulated in CG and annotated as \\u003cem\\u003eBGAL10\\u003c/em\\u003e. In Arabidopsis, \\u003cem\\u003eAtBGAL10\\u003c/em\\u003e mutants exhibit abnormal xyloglucan structure, resulting in growth defects and notably shortened stems\\u003csup\\u003e[\\u003cspan citationid=\\\"CR33\\\" class=\\\"CitationRef\\\"\\u003e33\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec19\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.7 Differential expression of genes within the chromosomal region containing \\u003cem\\u003ePcDw\\u003c/em\\u003e\\u003c/h2\\u003e \\u003cp\\u003eIn previous studies, a dominant gene (\\u003cem\\u003ePcDw\\u003c/em\\u003e) controlling dwarf trait in pear cultivar \\u0026lsquo;Le Nain Vert\\u0026rsquo; was mapped to scaffold00074 of \\u003cem\\u003eP. communis\\u003c/em\\u003e genome v1.0\\u003csup\\u003e[\\u003cspan citationid=\\\"CR8\\\" class=\\\"CitationRef\\\"\\u003e8\\u003c/span\\u003e]\\u003c/sup\\u003e, which harbors two SSR markers linked to the \\u003cem\\u003ePcDw\\u003c/em\\u003e locus. Here, we identified syntenic homologous regions of scaffold00074 in chromosome-scale genome of \\u003cem\\u003eP. communis\\u003c/em\\u003e (v2.0) and CG (\\u003cem\\u003eP. pyrifolia\\u003c/em\\u003e), and investigated expression patterns of genes within this chromosomal region in shoot apex between the dwarf germplasm and CG. A total of 52 genes were identified in this region and their potential functions were predicted based on homolog search against Arabidopsis genes (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig6\\\" class=\\\"InternalRef\\\"\\u003e6\\u003c/span\\u003e). Among them, 19 genes showed differential expression, of which 9 genes have functional annotation information. Of these nine genes, seven showed higher expression in the dwarf germplasm, whereas two showed higher expression in CG. (Supplementary Table\\u0026nbsp;6).\\u003c/p\\u003e \\u003cp\\u003eAmong the two DEGs upregulated in CG, \\u003cem\\u003eEVM0015682\\u003c/em\\u003e was annotated as a pectin methylesterase inhibitor (PEMI\\u003cem\\u003e)\\u003c/em\\u003e which can enhance brassinosteroid signaling, thereby promoting plant growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR34\\\" class=\\\"CitationRef\\\"\\u003e34\\u003c/span\\u003e]\\u003c/sup\\u003e. \\u003cem\\u003eEVM0011700\\u003c/em\\u003e was annotated as \\u003cem\\u003ePUB10-like\\u003c/em\\u003e which suppresses \\u003cem\\u003eMYC2\\u003c/em\\u003e activity and defense responses and promotes growth, making the antagonistic interaction between jasmonic acid (JA) and gibberellin (GA) more pronounced\\u003csup\\u003e[\\u003cspan citationid=\\\"CR22\\\" class=\\\"CitationRef\\\"\\u003e22\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003eAmong the seven DEGs upregulated in the dwarf germplasm, \\u003cem\\u003eEVM0008541\\u003c/em\\u003e, \\u003cem\\u003eEVM0027056\\u003c/em\\u003e, \\u003cem\\u003eEVM0004698\\u003c/em\\u003e, \\u003cem\\u003eEVM0022781\\u003c/em\\u003e and \\u003cem\\u003eEVM0038290\\u003c/em\\u003e were annotated as a member of the pathogenesis-related protein Bet v 1 family\\u003csup\\u003e[\\u003cspan citationid=\\\"CR35\\\" class=\\\"CitationRef\\\"\\u003e35\\u003c/span\\u003e]\\u003c/sup\\u003e, which inhibit plant growth in rice \\u003csup\\u003e[\\u003cspan citationid=\\\"CR36\\\" class=\\\"CitationRef\\\"\\u003e36\\u003c/span\\u003e]\\u003c/sup\\u003e. \\u003cem\\u003eEVM0021367\\u003c/em\\u003e belongs to the serine carboxypeptidase family, of which \\u003cem\\u003eBRS1\\u003c/em\\u003e regulates plant growth and development through modulating \\u003cem\\u003eBRI1\\u003c/em\\u003e signaling \\u003csup\\u003e[\\u003cspan citationid=\\\"CR37\\\" class=\\\"CitationRef\\\"\\u003e37\\u003c/span\\u003e]\\u003c/sup\\u003e. Moreover, \\u003cem\\u003eEVM0008593\\u003c/em\\u003e, belongs to the \\u003cem\\u003eDELLA\\u003c/em\\u003e proteins which are central suppressor of gibberellin signaling and restrict plant development, showed upregulated expression in the dwarf germplasm.\\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003c/div\\u003e \\u003cdiv id=\\\"Sec20\\\" class=\\\"Section2\\\"\\u003e \\u003ch2\\u003e3.8 Validation of RNA-Seq data by RT-qPCR\\u003c/h2\\u003e \\u003cp\\u003eTo validate the reliability of the RNA-Seq data, eight DEGs related to plant hormones, cell wall biosynthesis, and contained in chromosomal region harboring \\u003cem\\u003ePcDw\\u003c/em\\u003e locus were randomly selected, and their expression levels were measured by quantitative real-time PCR (RT-qPCR) (Fig.\\u0026nbsp;\\u003cspan refid=\\\"Fig7\\\" class=\\\"InternalRef\\\"\\u003e7\\u003c/span\\u003e). Pearson correlation coefficients (PCCs) between RT-qPCR and RNA-Seq expression profiles were calculated for each gene using the Pearson function in R. The results showed a high correlation between the RT-qPCR and RNA-Seq data for all selected genes, with an average PCC greater than 0.7, indicating the reliability of the RNA-Seq data.\\u003c/p\\u003e \\u003cp\\u003e \\u003c/p\\u003e \\u003c/div\\u003e\"},{\"header\":\"4 Discussion\",\"content\":\"\\u003cp\\u003eDecreasing plant height and maintaining compact canopy are crucial for achieving high-density planting in fruit tree cultivation. Dwarfing rootstocks can reduce tree height and canopy size and are desirable for high-density planting. However, the molecular mechanisms governing dwarf phenotype of dwarfing pear rootstocks have not been well studied. In this study, we compared transcriptome of shoot apex between the dwarf germplasm which inherited dwarf traits from LNV and pear cultivar CG with standard tree height. GO and KEGG enrichment analyses revealed that DEGs are enriched in plant hormone biosynthesis, signaling and transport, indicating that phytohormones play important roles in regulating tree height. Therefore, we further identified plant hormone-related genes in pear genome and investigated their expression patterns between the dwarf germplasm and CG.\\u003c/p\\u003e \\u003cp\\u003ePhytohormones play important roles in regulating plant growth and development. In this study, DEGs involved in phytohormone biosynthesis, transport, and signaling were identified. \\u003cem\\u003eYUCCA\\u003c/em\\u003e-mediated auxin biosynthesis is crucial for floral organ formation, vascular development, and plant architecture. Here, we found \\u003cem\\u003eEVM0005496 (YUCCA1)\\u003c/em\\u003e showed higher expression in CG. In addition, \\u003cem\\u003eEVM0020980 (TAA1)\\u003c/em\\u003e and \\u003cem\\u003eEVM0000187 (ABCB1)\\u003c/em\\u003e involved in auxin biosynthesis and transport also showed higher expression in CG, consistent with their important roles in promoting plant growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR38\\\" class=\\\"CitationRef\\\"\\u003e38\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR39\\\" class=\\\"CitationRef\\\"\\u003e39\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR40\\\" class=\\\"CitationRef\\\"\\u003e40\\u003c/span\\u003e]\\u003c/sup\\u003e. The BR biosynthesis gene \\u003cem\\u003eDWARF4 (EVM0042507)\\u003c/em\\u003e was upregulated in CG, in agreement with prior report that BR promotes bud outgrowth and growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR41\\\" class=\\\"CitationRef\\\"\\u003e41\\u003c/span\\u003e]\\u003c/sup\\u003e. \\u003cem\\u003eBZR1\\u003c/em\\u003e is a positive regulator of BR signaling\\u003csup\\u003e[\\u003cspan citationid=\\\"CR42\\\" class=\\\"CitationRef\\\"\\u003e42\\u003c/span\\u003e]\\u003c/sup\\u003e, which has been reported to be downregulated in dwarf varieties. However, in our data, BZR1 is upregulated in the dwarf germplasm. As the key components of the strigolactone signaling pathway, \\u003cem\\u003eEVM0017280 (MAX2)\\u003c/em\\u003e and \\u003cem\\u003eEVM0032611 (D14)\\u003c/em\\u003e, showed higher expression in the dwarf germplasm, supporting the association between increased level of SL and reduced plant height and branching\\u003csup\\u003e[\\u003cspan citationid=\\\"CR43\\\" class=\\\"CitationRef\\\"\\u003e43\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR44\\\" class=\\\"CitationRef\\\"\\u003e44\\u003c/span\\u003e]\\u003c/sup\\u003e. However, \\u003cem\\u003eSMXL\\u003c/em\\u003e family genes were also upregulated in the dwarf germplasm, suggesting complex feedback or post-translational regulation of SL signaling. For gibberellin metabolism, \\u003cem\\u003eEVM0011564 (KO1)\\u003c/em\\u003e and \\u003cem\\u003eEVM0009219 (GA20ox3)\\u003c/em\\u003e showed higher expression in CG, consistent with their roles in GA biosynthesis and thus promoting stem elongation and plant growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR45\\\" class=\\\"CitationRef\\\"\\u003e45\\u003c/span\\u003e][\\u003cspan citationid=\\\"CR46\\\" class=\\\"CitationRef\\\"\\u003e46\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e \\u003cp\\u003eDifferentially expressed transcription factors were mainly enriched in the \\u003cem\\u003eMYB\\u003c/em\\u003e, AP2/ERF, NAC, bHLH, and WRKY families. In previous studies, genes encoding growth-regulating factor (GRF) domain transcription factors and YABBY domain transcription factors were found to show downregulated expression in dwarf pear\\u003csup\\u003e[\\u003cspan citationid=\\\"CR8\\\" class=\\\"CitationRef\\\"\\u003e8\\u003c/span\\u003e]\\u003c/sup\\u003e. In our results, all \\u003cem\\u003eYABBY\\u003c/em\\u003e genes were also downregulated in the dwarf germplasm, whereas most \\u003cem\\u003eGRF\\u003c/em\\u003e genes were upregulated in the dwarf germplasm. \\u003cem\\u003eNACs\\u003c/em\\u003e and \\u003cem\\u003eTifys\\u003c/em\\u003e have been revealed to be upregulated in the dwarf pear lines\\u003csup\\u003e[\\u003cspan citationid=\\\"CR12\\\" class=\\\"CitationRef\\\"\\u003e12\\u003c/span\\u003e]\\u003c/sup\\u003e, consistent with our results.\\u003c/p\\u003e \\u003cp\\u003eNumerous DEGs related to cell wall biosynthesis, modification, and degradation were also identified. In CG, multiple cellulose synthases, xylan synthesis/modification genes (e.g., \\u003cem\\u003eCESA\\u003c/em\\u003e, \\u003cem\\u003eIRX\\u003c/em\\u003e, \\u003cem\\u003eGUX\\u003c/em\\u003e, and \\u003cem\\u003eESK1\\u003c/em\\u003e), and AGP biosynthesis genes were highly expressed, which may promote cell wall biosynthesis and cell growth, thereby supporting normal plant height. This supported previous studies that genes involved in cell wall biosynthesis are expressed at lower levels in dwarf plants.\\u003c/p\\u003e \\u003cp\\u003eThe \\u003cem\\u003ePcDw\\u003c/em\\u003e gene, which has been reported to control the dwarf phenotype of a French pear cultivar \\u0026lsquo;Le Nain Vert\\u0026rsquo;, was mapped between two SSR markers on scaffold00074 of \\u003cem\\u003eP. communis\\u003c/em\\u003e v1.0 genome. In this study, we identified homologous regions of scaffold00074 in chromosome-scale \\u003cem\\u003eP. communis\\u003c/em\\u003e v2.0 and CG genome and investigated their expression and functional involvement. Among them, \\u003cem\\u003eEVM0015682 (PEMI)\\u003c/em\\u003e exhibited higher expression in CG, which may enhance brassinosteroid signaling and consequently promote plant growth. \\u003cem\\u003eEVM0011700 (PUB10-like)\\u003c/em\\u003e was downregulated in the dwarf germplasm, which may enhance MYC2 activity, thereby promoting plant defense responses and inhibiting growth\\u003csup\\u003e[\\u003cspan citationid=\\\"CR34\\\" class=\\\"CitationRef\\\"\\u003e34\\u003c/span\\u003e]\\u003c/sup\\u003e. \\u003cem\\u003eEVM0008541\\u003c/em\\u003e, \\u003cem\\u003eEVM0027056\\u003c/em\\u003e, \\u003cem\\u003eEVM0004698\\u003c/em\\u003e, \\u003cem\\u003eEVM0022781\\u003c/em\\u003e, and \\u003cem\\u003eEVM0038290\\u003c/em\\u003e, members of the pathogenesis-related protein Bet v 1 family \\u003csup\\u003e[\\u003cspan citationid=\\\"CR35\\\" class=\\\"CitationRef\\\"\\u003e35\\u003c/span\\u003e]\\u003c/sup\\u003e, have been associated with reduced plant height, shorter panicles, and lower seed set when overexpressing\\u003csup\\u003e[\\u003cspan citationid=\\\"CR36\\\" class=\\\"CitationRef\\\"\\u003e36\\u003c/span\\u003e]\\u003c/sup\\u003e. Moreover, \\u003cem\\u003eEVM0008593\\u003c/em\\u003e, annotated as the DELLA protein, showed upregulated expression in the dwarf germplasm, consistent with previous report\\u003csup\\u003e[\\u003cspan citationid=\\\"CR12\\\" class=\\\"CitationRef\\\"\\u003e12\\u003c/span\\u003e]\\u003c/sup\\u003e In addition, \\u003cem\\u003eEVM0021367\\u003c/em\\u003e, a serine carboxypeptidase, may affect BR signaling, similar to \\u003cem\\u003eBRS1\\u003c/em\\u003e, whose regulation of \\u003cem\\u003eBRI1\\u003c/em\\u003e is critical for normal plant growth and development\\u003csup\\u003e[\\u003cspan citationid=\\\"CR37\\\" class=\\\"CitationRef\\\"\\u003e37\\u003c/span\\u003e]\\u003c/sup\\u003e.\\u003c/p\\u003e\"},{\"header\":\"5 Conclusion\",\"content\":\"\\u003cp\\u003eIn this study, we conducted comparative transcriptome analysis of shoot apex between the dwarf germplasm and cultivar CG. The dwarf germplasm exhibits a thicker cortex, longer cells, and irregular and loosely arranged cell structure. Functional terms involved in plant hormones biosynthesis and signal transduction were enriched in DEGs, indicating important roles of phytohormones in controlling dwarf phenotype of the dwarf germplasm. A set of DEGs involved in TFs, biosynthesis and signaling, and cell wall biosynthesis and degradation were identified, and their roles were clarified. By integrating our transcriptome data with previously reported molecular markers linked to the dwarf locus PcDW, several candidate genes were identified. Taken together, the results of this study contribute to elucidate the molecular mechanisms underlying pear dwarfism.\\u003c/p\\u003e\"},{\"header\":\"Declarations\",\"content\":\"\\u003cp\\u003e\\u003cstrong\\u003eEthics approval and consent to participate\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eNot applicable.\\u0026nbsp;\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eConsent for publication\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eNot applicable.\\u0026nbsp;\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eAvailability of data and materials\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eThe raw RNA-seq data have been deposited in the National Genomics Data Center (NGDC, https://www.cncb.ac.cn/?lang=en) under BioProject accession PRJCA059134 with CRA accession CRA039345.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eCompeting interests\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eThe authors declare that they have no competing interests.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eFunding\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eThis study was supported by the Seed Industry Promotion Project of Jiangsu (JBGS (2021)022) and Nanjing Agricultural University High-Level Talent Recruitment Start-up Fund. The bioinformatic analysis was supported by the Bioinformatics Center of Nanjing Agricultural University.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eAuthor\\u003c/strong\\u003e\\u003cstrong\\u003es\\u0026rsquo;\\u003c/strong\\u003e\\u003cstrong\\u003e\\u0026nbsp;contributions\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eYX, HHD and SL were responsible for data collection. YX conducted\\u0026nbsp;data analysis. QHL, HXL and KM participated in data analysis. SLZ, KJQ, and ZHX contributed to experimental materials collection and management. YX prepared the manuscript. XQ and QHL revised the manuscript. XQ conceived and supervised this study. All authors have read and approved the final manuscript.\\u003c/p\\u003e\\n\\u003cp\\u003e\\u003cstrong\\u003eAcknowledgments\\u003c/strong\\u003e\\u003cstrong\\u003e:\\u003c/strong\\u003e\\u003c/p\\u003e\\n\\u003cp\\u003eNot applicable\\u003c/p\\u003e\"},{\"header\":\"References\",\"content\":\"\\u003col\\u003e\\u003cli\\u003e\\u003cspan\\u003eOu C, Wang F, Wang J, Li S, Zhang Y, Fang M, Ma L, Zhao Y, Jiang S. A de novo genome assembly of the dwarfing pear rootstock Zhongai 1. Sci Data. 2019;6(1):281. \\u003cspan class=\\\"ExternalRef\\\"\\u003e\\u003cspan class=\\\"RefSource\\\"\\u003e10.1038/s41597-019-0291-3\\u003c/span\\u003e\\u003cspan address=\\\"10.1038/s41597-019-0291-3\\\" targettype=\\\"DOI\\\" class=\\\"RefTarget\\\"\\u003e\\u003c/span\\u003e\\u003c/span\\u003e.\\u003c/span\\u003e\\u003c/li\\u003e \\u003cli\\u003e\\u003cspan\\u003eWertheim SJ. 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Plant Physiol. 2013;163(2):929\\u0026ndash;45.\\u003c/span\\u003e\\u003c/li\\u003e\\u003c/ol\\u003e\"}],\"fulltextSource\":\"\",\"fullText\":\"\",\"funders\":[],\"hasAdminPriorityOnWorkflow\":false,\"hasManuscriptDocX\":true,\"hasOptedInToPreprint\":true,\"hasPassedJournalQc\":\"\",\"hasAnyPriority\":false,\"hideJournal\":false,\"highlight\":\"\",\"institution\":\"\",\"isAcceptedByJournal\":true,\"isAuthorSuppliedPdf\":false,\"isDeskRejected\":\"\",\"isHiddenFromSearch\":false,\"isInQc\":false,\"isInWorkflow\":false,\"isPdf\":false,\"isPdfUpToDate\":true,\"isWithdrawnOrRetracted\":false,\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"bmc-genomic-data\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":false,\"externalIdentity\":\"gtic\",\"sideBox\":\"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)\",\"snPcode\":\"\",\"submissionUrl\":\"https://www.editorialmanager.com/gtic/default.aspx\",\"title\":\"BMC Genomic Data\",\"twitterHandle\":\"BMC_series\",\"acdcEnabled\":true,\"dfaEnabled\":false,\"editorialSystem\":\"em\",\"reportingPortfolio\":\"BMC Series\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":true},\"keywords\":\"pear, dwarf germplasm, ‘Cuiguan’, comparative transcriptome, dwarfing mechanism\",\"lastPublishedDoi\":\"10.21203/rs.3.rs-9020477/v1\",\"lastPublishedDoiUrl\":\"https://doi.org/10.21203/rs.3.rs-9020477/v1\",\"license\":{\"name\":\"CC BY 4.0\",\"url\":\"https://creativecommons.org/licenses/by/4.0/\"},\"manuscriptAbstract\":\"\\u003ch2\\u003eBackground\\u003c/h2\\u003e \\u003cp\\u003eDwarfism is crucial for intensive cultivation and labor-saving management in modern orchard. However, the molecular mechanisms underlying pear tree dwarfing remain largely unclear. Here, we performed comparative transcriptome analysis between dwarf pear germplasm and pear cultivar \\u0026lsquo;Cuiguan\\u0026rsquo;.\\u003c/p\\u003e\\u003ch2\\u003eResult\\u003c/h2\\u003e \\u003cp\\u003eThe dwarf pear germplasm presents significantly shorter internode and branch length compared to \\u0026lsquo;Cuiguan\\u0026rsquo;. Histological analysis revealed that cortical cells in the dwarf pear germplasm are disordered and irregular, and longer than those of \\u0026lsquo;Cuiguan\\u0026rsquo;. Comparative transcriptome analysis of shoot apex from young shoots of the dwarf germplasm and \\u0026lsquo;Cuiguan\\u0026rsquo; was conducted and a total of 13,169 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that function terms related to plant hormone biosynthesis and signal transduction were overrepresented in DEGs. Genes involved in brassinosteroid (BR) and gibberellin (GA) inactivation and degradation were upregulated in the dwarf germplasm. DEGs involved in transcription regulation and cell wall formation were also identified, which play potential roles in tree dwarfing. In addition, expression level of genes within the chromosomal region containing \\u003cem\\u003ePcDw\\u003c/em\\u003e locus, which has been reported as the dominant gene controlling dwarf trait, was investigated in both the dwarf pear germplasm and \\u0026lsquo;Cuiguan\\u0026rsquo;. Based on comparative analysis, 9 genes in this region are considered to be closely associated with dwarf traits.\\u003c/p\\u003e\\u003ch2\\u003eConclusions\\u003c/h2\\u003e \\u003cp\\u003eOverall, the results of this study provide insights for understanding the genetic and molecular mechanisms underlying pear tree dwarfing.\\u003c/p\\u003e\",\"manuscriptTitle\":\"Comparative transcriptome analysis provides insights into the dwarfing mechanism of pear trees\",\"msid\":\"\",\"msnumber\":\"\",\"nonDraftVersions\":[{\"code\":1,\"date\":\"2026-03-20 13:14:51\",\"doi\":\"10.21203/rs.3.rs-9020477/v1\",\"editorialEvents\":[{\"type\":\"communityComments\",\"content\":0},{\"type\":\"decision\",\"content\":\"Revision requested\",\"date\":\"2026-03-31T08:23:58+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-03-30T08:46:30+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-03-28T12:19:22+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-03-26T15:03:21+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2026-03-25T02:46:33+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"299860251963520052572922266281741837571\",\"date\":\"2026-03-20T01:05:06+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"143110674137912176362272649029045244877\",\"date\":\"2026-03-18T10:02:11+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"292152949698728921727170802526210415717\",\"date\":\"2026-03-18T06:50:51+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"269670447733363552925212561918152547490\",\"date\":\"2026-03-18T03:42:12+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewersInvited\",\"content\":\"\",\"date\":\"2026-03-18T01:00:31+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorInvited\",\"content\":\"\",\"date\":\"2026-03-12T16:49:50+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorAssigned\",\"content\":\"\",\"date\":\"2026-03-12T11:19:17+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"checksComplete\",\"content\":\"\",\"date\":\"2026-03-12T11:18:52+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"submitted\",\"content\":\"BMC Genomic Data\",\"date\":\"2026-03-03T12:39:24+00:00\",\"index\":\"\",\"fulltext\":\"\"}],\"status\":\"published\",\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"bmc-genomic-data\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":false,\"externalIdentity\":\"gtic\",\"sideBox\":\"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)\",\"snPcode\":\"\",\"submissionUrl\":\"https://www.editorialmanager.com/gtic/default.aspx\",\"title\":\"BMC Genomic Data\",\"twitterHandle\":\"BMC_series\",\"acdcEnabled\":true,\"dfaEnabled\":false,\"editorialSystem\":\"em\",\"reportingPortfolio\":\"BMC Series\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":true}}],\"origin\":\"\",\"ownerIdentity\":\"53403a60-bda9-410d-a2dd-8db2c4b06bc1\",\"owner\":[],\"postedDate\":\"March 20th, 2026\",\"published\":true,\"recentEditorialEvents\":[],\"rejectedJournal\":[],\"revision\":\"\",\"amendment\":\"\",\"status\":\"under-review\",\"subjectAreas\":[],\"tags\":[],\"updatedAt\":\"2026-05-11T12:12:51+00:00\",\"versionOfRecord\":[],\"versionCreatedAt\":\"2026-03-20 13:14:51\",\"video\":\"\",\"vorDoi\":\"\",\"vorDoiUrl\":\"\",\"workflowStages\":[]},\"version\":\"v1\",\"identity\":\"rs-9020477\",\"journalConfig\":\"researchsquare\"},\"__N_SSP\":true},\"page\":\"/article/[identity]/[[...version]]\",\"query\":{\"redirect\":\"/article/rs-9020477\",\"identity\":\"rs-9020477\",\"version\":[\"v1\"]},\"buildId\":\"XKTyCvWXoU3ODBz1xrDgd\",\"isFallback\":false,\"isExperimentalCompile\":false,\"dynamicIds\":[84888],\"gssp\":true,\"scriptLoader\":[]}","source_license":"CC-BY-4.0","license_restricted":false}