Scientia Horticulturae最新文献

{"title":"Selecting superior genotypes to enhance yield and fruit quality in Australian passion fruit","authors":"Xinhang Sun ,&nbsp;Vivi Arief ,&nbsp;Paul Gauthier ,&nbsp;Pragya Dhakal Poudel ,&nbsp;Patrick Mason ,&nbsp;Rajeev Varshney ,&nbsp;Bruce Topp ,&nbsp;Mobashwer Alam","doi":"10.1016/j.scienta.2025.114411","DOIUrl":"10.1016/j.scienta.2025.114411","url":null,"abstract":"<div><div>Passion fruit (<em>Passiflora edulis</em>) holds significant economic value due to its distinct flavour, aroma, rich nutritional composition, and notable medicinal benefits. Despite its economic importance, the passion fruit industry is constrained by the limited availability of improved cultivars, which adversely affects yield, fruit quality, and profitability. Breeding efforts aimed at improving passion fruit are complex due to the polygenic nature of yield and quality traits, as well as the genetic correlations among them. This study evaluated nine agronomic traits (fruit weight and number, pulp weight and content, fruit length and diameter, soluble solids, skin thickness and yield) across 10 genotypes to estimate heritability and genetic correlations and to identify promising candidates for yield and quality improvement. Heritability estimates ranged from 0.58 for fruit number to 0.95 for pulp weight. Strong and positive genetic correlations were observed among traits related to fruit size and weight, ranging from 0.94 (fruit length–fruit diameter) to 0.97 (fruit weight–fruit diameter). Based on the predicted genetic values of nine fruit traits, different genotype rankings were obtained. The top 20 % of genotypes (PF102 and PF115) were identified using a selection index for fruit yield and soluble solids, achieving gains of 59.11 % and 6.68 %, respectively. Additionally, the study assessed weight loss and storage quality, revealing that PF101 had the longest shelf life, lasting 40 days. These findings provide valuable insights for selecting genotypes in passion fruit breeding programs aimed at improving yield, quality, and post-harvest performance.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114411"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158598","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":"Integrated transcriptomic and metabolomic analysis reveals flavonoid-mediated cold adaptation in rootstock ‘Totosga’","authors":"Zongyi Zhang ,&nbsp;Junli Sun ,&nbsp;Wenting Zhai ,&nbsp;Chunmei Zhu ,&nbsp;Zhiyu Liu ,&nbsp;Dongliang Zhang ,&nbsp;Anqi Xie ,&nbsp;Wenchao Shi ,&nbsp;Shujun Liu ,&nbsp;Jianrong Feng ,&nbsp;Baolong Zhao","doi":"10.1016/j.scienta.2025.114414","DOIUrl":"10.1016/j.scienta.2025.114414","url":null,"abstract":"<div><div>To investigate chilling injury mitigation in off-season solanaceousvegetable production, this study conducted physiological and multi-omics analyses on six rootstock cultivars—'Totosga' (TTS), 'Jingfeng 808′ (JF), 'Torubam' (TLB), 'Qiangli' (QL), 'Jinzuan No.1′ (JZ), and 'Weiershengen' (WS)—under low-temperature stress. Among these, the cold-tolerant genotype 'Totosga' exhibited superior photosynthetic integrity, membrane stability, and antioxidant enzyme activity. Comparative transcriptomic and metabolomic profiling identified 2517 differentially expressed genes (1015 upregulated; 1502 downregulated) and 2728 differential metabolites (1465 increased; 1263 decreased) under cold stress. Transcriptomic alterations predominantly affected photosynthesis-related pathways and calcium-mediated signal transduction, whereas metabolomic changes were concentrated in secondary metabolic processes. Integrative omics analysis revealed significant enrichment in flavonoid biosynthesis, identifying eight hub genes (e.g., <em>PAL2, CHS2, FLS</em>) and 16 key metabolites (e.g., isoliquiritigenin, calycosin) as regulatory components. Mechanistic investigations demonstrated that 'Totosga' enhances cold adaptation through coordinated flavonoid metabolic reprogramming, characterized by (1) flavanol biosynthesis suppression, (2) isoflavonoid pathway activation, and (3) glycosylation/hydroxylation modifications for metabolite stabilization. Therefore, these findings elucidate the molecular basis of rootstock cold adaptation and provide valuable genetic resources for developing stress-resilient solanaceous cultivars.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114414"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158600","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":"Corrigendum to “Fish manure as a potential feedstock for organic hydroponic nutrient solutions: The effect of fish feed composition and fertilizer amendment on the growth performance of lettuce” [Scientia Horticulturae, Volume 350, August 2025, 114309]","authors":"Anıl Axel Tellbüscher ,&nbsp;Radek Gebauer ,&nbsp;Martin Šeda ,&nbsp;Tobias Goldhammer ,&nbsp;Ondřej Nikl ,&nbsp;Koushik Roy ,&nbsp;Werner Kloas ,&nbsp;Jan Mráz","doi":"10.1016/j.scienta.2025.114361","DOIUrl":"10.1016/j.scienta.2025.114361","url":null,"abstract":"","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114361"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145267389","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":"Corrigendum to “Synergistic interaction in mixed pant growth promoting rhizobacteria consortium enhances biofilm formation and rhizosphere colonization to promote tomato (Solanum lycopersicum) growth” [Scientia Horticulturae, Volume 351, September 2025, 114383]","authors":"Dandan Wang ,&nbsp;Nan Zeng ,&nbsp;Jiahe Pang ,&nbsp;Chunji Li ,&nbsp;Dingcun Zhang ,&nbsp;Junliang Ge ,&nbsp;Die Zhao ,&nbsp;Jinmei Li ,&nbsp;Ruoyan Ran ,&nbsp;Xiang Gao ,&nbsp;Rutao Gai ,&nbsp;Ziqi Cao ,&nbsp;Xinyue Bi ,&nbsp;Ning Zhang ,&nbsp;Bingxue Li","doi":"10.1016/j.scienta.2025.114398","DOIUrl":"10.1016/j.scienta.2025.114398","url":null,"abstract":"","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114398"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145261745","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":"Synergistic interaction in mixed pant growth promoting rhizobacteria consortium enhances biofilm formation and rhizosphere colonization to promote tomato (Solanum lycopersicum) growth","authors":"Dandan Wang ,&nbsp;Nan Zeng ,&nbsp;Jiahe Pang ,&nbsp;Chunji Li ,&nbsp;Dingcun Zhang ,&nbsp;Junliang Ge ,&nbsp;Die Zhao ,&nbsp;Jinmei Li ,&nbsp;Ruoyan Ran ,&nbsp;Xiang Gao ,&nbsp;Rutao Gai ,&nbsp;Ziqi Cao ,&nbsp;Xinyue Bi ,&nbsp;Ning Zhang ,&nbsp;Bingxue Li","doi":"10.1016/j.scienta.2025.114383","DOIUrl":"10.1016/j.scienta.2025.114383","url":null,"abstract":"<div><div>While plant growth-promoting rhizobacteria (PGPR) consortia show enhanced benefits over single strains, the systematic design of functionally complementary synthetic communities and their synergistic mechanisms through biofilm-mediated root colonization remain poorly explored. This study aimed to screen and construct functionally complementary PGPR consortia, systematically evaluate their synergistic effects on biofilm formation in the tomato rhizosphere, and elucidate the underlying mechanisms regulating plant growth through enhanced root colonization and metabolic interactions. Three PGPR strains —<em>Pantoea ananatis</em> D1–28, <em>Bacillus aryabhattai</em> LAD, and <em>Burkholderia cepacia</em> 4–5—were selected for individual and combinatorial inoculation experiments. The results demonstrated that the D1–28/LAD combination exhibited significant synergistic advantages in both biofilm formation and plant growth promotion. This consortium markedly enhanced rhizosphere colonization and the synthesis of growth-promoting factors (such as N, P, siderophores, and IAA), thereby significantly improving tomato growth and up-regulating auxin biosynthesis and nitrogen transporter gene expression in roots. At an inoculum concentration of 10⁶ cfu·mL⁻¹, the fresh and dry weights of tomato shoots increased by 186.40 % and 278.57 %, respectively, while root fresh and dry weights increased by 327.62 % and 543.68 %. Plant height, root length, root surface area, and root volume increased by 117.19 %, 207.29 %, 531.36 %, and 525.69 %, respectively. This study provides theoretical insights into the role of microbial interactions in plant growth promotion and lays a technical foundation for the development of efficient and stable microbial biofertilizers, with promising applications in sustainable agriculture.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114383"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005334","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":"Stomatal Number and Size in Horticultural Tree Species: Seasonal and Varietal Variation to face different climatic conditions","authors":"Simona Pitardi ,&nbsp;Agostino Chiriacò ,&nbsp;Mario Pellegrino,&nbsp;Alessandro Pesole,&nbsp;Andrea Mazzeo,&nbsp;Giuseppe Ferrara","doi":"10.1016/j.scienta.2025.114389","DOIUrl":"10.1016/j.scienta.2025.114389","url":null,"abstract":"<div><div>Stomatal traits play a fundamental role in plant gas exchange, balancing CO₂ uptake and water loss to optimize photosynthesis and water use efficiency (WUE). This study investigated stomatal characteristics in six horticultural tree species (grape, pomegranate, pecan, carob, mulberry and lemon) grown either in the University of Bari repository or in commercial orchards. Stomatal density (SD) and size (length, width and area) (SS) in Southern Italy over two growing seasons (2019 and 2020) were analysed by coating both the abaxial and adaxial sides of the leaves (and leaflets in the case of pecan and carob) with clear nail polish which was then removed with a transparent adhesive tape. The results revealed significant interspecific and intraspecific variations, highlighting species-specific adaptive strategies of either varieties or clones. Grapevine exhibited the largest stomata area (average 488 μm²), with a wide inter-varietal variability, ranging from 284 μm² in Verdeca #19 to 726 μm² of Negramaro #12, whereas lemon and pomegranate had the smallest ones (120-192 μm²). The SD ranged from 165/mm² in grapevine to 712/mm² in lemon, with intermediate values in carob (214/mm²), mulberry (468/mm²), pecan (505/mm²), and pomegranate (593/mm²). Seasonal effects were species-dependent: pecan and grapevine consistently showed a reduction in SD, decreasing from 555 to 461 and from 178 to 152 stomata/mm² respectively, while grapevine also exhibited a decrease in SS, from 508 μm² in 2019 to 481 μm² in 2020. Conversely, pomegranate increased both SD (576 to 608 stomata/mm²) and SS (156 to 201 μm²) in 2020 with respect to 2019, suggesting a different adaptive strategy since the 2019 was a drier summer season with respect to 2020. These findings underscore the role of stomatal traits in species as a tool for a better resilience to climatic variability. The results also provide valuable insights into optimizing fruit tree selection for the different agricultural areas, with important implications for a sustainable agriculture in the context of climate change where water availability is a key factor.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114389"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047256","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":"Development of informative SNP markers for Capsicum species identification using phenotypic and genomic data","authors":"Nayoung Ro ,&nbsp;Mesfin Haile ,&nbsp;Hye-Myeong Yoon,&nbsp;Dong-Su Yu,&nbsp;Ho-Cheol Ko,&nbsp;Gyu-Taek Cho,&nbsp;Hee-Jong Woo,&nbsp;Pilmo Sung","doi":"10.1016/j.scienta.2025.114417","DOIUrl":"10.1016/j.scienta.2025.114417","url":null,"abstract":"<div><div>Accurate identification of <em>Capsicum</em> species is essential for effective germplasm conservation, breeding, and taxonomic research. However, traditional classification based on morphological traits is often complicated by overlapping features and interspecific hybridization. In this study, 316 <em>Capsicum</em> accessions representing five species were analyzed, revealing distinct, species-specific corolla color patterns. Although corolla color was initially considered for genome-wide association studies (GWAS), strong population structure caused by species differentiation confounded interpretation of trait-locus associations. Instead, phenotypic traits and genome-wide nucleotide variation were leveraged to identify a subset of informative single nucleotide polymorphisms (SNPs) useful for species discrimination. From an initial pool of 82 candidate SNPs, four were selected based on discriminatory power and allele distribution, while two additional markers were incorporated from broader variant data to enhance classification accuracy. The resulting six-marker panel demonstrated high performance in an independent validation set of 333 accessions, achieving 95.6 to 100 percent accuracy, sensitivity, and specificity across species. Phylogenetic clustering using the selected SNPs corresponded closely with known taxonomic relationships. Furthermore, the markers successfully classified 50 previously unassigned accessions. These SNPs provide a reliable and cost-effective molecular tool for <em>Capsicum</em> species identification, with practical applications in germplasm management at gene banks and in breeding programs.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114417"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158597","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":"Long-term performance of ‘Valencia’ sweet orange grafted onto nine rootstocks under two subtropical environments in Brazil: Effects of orchard age on growth, yield, fruit quality, and planting estimates","authors":"Deived Uilian de Carvalho ,&nbsp;Maria Aparecida Cruz-Bejatto ,&nbsp;Caroline Tardivo ,&nbsp;Inês Fumiko Ubukata Yada ,&nbsp;Rui Pereira Leite Junior ,&nbsp;Zuleide Hissano Tazima","doi":"10.1016/j.scienta.2025.114405","DOIUrl":"10.1016/j.scienta.2025.114405","url":null,"abstract":"&lt;div&gt;&lt;div&gt;‘Valencia’ sweet orange is a cornerstone of the global citrus industry, widely cultivated for both juice-processing and fresh fruit markets. Rootstock selection plays a critical role in determining long-term tree performance, yet comparative multi-environment studies spanning different orchard ages remain limited. This 17-year field trial (2000–2017) evaluated the horticultural performance of ‘Valencia’ trees grafted onto nine rootstocks – ‘Rangpur’ lime, ‘Swingle’ citrumelo, ‘Volkamer’ lemon, ‘Caipira DAC’ orange, ‘Cleopatra’ and ‘Sunki’ mandarins, ‘Trifoliate’ orange, ‘Carrizo’, and ‘Fepagro C-13′ citranges – at two contrasting locations in Paraná, Brazil (Londrina and Paranavaí). Trees were assessed over three orchard maturity phases: establishment (3–7 years old trees), full production (8–13 years), and aging (14–17 years; evaluated in one location only). Vegetative growth, yield performance, fruit quality attributes, and estimates of planting density, productivity, and total soluble solids (TSS) yield were evaluated over time. Data were analyzed using mixed-effects models for each orchard age, based on a randomized block design structured as a 9 × 2 factorial arrangement (rootstock × location), with six replicates and four trees per plot. ‘Cleopatra’ induced vigorous tree growth across the orchard’s lifespan, while ‘Trifoliate’ reduced tree size of ‘Valencia’, enhancing yield efficiency and supporting higher planting density. ‘Carrizo’, ‘Swingle’, and ‘Fepagro C-13′ induced superior cumulative yields and consistent productivity across orchard ages. In contrast, ‘Sunki’ and ‘Caipira DAC’ performed poorly, particularly under Paranavaí’s warm-dry climate, accentuating yield instability. ‘Volkamer’ showed a marked decline in yield during the aging phase in Londrina, highlighting its limitations for long-term cultivation. Rootstock × location interactions significantly influenced tree performance, with Londrina conditions favoring vegetative growth and delayed peak yield, while Paranavaí promoted early bearing and improved yield efficiency. Juice quality and technological indices were highest for fruit from trees on ‘Carrizo’, ‘Swingle’, and ‘Trifoliate’, revealing their suitability for juice-oriented production in subtropical regions. Overall, rootstock performance varied markedly with genotype and location, emphasizing the importance of matching rootstock selection to local conditions. ‘Carrizo’ and ‘Swingle’ provided superior long-term yields, while ‘Cleopatra’ favored vegetative growth. Conversely, ‘Volkamer’, ‘Sunki’, and ‘Caipira DAC’ rootstocks showed poor long-term yield performance, particularly in Paranavaí. Rootstock choice may also affect susceptibility to pests and diseases by influencing canopy size and shoot flushing pattern. This study provides robust long-term evidence to guide rootstock selection for sustainable cultivation of ‘Valencia’ orange, optimizing tree vigor, yield stability, and fruit quality across orchard a","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114405"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158599","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":"Integrated transcriptomic and metabolomic analyses reveal the mechanisms underlying flower colour change from green to white in tree peony","authors":"Lei Liu ,&nbsp;Xiaomei Peng ,&nbsp;Yingdan Yuan ,&nbsp;Qianqian Zhang ,&nbsp;Wenqing Jia ,&nbsp;Yanqing Wu ,&nbsp;Changmei Du ,&nbsp;Jianhua Yue","doi":"10.1016/j.scienta.2025.114393","DOIUrl":"10.1016/j.scienta.2025.114393","url":null,"abstract":"<div><div>Tree peonies with green flowers are rare, because they appear green at the initial blooming stage (CH) but turn white at the full blooming stage (SH). As limited information is available on the mechanisms underlying flower colour change in tree peonies, we performed transcriptomic and metabolomic analyses using the petals of <em>Paeonia suffruticosa</em> cultivar ‘Lvmuyinyu’ at the CH and SH stages. During flower development and blooming, flower colour changed from green to white, and the chlorophyll and anthocyanin content in the petals decreased sharply. The expression levels of chlorophyll synthesis genes and degradation genes were consistent with changes in the chlorophyll and anthocyanin levels. Upon non-target metabolomic analysis, a total of 86 differentially expressed metabolites related to flower colour change were identified. These metabolites were mainly involved in anthocyanin, secondary metabolite, flavonoid, and flavonol biosynthesis. We also identified 1318 differentially expressed genes (DEGs), of which 821 DEGs were upregulated and 497 were downregulated; and 12 differentially expressed MicroRNAs (DEMs), of which 2 were downregulated and 10 were upregulated. Functional analysis revealed that the targets of these DEGs and DEMs were primarily enriched in plant hormone signal transduction, starch and sucrose metabolism, endocytosis, and ether lipid metabolism. Integrated analysis of DEG and DEM profiles predicted nine miRNA–mRNA pairs, suggesting that these regulatory factors may be involved in flower colour change in tree peony. These findings are significant for the directional improvement of flower colour and the cultivation of new tree peony cultivars.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114393"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093833","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":"Genome-wide identification and comparative analyses of NLR gene families in Cucumis sativus and its related species","authors":"Shu-Yan Xie ,&nbsp;Min Wang ,&nbsp;Songguang Yang ,&nbsp;Qingwu Peng ,&nbsp;Wenrui Liu ,&nbsp;Jinqiang Yan ,&nbsp;Jinsen Cai ,&nbsp;Dasen Xie ,&nbsp;Biao Jiang ,&nbsp;Yu’e Lin ,&nbsp;Lin Chen","doi":"10.1016/j.scienta.2025.114382","DOIUrl":"10.1016/j.scienta.2025.114382","url":null,"abstract":"<div><div>Cucumber (<em>Cucumis sativus</em> L.) is a globally significant economic crop vulnerable to a multitude of diseases. Its two relatives, <em>C. sativus</em> var. <em>hardwickii</em> and <em>C. hystrix</em>, possess strong disease resistances and are valuable for cucumber resistance breeding<em>. Nucleotide binding site leucine-rich repeat</em> (<em>NLR</em>) genes are crucial in regulating resistance against phytopathogens and insects. However, their characteristics and resistance mechanisms in cucumber and its wild relatives remain poorly understood. Therefore, we conducted a comprehensive genome-wide analysis of the <em>NLR</em> gene families in cucumber, <em>C. sativus</em> var. <em>hardwickii</em>, and <em>C. hystrix</em> using bioinformatics tools. A total of 63, 67, and 89 <em>NLR</em> genes were identified in the three genomes and were categorized into <em>N, NL, TNL, CNL</em>, and <em>RNL</em> classes. More than 50 % of the <em>NLRs</em> contained only 1–3 exons, and most <em>cis-acting</em> regulatory elements in the <em>NLR</em> gene promoters were disease resistance related- and phytohormone-responsive. Cucumber had a closer synteny relationship with <em>C. sativus</em> var. <em>hardwickii</em> than with <em>C. hystrix</em>, and unique motifs were found in <em>C. hystrix</em> NLR proteins<em>.</em> Moreover, the expression patterns of the <em>NLR</em> genes in cucumber and <em>C. hystrix</em> demonstrated specific transciptional responses and genotype/tissue-dependent expression variations under biotic and abiotic stresses, suggesting distinct defense adaptation strategies. Additionally, this study revealed the diversity and molecular phylogenetic relationships of 830 <em>NLR</em> genes in 14 cucurbit species. Overall, these findings advance our understanding of plant defense mechanisms and broaden the <em>NLR</em> gene pool that could be utilized in cucumber resistance breeding.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"351 ","pages":"Article 114382"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145047257","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}