Scientia Horticulturae最新文献

{"title":"Comparative transcriptomic analysis reveals distinct drought-response patterns in Chrysanthemum morifolium ‘Jinsihuangju’ and Chrysanthemum chanetii","authors":"Xin Zhang,&nbsp;Yong-Zhi Yang,&nbsp;Zheng-Nan Li","doi":"10.1016/j.scienta.2026.115204","DOIUrl":"10.1016/j.scienta.2026.115204","url":null,"abstract":"<div><div>To elucidate the differential responses of chrysanthemum materials to drought stress and their underlying molecular regulatory mechanisms, this study used <em>Chrysanthemum chanetii</em> H. Lév. (XHJ) and <em>Chrysanthemum morifolium</em> ‘Jinsihuangju’ (JSHJ). Phenotypic observation, physiological measurements, transcriptome sequencing, GO/KEGG enrichment analyses, and qRT-PCR validation were integrated to systematically compare their drought-response characteristics. The results showed that drought stress induced more severe wilting and canopy shrinkage in JSHJ, whereas XHJ maintained a relatively intact canopy structure. Physiological analysis showed that the activities of POD, SOD, and APX, as well as the contents of Pro, SS, and SP, increased in both materials, indicating that antioxidant defense and osmotic adjustment jointly participated in drought responses. Transcriptome analysis generated 60,531 nonredundant transcripts, with 3,502 and 3,792 drought-responsive DETs in JSHJ and XHJ, respectively. A factorial material × treatment analysis further identified 630 transcripts with significantly different drought responses. KEGG enrichment showed that DETs were mainly involved in photosynthesis, carbon and carbohydrate metabolism, antioxidant defense, energy metabolism, and signal transduction. Major candidate regulatory families included AP2/ERF, bHLH, MYB, NAC, WRKY, bZIP, and RLK-Pelle. qRT-PCR showed overall consistency with RNA-seq expression patterns for the selected genes. Integrated analysis showed that XHJ maintained lower absolute MDA levels and better canopy integrity, whereas JSHJ exhibited stronger antioxidant and transcriptional responses. These findings provide candidate transcript resources and a comparative framework for genetic mapping and breeding-oriented evaluation of drought-associated traits in chrysanthemum.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"368 ","pages":"Article 115204"},"PeriodicalIF":4.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149092303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cytological mechanisms underlying fertility differences in allotetraploid tree peonies","authors":"Run-ze Ji,&nbsp;Kun-yan Li,&nbsp;Yu-jie Xu,&nbsp;Rui-qing Zhang,&nbsp;Xiao-han Meng,&nbsp;Yuan Zhong,&nbsp;Fang-yun Cheng","doi":"10.1016/j.scienta.2026.115201","DOIUrl":"10.1016/j.scienta.2026.115201","url":null,"abstract":"<div><div>Tetraploidization is a critical pathway for fertility restoration in inter-subsectional hybrid tree peonies (<em>Paeonia</em> × <em>lemoinei</em>). However, mechanisms underlying the male sterility or reduced fertility observed in some allotetraploid tree peonies remain unclear. In this study, three allotetraploid tree peonies (07-LB-30, 07-LB-22, and 07-LB-56) with different fertility levels were investigated by observing meiosis behavior and anther development, characterizing pollen morphology and viability, and analyzing chromosomal composition via genomic <em>in situ</em> hybridization (GISH). We found that the fertility differences among the three materials did not align with their overall frequency of meiotic irregularities, suggesting that meiotic disturbance could not necessarily lead to fertility defects in these allotetraploids. Despite forming 17.57% normal tetrads, 07-LB-22 exhibited defective tapetum development and subsequent thorough pollen abortion, which more possibly result in its male sterility. Similarly, although 07-LB-56 generated a moderate proportion (38.90%) of normal tetrads, its severe chromosomal pairing disorders, which may lead to a high frequency of aneuploid gametes, are supposed to account for its reduced fertility. GISH revealed that 07-LB-56 possesses an AAAB type chromosomal composition, distinct from the near-AABB configuration of the other two materials. This asymmetric subgenomic composition could cause genomic imbalance, thereby giving rise to pairing failure and reduced fertility. The AAAB-type allotetraploid tree peony might originate from backcrossing between inter-subsectional hybrid tree peonies (<em>P.</em> × <em>lemoinei</em>, AABB or AB) and common tree peonies (<em>P. suffruticosa</em>, AA), suggesting a potential pathway for tetraploidization in tree peonies. This study elucidated the mechanisms underlying fertility differences in three allotetraploid tree peonies, and proposed a backcrossing pathway for tetraploidization, providing valuable theoretical bases for polyploid breeding in tree peonies.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"368 ","pages":"Article 115201"},"PeriodicalIF":4.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149085381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large-scale population genomics reveals genetic diversity and evolutionary history of Saxifraga stolonifera","authors":"Shimei Tang,&nbsp;Jialin Luo,&nbsp;Xing Zhang,&nbsp;Zhilin Chen,&nbsp;Daike Tian","doi":"10.1016/j.scienta.2026.115178","DOIUrl":"10.1016/j.scienta.2026.115178","url":null,"abstract":"<div><div><em>Saxifraga stolonifera</em> is widely distributed across the subtropical monsoon regions of China and has been extensively utilized for its medicinal and horticultural importance. A comprehensive assessment of its genetic variation can clarify both the extent and spatial patterns of diversity within available germplasm, thus supporting the identification of representative and diverse materials for future utilization. Here, we analyzed genetic diversity and population structure in <em>S. stolonifera</em> by examining 49 populations sampled throughout China, based on single nucleotide polymorphism (SNP) markers. Phylogenetic inference combined with population structure analysis indicated relatively low levels of genetic diversity but pronounced genetic differentiation, allowing the samples to be classified into five distinct genetic groups (π = 0.00,394–0.00,959; <em>F</em>_ST = 0.221–0.513). Estimates from molecular dating together with ancestral range reconstruction suggest that Chinese populations of <em>S. stolonifera</em> likely originated in eastern China during the late Miocene, followed by a westward expansion and diversification. In addition, we detected pronounced patterns of both geographic and environmental isolation in <em>S. stolonifera</em>, as well as limited interspecific gene flow with species in <em>S.</em> sect. <em>Irregulares</em>, and only limited gene exchange was observed among populations of <em>S. stolonifera</em>. These findings enhance our understanding of the diversity patterns of <em>S. stolonifera</em> and offer important perspectives on its evolutionary trajectory and clarify how geographic isolation and gene flow have contributed to the formation of its present genetic structure.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"368 ","pages":"Article 115178"},"PeriodicalIF":4.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149085385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated analysis identifies antioxidant-associated phytochemicals and candidate flavonoid co-expression networks in Iris sanguinea flowers","authors":"Gongfa Shi,&nbsp;Nuo Xu,&nbsp;Jie Yan,&nbsp;Ying Guo,&nbsp;Ling Wang,&nbsp;Lijuan Fan","doi":"10.1016/j.scienta.2026.115260","DOIUrl":"10.1016/j.scienta.2026.115260","url":null,"abstract":"<div><div><em>Iris sanguinea</em> is an ornamental perennial whose floral antioxidant-associated phytochemicals remain poorly characterized. In this study, previously published broad-targeted metabolomic and transcriptomic datasets generated from flower-bud perianth tissues of five flower-color materials were reanalyzed and integrated with newly measured DPPH, ABTS, and FRAP activities and total flavonoid, total phenolic, and total proanthocyanidin contents obtained from the same biological sampling batch. The wild-type blue-purple-flowered material IS showed the strongest overall antioxidant capacity, which was more closely associated with total flavonoid and total phenolic contents than with total anthocyanin or proanthocyanidin contents. Correlation analysis and weighted gene co-expression network analysis jointly identified eight high-confidence antioxidant-associated metabolites, including five flavonoids. Targeted UPLC–MS/MS analysis using authentic standards further confirmed and quantified spinosin in <em>I. sanguinea</em> flowers and identified it as the most abundant quantified flavonoid in IS (2718.25 μg g ^− 1 DW), substantially exceeding vicenin-2 (469.72 μg g ^− 1 DW) and vitexin (223.90 μg g ^− 1 DW). Reanalysis of gene-expression profiles identified 13 candidate structural genes and 82 core candidate transcription factors associated with the five key antioxidant flavonoids. These findings characterize antioxidant-related phytochemical variation among <em>I. sanguinea</em> flower-color materials and provide candidate metabolites and genes for subsequent functional validation and antioxidant-oriented horticultural quality evaluation.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"368 ","pages":"Article 115260"},"PeriodicalIF":4.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149232216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal responses of two grapevine cultivars to water deficit and microbial inoculation: linking plant physiology, elemental composition, and soil microbiomes","authors":"Gabriella Vinci,&nbsp;Alberto Calderan,&nbsp;Francesco Flagiello,&nbsp;Arianna Lodovici,&nbsp;Maraike Probst,&nbsp;Christian Rinke,&nbsp;Marianna Fasoli,&nbsp;Laura Zanin,&nbsp;Paolo Sivilotti","doi":"10.1016/j.scienta.2026.115252","DOIUrl":"10.1016/j.scienta.2026.115252","url":null,"abstract":"<div><div>Water deficit impacts grapevine development, yield, and nutrient uptake. Beneficial microorganisms can promote plant growth and nutrient status and enhance tolerance to abiotic stresses. This study evaluated the combined effects of water deficit and microbial treatment on the physiological and nutritional status of two <em>Vitis vinifera</em> L. cultivars.</div><div>Two-year-old Cabernet Sauvignon and Grenache plants grafted on SO4 were cultivated in pots under semi-environmental conditions. Plants were treated with a commercial bacterial and fungal inoculum and subjected to water deficit for two consecutive years, in 2023 and 2024, respectively.</div><div>Water deficit reduced shoot growth in both years, with a reduction of approximately 40 % in both Cabernet Sauvignon and Grenache in 2024. The moderate water deficit in 2023 (33 % lysimeter evapotranspiration, ET_lys) had a mild effect on plant water status, while the more severe water deficit in 2024 (25 % ET_lys) reduced transpiration and stem water potential, with both cultivars reaching values below -1 MPa. Multielemental analyses revealed that the elemental composition was primarily affected by water regime, followed by microbial treatment: water deficit increased nutrient concentration in leaves and roots, while the effect of microbial inoculation on elemental composition was more pronounced in Grenache, especially under water deficit. Finally, the microbial community composition differed primarily between soil and rhizosphere compartments and water regime. Differential abundance analysis revealed a significant reduction in Glomeromycota under water deficit. The study contributes to optimizing water use and reducing the use of synthetic fertilizers for a more sustainable and efficient input management.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"368 ","pages":"Article 115252"},"PeriodicalIF":4.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149232219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of drought stress sensitivity of kiwifruit rootstocks and grafting combinations through integrated physiological and phenotyping analysis","authors":"Maria Calabritto,&nbsp;Alba N. Mininni,&nbsp;Angelo Petrozza,&nbsp;Stephan Summerer,&nbsp;Francesco Cellini,&nbsp;Roberto Di Biase,&nbsp;Rocco Sarli,&nbsp;Bartolomeo Dichio","doi":"10.1016/j.scienta.2026.115221","DOIUrl":"10.1016/j.scienta.2026.115221","url":null,"abstract":"<div><div>Kiwifruit has a high-water requirement and is sensitive to reduced water availability. Many kiwifruit growing areas are expected to face increasing water scarcity due to climate change. Although the effects of drought stress on kiwifruit have been widely studied, the sensitivity of different genotypes to drought remains poorly described. The present study evaluated the physiological and phenotypic drought responses of three kiwifruit rootstocks (‘Bounty71’, <em>Actinidia macrosperma</em>; ‘D1’ and ‘Hayward’, <em>Actinidia chinensis</em> var. <em>deliciosa</em>) and scion/rootstock combinations, in which a yellow-fleshed cultivar (‘Zesy002’, <em>A. chinensis</em> var. <em>chinensis</em>) was grafted on each rootstock.</div><div>A pot experiment was conducted using non-destructive RGB imaging combined with leaf gas exchange measurements. Potted vines were subjected to continuous well-watered conditions or to a mild drought stress cycle, imposed by progressively reducing pot water availability (up to 65% field capacity), followed by five days of full re-watering.</div><div>Based on physiological measurements, Hayward and D1 rootstocks were more affected by drought than Bounty71. Drought-induced physiological (reduced stomatal conductance and photosynthetic rate, increased intrinsic water use efficiency, and decreased instantaneous carboxylation efficiency) and phenotypic (changes in projected shoot area and leaf color) responses differed among genotypes, with Hayward identified as the most drought-sensitive. However, the complete recovery of both physiological and phenotypic parameters suggests the ability of all combinations to cope with short-term and mild drought.</div><div>The results support the use of phenotypic tools combined with leaf gas exchange measurements for a comprehensive screening of drought sensitivity in kiwifruit genotypes.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"368 ","pages":"Article 115221"},"PeriodicalIF":4.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149202217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HZP66 and ERF122 are involved in flavonoid metabolism of kiwifruit regulated by ethylene and 1-MCP","authors":"Hao Ni,&nbsp;Han Dai,&nbsp;Yi-hang Zhang,&nbsp;Zi-yi Wei,&nbsp;Yu-cheng Zhang,&nbsp;Hao-miao Ding,&nbsp;Wei Chen,&nbsp;Zhen-feng Yang,&nbsp;Wei Wu","doi":"10.1016/j.scienta.2026.115250","DOIUrl":"10.1016/j.scienta.2026.115250","url":null,"abstract":"<div><div>Flavonoids are the core nutritional components and key indicators for quality evaluation of kiwifruit. Ethylene and 1-methylcyclopropene (1-MCP) treatments, as common postharvest regulation technologies, have been proven to promote flavonoid accumulation, but their underlying molecular mechanisms remain unclear. To elucidate the transcriptional regulatory mechanism of flavonoid metabolism in postharvest kiwifruit, this study used ‘Hongyang’ kiwifruit as material, and established ethylene, 1-MCP and control groups. A systematic analysis was conducted by integrating physiological assays, transcriptome analysis, dual-luciferase assay and electrophoretic mobility shift assay (EMSA). A total of 285 differentially expressed genes were screened, and 10 potential transcription factors were identified. Among them, ERF122 and HZP66 could directly activate the promoters of <em>AcPAL1</em> and <em>AcPAL2</em> respectively, the key structural genes involved in flavonoid biosynthesis. These findings refine the molecular regulatory network of flavonoid metabolism in kiwifruit, and also provide theoretical support and molecular targets for kiwifruit breeding and postharvest quality regulation.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"368 ","pages":"Article 115250"},"PeriodicalIF":4.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149208997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of boron nutrition on yield and kernel quality of macadamia and optimization of boron fertilization","authors":"Yanyun Pang, Mengjiang Huang, Jingqi Xu, Xiang Zheng, Dan Li, Rui Shi, Peizhen Chen","doi":"10.1016/j.scienta.2026.115136","DOIUrl":"https://doi.org/10.1016/j.scienta.2026.115136","url":null,"abstract":"<ce:italic>Macadamia</ce:italic> is an economically important tree crop in Yunnan, China, where boron deficiency may constrain fruit set, yield, and kernel quality. This study integrated a field experiment with six-year-old ‘A4’ trees and a hydroponic experiment using ‘H2’ root-stock seedlings to evaluate boron responses across the soil-root-leaf-fruit continuum. Soil-applied Borax-Plus was tested at 20, 40, and 60 g plant<ce:sup loc=\"post\">–1</ce:sup>, while combined treatments received 20 g plant<ce:sup loc=\"post\">–1</ce:sup> soil-applied Borax-Plus combined with 0.1%, 0.3%, or 0.5% foliar Solubor. Boron application increased soil available B, whereas higher soil rates slightly reduced soil pH and exchangeable Ca. Hydroponic application of 0.5 mg <ce:small-caps>l</ce:small-caps><ce:sup loc=\"post\">–1</ce:sup> B promoted root development. In the field, boron altered leaf morphology, photosynthetic pigments, and mineral nutrient status in a dose- and trait-dependent manner, while several treatments improved yield and fruit development. Combined soil-foliar application also influenced fruit disease incidence and kernel nutritional quality. Membership function analysis identified 20 g plant<ce:sup loc=\"post\">–1</ce:sup> Borax-Plus combined with 0.1% Solubor (T4) as the best overall treatment. These findings indicate that appropriate boron supply can coordinate soil, root, leaf, and fruit responses and provide a practical basis for boron management in <ce:italic>Macadamia</ce:italic> grown on acidic red soils.","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"79 1","pages":"115136"},"PeriodicalIF":4.3,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exogenous putrescine enhances drought tolerance by improving growth and antioxidant responses in Petunia × hybrida cv. Grandiflora","authors":"Maryam Shahnavazi, Mahyar Gerami, Davood Akbari Nodehi, Fazl Shirdel Shahmiri, Mahboubeh Davoudi Pahnekolayi","doi":"10.1016/j.scienta.2026.115144","DOIUrl":"https://doi.org/10.1016/j.scienta.2026.115144","url":null,"abstract":"Polyamines (PAs) are small aliphatic compounds that function as important plant biostimulants, contributing to growth regulation, development, and responses to environmental stresses. Among these compounds, putrescine (Put) has gained considerable attention for its potential role in improving plant tolerance to abiotic stresses, especially drought conditions. This study investigated the effects of varying irrigation intervals and exogenous Put application on growth performance and antioxidant responses of <ce:italic>Petunia × hybrida</ce:italic> cv. Grandiflora. The experiment was conducted using a factorial completely randomized design with three replications, including four irrigation regimes (2, 4, 6, and 8-day intervals) and four Put concentrations (0, 0.5, 1.0, and 1.5 mM). Extended irrigation intervals negatively affected plant growth parameters and photosynthetic pigment levels, demonstrating the detrimental effects of water limitation. However, Put treatment mitigated drought-induced damage and improved several physiological traits. The highest soluble sugar accumulation and guaiacol peroxidase activity were recorded in plants subjected to an 8-day irrigation interval with 1.5 mM Put. Catalase activity was greatest under severe drought conditions without Put supplementation, while carotenoid content was lowest in plants treated with 0.5 mM Put under adequate irrigation. Altogether, the significant interaction between irrigation frequency and Put concentration on growth and biochemical characteristics indicates that Put application may enhance drought tolerance and support physiological stability in petunia under water-limited conditions.","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"36 1","pages":"115144"},"PeriodicalIF":4.3,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of NLR genes across eight Rubus genomes reveals conserved synteny and lineage-specific diversification","authors":"Ankit Pokhrel, Zhanao Deng","doi":"10.1016/j.scienta.2026.115124","DOIUrl":"https://doi.org/10.1016/j.scienta.2026.115124","url":null,"abstract":"Nucleotide-binding leucine-rich repeat (<ce:italic>NLR</ce:italic>) genes encode the largest family of plant immune receptors and play central roles in disease resistance. Despite the economic importance, no systematic genome-wide characterization of <ce:italic>NLR</ce:italic> genes has been conducted in raspberries. Here, we performed a comprehensive comparative analysis of <ce:italic>NLR</ce:italic> genes across eight raspberry (<ce:italic>Rubus)</ce:italic> species and identified 147 to 395 <ce:italic>NLR</ce:italic> genes per species. Complete <ce:italic>NLR</ce:italic> structures (CNL, TNL, and RNL) accounted for 68.2% of identified genes, with CNL and TNL being predominant. Chromosomal distribution analysis revealed conserved hotspots on chromosomes 2, 5, and 7, with RNL and TNL genes preferentially localized to chromosomes 1 and 2. Genome-wide synteny analysis identified 2798 <ce:italic>NLR</ce:italic> syntenic pairs, predominantly between members of the same subclass, indicating extensive evolutionary conservation across <ce:italic>Rubus</ce:italic>. Tandem duplication was the primary driver of <ce:italic>NLR</ce:italic> expansion in most species, while dispersed duplication occurred more in <ce:italic>R. idaeus, R. hirsutus</ce:italic>, and <ce:italic>R. occidentalis</ce:italic>. Gene family evolution analysis further revealed lineage-specific patterns of expansion and contraction, with significant <ce:italic>NLR</ce:italic> contractions in <ce:italic>R. occidentalis</ce:italic> and <ce:italic>R. chingii</ce:italic> and net expansions in <ce:italic>R. idaeus</ce:italic> and <ce:italic>R. sachalinensis</ce:italic>. Expression profiling showed that more <ce:italic>NLR</ce:italic> genes were expressed in leaves and young fruits than in mature fruit, and comparison of resistant (‘Latham’) and susceptible (‘Glen Moy’) raspberry cultivars following <ce:italic>Phytophthora rubi</ce:italic> infection revealed downregulated and upregulated <ce:italic>NLR</ce:italic>s for future functional studies. Together, these findings provide new insights into the organization, evolution, and expression of <ce:italic>NLR</ce:italic> genes in raspberries and establish a comparative genomic resource for investigating disease-resistance genes in raspberries and related species.","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"491 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148884252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}