Search Results (476)

Rusty root rot of ginseng (Panax ginseng) caused by Ilyonectria spp. infection is a devastating soil-borne disease restricting the sustainable production of garden-cultivated ginseng (GCG) in Northeast China and causes severe yield and economic losses; GCG is far more susceptible to this pathogen than forest-cultivated ginseng (Lin-Xia-Shan-Shen, LXSS). Ginsenosides, the signature triterpenoid saponin defensive metabolites of ginseng, are characteristic dammarane-type triterpenoid defensive saponins represented by Re, Rg₂, Rb₁, Rd, and Rg₁. These compounds are continuously secreted into the rhizosphere and widely participate in plant–microbe interactions, yet their functional roles in mediating Ilyonectria infection remain poorly clarified. This study aimed to clarify how rhizospheric ginsenosides regulate the infection process of pathogenic Ilyonectria strains. Two pathogenic strains, Ilyonectria sp. SYM-1 and Ilyonectria sp. SYM-2, were found isolated from diseased GCG roots and verified as causal agents via morphological observation, molecular ITS identification and artificial inoculation infection experiments. Interestingly, the concentrations of five ginsenosides, Re, Rg₂, Rb₁, Rd, and Rg₁, in the rhizospheric soil of GCG with rusty root rot were significantly higher than those in the rhizospheric soil of healthy LXSS plants. In addition, the concentrations of ginsenosides in the LXSS rhizospheric soils decreased with increasing age of plants. Non-nutritive suspension co-culture assays showed that high concentrations of the ginsenosides Rg₁ and Rd significantly promoted spore germination of the strains SYM-1 and SYM-2. However, Rb₁ had a certain inhibitory effect on the growth of Ilyonectria sp. SYM-2. Host inoculation experiments further indicated that infection with either fungus significantly reduced the concentrations of ginsenosides produced in ginseng roots. These results demonstrate that the pathogenic fungi SYM-1 and SYM-2 of Ilyonectria can adapt to and utilize ginsenosides. Collectively, these findings prove that the two pathogenic Ilyonectria strains have evolved the capacity to adapt to and exploit rhizospheric ginsenosides to facilitate their infectivity. From an application perspective, reducing rhizospheric ginsenoside release may represent a promising theoretical strategy for ginseng cultivation and germplasm improvement, which warrants further verification by field or greenhouse experiments for validation. Full article

European plum (Prunus domestica L.) breeding for competitive production increasingly requires donor parents that combine attractive, market-oriented fruit quality with stable trait expression. This study evaluated a set of 36 phenotypically highly different cultivars from the germplasm collection maintained at the Research and Breeding Institute of Pomology Holovousy Ltd. (the Czech Republic). First, genetic analyses based on SSR marker data were performed to assess the diversity and kinship relationships within the selected collection of plum varieties. Several parentage combinations were successfully identified for cultivars with previously undocumented origins. Population-level analyses confirmed broad genetic diversity and separated the collection into four genetically distinct groups. Phenotypes were obtained on fruits ripened on trees from a non-irrigated orchard on myrobalan rootstock over five consecutive years (2019–2023). Pomological and related quality traits were recorded using nine-point UPOV-based rating scales together with instrumental measurements. The dataset included fruit size and shape descriptors, skin and flesh color, wax bloom, soluble solids (°Brix), firmness, bruising resistance, stone separability, and sensory attributes (flavor, aroma, juiciness, texture, and acidity). Interannual variability was quantified using coefficients of variation, and relationships among traits were explored using Pearson correlations. The results revealed broad phenotypic diversity among the individual varieties and also their genetic groups. Finally, phenotypes were associated with genotypes, and the most genetically determined traits were identified. Multi-year stability profiling supported the identification of candidate elite donor cultivars that combine favorable attributes for the fresh market and/or traits relevant to processing. These findings provide a practical pre-breeding shortlist and quantitative trait targets to support crossing design and selection under central European conditions. Full article

Potato is a globally important staple, but postharvest diseases such as dry rot, caused by Fusarium spp., threaten production and lead to major economic losses and food safety risks. Limited resistant cultivars highlight the need for phenotypic screening and integration with genomic tools to improve resistance and breeding efficiency. A total of 336 potato genotypes, including 295 commercial varieties and 41 breeding clones, were evaluated under post-harvest conditions following artificial inoculation. Tubers were inoculated with Fusarium sambucinum, and lesion penetration measured to classify susceptibility. Overall, this study provides one of the most comprehensive phenotypic evaluations of dry rot resistance in potato germplasm to date. While no variety was fully resistant, the identification of both moderately susceptible and highly susceptible cultivars offers valuable insights for breeding programs and contributes to the development of more resilient potato production and storage systems. In addition, this phenotypic screening can be integrated with genomic tools to accelerate breeding for improved resistance and postharvest performance. Full article

Thai aromatic coconut faces persistent breeding challenges arising from limited genetic diversity, complex trait trade-offs, and increasing climate vulnerability. These constraints highlight the need for comprehensive phenotypic characterization to improve understanding of trait variation and support the identification of key traits associated with yield and quality improvement. This study aimed to dissect trait architecture and associations in Thai aromatic coconut using an integrated multivariate and machine learning framework. Two populations of Thai aromatic coconut, Ratchaburi (RB) and Pak Phanang (PP), were evaluated through comprehensive phenotypic characterization. Thirty-seven morphological, reproductive, and soil-influenced traits were evaluated using analysis of variance, broad-sense heritability estimates, Pearson correlation analysis, principal component analysis (PCA), hierarchical clustering, and machine learning models. The PP population exhibited superior water yield, indicated by a strong positive correlation between water content and TWW, and larger fruit size, but showed a pronounced trade-off with kernel weight. High phenotypic variability was observed for key traits (CV > 39%), accompanied by moderate to high heritability estimates. Principal component analysis revealed that PC1, PC2, and PC3 explained 32.2%, 13.0%, and 11.1% of the total phenotypic variation, respectively, accounting for a cumulative 56.3% of the observed variation among accessions. Random Forest models achieved high predictive accuracy for total water weight (R² = 0.942), with water content (WC), fruit weight (FW), fruit diameter (FD), fruit length (FL), and hole spacing (HS) identified as the most influential predictors. Overall, the findings provide a non-destructive phenotypic framework for germplasm evaluation and trait-based selection in Thai aromatic coconut. Full article

Aphis craccivora is a major piercing–sucking insect pest in faba bean (Vicia faba L.) production and severely restricts yield and quality. To identify aphid-resistant genetic resources and clarify the key physiological and biochemical mechanisms underlying resistance and susceptibility, 937 faba bean germplasm accessions were evaluated using a stepwise strategy comprising natural field screening, precise net-house re-screening, laboratory validation based on aphid life-table parameters, and physiological and biochemical characterization of representative resistant and susceptible accessions. After final laboratory validation, three resistant and three susceptible accessions were selected and subjected to aphid feeding for 0 h (CK), 36 h, and 72 h. Eleven physiological and biochemical traits were dynamically analyzed, including the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and phenylalanine ammonia-lyase (PAL), as well as the contents of soluble protein, soluble sugar, free amino acids, tannins, total phenolics, flavonoids, and lignin. Three stable aphid-resistant accessions were ultimately identified. Laboratory life-table analysis showed that the net reproductive rate of aphids on resistant accessions was significantly lower than that on susceptible accessions, with R₀ decreasing from 53.63 to 25.08, representing a reduction of 53.2%. The intrinsic rate of increase decreased by 26.7%, whereas the mean generation time increased by 10.7%, confirming the reliability of the screening results. Physiological and biochemical analyses showed that aphid feeding induced significant and time-dependent increases in SOD, POD, CAT, and PAL activities and in tannin, total phenolic, flavonoid, and lignin contents in resistant accessions, whereas these defense responses were weak in susceptible accessions. In contrast, susceptible accessions showed abnormal accumulation of soluble sugars and free amino acids, whereas resistant accessions maintained these nutrients at low levels. Lignin exhibited both constitutive and inducible defense characteristics in resistant accessions and emerged as a prominent candidate indicator for aphid resistance in faba bean. This study establishes an effective technical pipeline for screening aphid-resistant faba bean germplasm and reveals a coordinated defense network involving antioxidant enzymes, phenylpropanoid metabolism, secondary metabolites, and physical barriers. These findings provide elite parental germplasm and theoretical support for aphid-resistance breeding in faba bean. Full article

Plot combine harvesters are specialized machines used in breeding trials, germplasm evaluation, and small-batch seed harvesting. Compared with conventional field combine harvesters, they have higher requirements for sample independence, grain integrity, seed purity, low residual grain, rapid plot switching, and plot-level data reliability. However, existing studies remain relatively fragmented, and many studies mainly focus on individual components, whereas analyses of whole-machine coordination, residual-grain control, crop adaptability, and data integration remain insufficient. This paper presents a structured review of the research progress in plot combine harvesters from an agricultural-engineering perspective, covering representative international and domestic models, headers, threshing and separation systems, cleaning systems, residual-seed removal devices, simulation methods, intelligent monitoring, and seed-quality sensing. Existing evidence indicates that plot combine harvesters are developing toward whole-machine low-residue design, coordinated threshing–cleaning–conveying optimization, standardized evaluation methods, sample identification, data traceability, and long-term field validation under continuous multi-plot harvesting conditions. Key challenges include coordinating small-batch intermittent material flow, controlling residual grain during frequent plot switching, balancing threshing completeness with seed protection, improving adaptability to different crops and breeding materials, and validating intelligent sensing technologies under field conditions. This paper provides an engineering reference for improving the mechanization, precision, and intelligence of breeding-trial harvesting equipment. Full article

Drought stress is a major constraint on alfalfa (Medicago sativa L.) production. Screening for drought tolerance at the seedling stage can accelerate the identification of resilient germplasm. In this study, six alfalfa cultivars were selected and subjected to drought stress at the seedling stage. Morphological traits (stem diameter, plant height, biomass, and root–shoot ratio) and oxidative/antioxidant indicators (malondialdehyde (MDA), superoxide (O₂•⁻), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), glutathione reductase (GR), and ascorbate peroxidase (APX) activity) were quantified in leaves and roots. Drought stress significantly reduced plant height (by up to 42.4% in ZL2) and biomass (by up to 30% in some cultivars), but increased the root–shoot ratio (by 50–166%). MDA and O₂•⁻ levels increased by 10–174% in leaves and 8–65% in roots across cultivars. Antioxidant enzyme activities rose markedly: SOD by 23–125% in leaves and 2–100% in roots; POD by 47–240% (leaves) and 38–166% (roots); CAT by 9–129% (leaves) and 30–227% (roots); GR by 35–107% (leaves) and 23–172% (roots); APX by 8–175% (leaves) and 3–89% (roots), indicating a coordinated leaf–root antioxidant defense. Transcriptome analysis of the tolerant cultivar ZM3 revealed 853 differentially expressed genes, which were enriched in pathways such as the non-homologous end-joining DNA repair pathway. Multivariate assessment of seedling-stage performance identified ZM3 and ZL2 as the most drought-tolerant cultivars. Collectively, these findings provide germplasm leads and empirical evidence for coordinated leaf–root antioxidant strategies in alfalfa, informing the selection and improvement of drought-tolerant cultivars. Full article

Apple (Malus domestica Borkh.) rootstocks play a key role in modern intensive orchard systems, where their accurate identification is essential for breeding, nursery production, and certification of planting material. This is particularly important in Kazakhstan, a recognized center of origin of cultivated apple, where local germplasm remains insufficiently characterized at the molecular level. In this study, we integrated simple sequence repeat (SSR) genotyping and morphological trait analysis to develop a reliable approach for the identification of clonal apple rootstocks cultivated in Kazakhstan. Five widely used rootstocks (Zhetysu 5, ARM-18, B-7-35, M9, and B9) were analyzed using 17 polymorphic SSR markers and 30 vegetative traits. SSR analysis revealed moderate genetic polymorphism (PIC = 0.28–0.54; He = 0.35–0.58) and enabled clear discrimination among all studied genotypes. Cluster analysis based on genetic distances grouped rootstocks according to their genetic similarity, reflecting their origin and differentiation. Morphological evaluation demonstrated significant phenotypic variability and identified correlations among key vegetative traits related to plant vigor and leaf development. The integration of molecular and morphological data allowed the development of comprehensive genotype profiles (“molecular–morphological passports”) for each rootstock, ensuring their reliable identification. The proposed approach provides a practical framework for the certification of planting material and the management of apple genetic resources in Kazakhstan. It can be applied to improve nursery systems, support breeding programs, and ensure the production of true-to-type planting material in modern horticulture. Full article

Pumpkin (Cucurbita spp.) is a globally significant vegetable crop known for its high nutritional value and remarkable phenotypic diversity. Yet, the surge in new cultivar releases has overwhelmed traditional morphological descriptors, creating critical gaps in variety purity control and breeders’ rights enforcement. Despite the established utility of SNP markers as the gold standard for genetic analysis, a dedicated high-resolution molecular database for modern pumpkin cultivars remains unavailable. To address this gap, we conducted whole-genome resequencing (WGS) on 94 representative pumpkin cultivars (spanning C. moschata, C. maxima, and C. pepo). Clean reads were mapped to the Cucurbita maxima reference genome. We employed a stringent pipeline to identify genomic variants and utilized STRUCTURE software, Principal Component Analysis (PCA), and Neighbor-Joining (NJ) trees to evaluate population stratification. Linkage disequilibrium (LD) decay and DNA fingerprinting barcodes were also developed. A total of 8,873,150 high-quality variants were identified, including 7,345,007 SNPs and 1,528,143 InDels, with an average SNP density of 21,281.50 SNPs/Mb. Population analysis consistently categorized the 94 cultivars into two primary subpopulations (G1 and G2). The first two PCs accounted for 74.06% of the total genetic variance. Further analysis revealed that G1 possessed a more complex genetic architecture and slower LD decay compared to G2, suggesting distinct selection histories. Finally, we screened for highly informative biallelic SNPs to construct a DNA fingerprinting database, enabling precise sample discrimination through unique chromatic barcodes. This study fills a critical gap in pumpkin genomics by establishing a high-density SNP database and a robust fingerprinting system. These resources provide a definitive tool for variety certification, seed purity testing, and the advancement of molecular-assisted breeding in pumpkin. Full article

Enormous genetic diversity exists in rice germplasm, including wild and weedy relatives, though they remain unexplored within in situ or ex situ collections. Characterisation and utilisation of the available biodiversity in plant breeding is essential for the detection of novel traits or genes for climate resilience. In this study, 97 rice genotypes, including 90 rice accessions belonging to various Oryza species and 7 check cultivars with an O. sativa background, were characterised for quantitative morphological characters following the guidelines based on distinctiveness, uniformity and stability (DUS) test by the Protection of Plant Varieties and Farmers’ Rights Authority (PPVFRA), India. Characterisation of the genotypes based on 39 important DUS morphological descriptors revealed polymorphism in 35 traits, confirming high morphological diversity among wild rice accessions and distinguishing and unique traits from other wild accessions for the utilisation in pre-breeding programmes. Genotypes such as WD5_6, WD10_4, and WD3_3 consistently expressed a favourable combination of broad and long leaves, extended panicle length, and well-branched panicles with higher panicle number. In addition, these genotypes showed purple pigmentation across multiple vegetative and reproductive organs, indicating stable and enhanced anthocyanin accumulation. Accessions WD10_4 and WD3_3 also represent valuable donors for panicle architecture and yield component enhancement, while genotypes such as WD17_15 and WD12_8 may serve as specific donors for panicle length and branching traits. Characterisation studies and detection of unique traits provide the empirical foundation for conservation decisions, taxonomic clarity, and pre-breeding applications. Interspecific crosses in the genetic background of elite cultivars with donor species viz., O. barthii, O. glaberrima and O. rufipogon were developed as pre-breeding materials for further crop improvement as well as for the identification of novel genes of agronomic importance. Full article

The Northwest soybean production region (covering Shanxi, Shaanxi, Gansu, Ningxia, Xinjiang, central and western Inner Mongolia and northern parts of Hebei) possesses vast cultivated land resources and advantageous light–temperature conditions, endowing soybean with substantial yield potential. In this study, two natural soybean populations originating from this region were used to systematically investigate the phenotypic variation in two important agronomic traits, plant height (PH) and main stem node number (NN). The results showed abundant genetic variation for both traits. Through genome-wide association analysis (GWAS) and employing a joint detection across multi-environments (control false positives), 5 SNPs significantly associated with PH and 18 SNPs significantly associated with NN were identified, among which four SNPs were detected associated with both traits. Candidate genes were further screened within the ±100 kb intervals flanking lead SNPs at association peaks. By integrating gene expression levels of different soybean tissues and their correlations with the phenotypes, two candidate genes associated with both PH and NN were determined. These findings provide a theoretical basis for the identification and utilization of soybean germplasm resources in Northwest China, and lay a solid foundation for breeding high-yield and high-quality soybean varieties through molecular breeding. Full article

High-density SNP chips have been demonstrated to be effective instruments for simultaneously genotyping large numbers of loci, thereby facilitating genome-scale analyses and advancing genomic selection (GS) in poultry and livestock. The meat-type duck, an economically valuable poultry species in China, has so far lacked precise and high-throughput genotyping systems, which has constrained the broader implementation of GS and genome-wide association analyses (GWASs) and consequently slowed genetic progress. In this study, we developed and validated a novel SNP array based on Genotyping-by-Targeted-Sequencing (GBTS) technology. The array comprises 40,875 SNP markers evenly distributed across 32 duck chromosomes. Using data generated from this array, genomic heritability estimates were obtained for six economic traits in a cultured duck population (n = 400), with values of 0.61 ± 0.09, 0.69 ± 0.08, 0.80 ± 0.08, 0.11 ± 0.09, 0.14 ± 0.08, 0.31 ± 0.09 for age at first egg (AFE), egg production number at 38 weeks (EN38w), egg weight at 38 weeks (EW38w), body weight at 35 days (BW35d), shank length at 35 days (SL35d) and thickness of breast muscle at 40 days (TB40d). A total of 163 significant SNPs associated with economic traits were identified through GWAS, and annotation revealed 28 candidate genes related to five of these traits. Moreover, the prediction accuracy of ssGBLUP for AFE, EN38w, EW38w, BW35d, SL35d, and TB40d reached 0.55 ± 0.16, 0.56 ± 0.12, 0.57 ± 0.08, 0.25 ± 0.19, 0.31 ± 0.19, and 0.47 ± 0.17, respectively—values that exceeded those obtained using BLUP. Population genomic analyses of 400 ducks demonstrated that this SNP array provides improved genomic prediction accuracy over pedigree-based BLUP for most analyzed traits. Overall, the developed SNP array provides a robust, high-efficiency, and cost-effective genotyping platform that will accelerate genetic progress and promote the sustainable development of the meat-type duck industry. Full article

Background: The phylogenetic placement and chloroplast-inferred maternal relationships of commercial pluot cultivars remain unclear, largely because plastome-level evidence is limited for assessing their affinities with Prunus salicina and Prunus ussuriensis. Although chloroplast genome structure has been well characterized in angiosperms and in several Prunus species, complete plastome resources and comparative genomic evidence for commercial pluot cultivars remain scarce. Methods: Here, we assembled the complete chloroplast genomes of six commercial pluot cultivars and performed comparative genomic, phylogenomic, and divergence time analyses using representative Prunus species. Results: All genomes exhibited the typical circular quadripartite structure and ranged from 157,865 to 158,138 bp in length. Genome organization, GC content, and gene content were highly conserved, whereas the IR regions showed an elevated GC content of approximately 42.6%, owing to rRNA gene enrichment. IR boundary comparison revealed contraction at the IRb/SSC boundary in P. ussuriensis, while pluot cultivars were structurally more similar to P. salicina. In total, 370 SSR loci and four hypervariable regions, namely rpoB–trnC-GCA, petN–psbM, trnV-UAC–trnM-CAU, and trnP-UGG–psaJ, were identified as candidate molecular markers for Prunus germplasm identification and genetic analysis. Phylogenomic analysis resolved four major clades within Prunus and showed that ‘Flavor King’, ‘Flavor Supreme’, and ‘Flavor Queen’ grouped with P. ussuriensis, whereas ‘Flavorosa’, ‘Dinosaur Egg’, and ‘Flavorich’ grouped with P. salicina. Conclusion: Overall, this study provides the first comparative plastome analysis of six commercial pluot cultivars and offers chloroplast-level evidence for their maternal affinities within Prunus, together with useful marker resources for cultivar identification and germplasm evaluation. Full article

Accurate characterization of closely related Ilex taxa is essential for the conservation, documentation, and utilization of plant genetic resources. In this study, five Ilex taxa from eastern China (Ilex rotunda Thunb., Ilex chinensis, Ilex cornuta Lindl. & Paxt., Ilex cornuta ‘Fortunei’, and Ilex latifolia Thunb.) were evaluated using an integrated framework combining fruit morphometric traits, CIELAB color parameters, and electronic-nose (E-nose) volatile fingerprints. Fruit transverse diameter, longitudinal diameter, single-fruit weight, fruit shape index, and peel color traits (L*, a*, b*, and chroma, C*) differed significantly among taxa (one-way ANOVA, all p < 0.001). I. cornuta produced the largest and heaviest fruits, I. chinensis showed the most elongated fruit shape, and I. rotunda exhibited the highest redness and chroma values. Chemometric analyses of E-nose responses further improved taxon discrimination and revealed clear divergence in volatile-response patterns. Trait-space relationships were broadly consistent with the preset phylogenetic framework, with I. rotunda showing the greatest divergence and I. cornuta and I. cornuta ‘Fortunei’ showing the closest similarity. These findings indicate that integrated fruit phenotyping and rapid volatile profiling provide a practical approach for Ilex germplasm identification, comparative evaluation, and resource documentation, with potential value for conservation planning and horticultural utilization. Full article

Cotton is one of the world’s important cash crops and occupies a significant position in agricultural production and the national economy. However, insect pests severely affect the growth, yield and quality of cotton. To ensure high and stable cotton yields, the cultivation of insect-resistant transgenic cotton via transgenic technology can not only effectively reduce the impact of chemical pesticides on crops but also exert excellent control effects against pests such as cotton bollworms. In this study, the plant expression vector pC2300-VEC harboring the target genes epsps, cry1Ac and vip3A was introduced into the genome of the recipient cotton cultivar CCRI 24 via Agrobacterium-mediated transformation. The obtained transgenic cotton plants were subjected to the identification of target genes and target traits, and the insect-resistant transgenic cotton line BrsC35 was ultimately obtained. PacBio sequencing combined with conventional molecular characterization methods was used to analyze its insertion site, copy number and other characteristics, providing a new germplasm for insect-resistant transgenic cotton. Full article