Search Results (1,774)

Stem blight, caused by Phomopsis asparagi, is the most serious disease affecting the cultivation of asparagus (Asparagus officinalis L.) in the warm regions of East and Southeast Asia, including Japan. Although Asparagus kiusianus, a wild species endemic to Japan, shows strong resistance to this disease and is cross-compatible with cultivated asparagus, the genetic basis of this resistance remains unclear. In this study, we used BC₁ populations from interspecific crosses between A. officinalis and A. kiusianus to dissect stem blight resistance inheritance and identify markers suitable for marker-assisted selection. Disease severity was evaluated using P. asparagi inoculation, and RAD sequencing was used to construct a linkage map and perform QTL analysis. Segregation patterns suggested that resistance was controlled by major genes and polygenic factors which depended on the cross combination. A major QTL was detected on chromosome 1 and SNP_PRK showed a significant association (LOD > 3). A dCAPS marker derived from SNP_PRK was associated with resistance, with approximately 80% of individuals carrying the associated genotype showing resistance. CAPS marker PR1 distinguished the same genotype classes and produced results consistent with those obtained using PRK in the evaluated materials. PR1 may therefore facilitate resistant individual selection in breeding programs. Full article

Red-flowered strawberries possess both floral and foliage ornamental characteristics, making them highly promising as landscape groundcovers and potted ornamental plants. To establish a standardized ornamental evaluation system and screen for superior germplasm, this study used 18 strawberry accessions from China and abroad as experimental materials. Twelve core ornamental indicators were selected across three dimensions: flowering period, morphological traits, and disease resistance. The Analytic Hierarchy Process (AHP) was employed to construct a multi-level ornamental value evaluation model. The results indicate the following weight rankings across the constraint layers: morphological traits (60.66%) > flowering period (27.71%) > disease resistance (11.63%). Among these, flower color (21.96%), plant flowering period (16.41%), corolla diameter (15.69%), and single-flower flowering duration (11.30%) were the core indicators determining ornamental value. The comprehensive score rankings showed that the accessions ‘140’, ‘Pink Panda’, ‘Summer Breeze-Cherry’, and ‘Summer Breeze-Rose’ exhibited the best overall ornamental performance. These accessions feature vibrant flower colors, a prolonged flowering period, abundant blooms, and good disease resistance. ‘Frisan’ and ‘246’ had the lowest composite scores, exhibiting significant shortcomings in ornamental traits. The AHP-based evaluation system established in this study provides a quantitative tool for ornamental trait assessment in red-flowered strawberries. The four elite accessions identifed using this system—‘140’, ‘Pink Panda’, ‘Summer Breeze-Cherry’, and ‘Summer Breeze-Rose’—can serve as priority candidates for protected landscape applications and container gardening in subtropical southern China. Full article

MicroRNAs play crucial roles in plant growth, development, and disease resistance. Transcriptome screening previously identified three late blight-responsive miRNAs (sly-miR172a, sly-miR156e, and sly-miR395a) in tomato whose biological functions remain uncharacterized. Here, CRISPR/Cas9 editing vectors targeting each miRNA were transformed into the tomato cultivar ‘Micro-Tom’. sly-miR395a showed the highest T0 editing efficiency (77.78%), followed by sly-miR172a (48.00%) and sly-miR156e (40.74%). T1 segregation ratios were approximately 1:12.3, 1:1.83, and 1:13 for the three targets. Stable T2 homozygous lines were obtained, and qRT-PCR confirmed average mature miRNA inhibition rates of 78.00%, 79.50%, and 87.50%. To assess editing specificity, genome-wide off-target prediction and Sanger sequencing of top high-risk loci were performed; no unintended indels were detected, confirming sgRNA specificity. Agronomic phenotyping revealed divergent developmental phenotypes: sly-miR172a knockout caused dwarfism, leaf senescence and reduced flower number; sly-miR156e mutants exhibited taller plants and increased floral production; sly-miR395a mutants had normal vegetative growth but fewer flowers. Resistance assays demonstrated distinct responses to Phytophthora infestans. Loss of sly-miR172a increased pathogen biomass by 1.6–2.3-fold and aggravated susceptibility, likely by de-repressing AP2/TOE to disrupt oxidative homeostasis. In contrast, both sly-miR156e and sly-miR395a negatively regulate late blight resistance. This could be because sly-miR156e knockout relieved the repression of SPL transcription factors, significantly restricting pathogen proliferation and lesion formation, and notably broke the canonical plant growth–defense trade-off to achieve simultaneous improvement of agronomic traits and disease resistance. sly-miR395a knockout enhanced tomato immunity potentially by activating sulfur metabolism-related pathways to accumulate defensive metabolites, with negligible adverse effects on vegetative growth. Nevertheless, this study has several limitations: the proposed regulatory cascades, including miRNA–AP2, miRNA–SPL, and miRNA–sulfur metabolism modules remain hypothetical without direct molecular validation of target interactions. Collectively, this study genetically validates that sly-miR172a, sly-miR156e, and sly-miR395a exert divergent functions in regulating tomato growth and immunity against late blight, providing valuable germplasm and gene resources for tomato disease-resistance breeding. Full article

Fusarium ear rot (FER), caused by Fusarium verticillioides (F. verticillioides), is a major disease of maize that reduces grain yield and quality globally. However, few major loci for FER have been verified and cloned. Resistance to FER is a quantitative trait influenced by environmental conditions, and maize genotypes completely resistant to the pathogen remain unknown. To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred line (RIL) population consisting of 257 progenies was developed by crossing the resistant line BT with the susceptible line Xi502. This population was genotyped using a set of 6807 high-density single nucleotide polymorphism (SNP) markers developed in this study. As a result, a total of five QTLs were identified by linkage mapping across three years, located on five chromosomes, and explaining 4.38–13.13% of the phenotypic variation. Among these was a major QTL, qFER5-2. Located on chromosome 5 within the interval 185568562–185574073, qFER5-2 explained 13.13% of the total phenotypic variance. The two candidate genes within qFER5-2 exhibited distinct expression profiles between the BT and Xi502 inbred lines, suggesting their potential association with FER resistance. Collectively, these findings provide candidate genetic resources for further investigation and offer potentially useful materials for maize disease resistance breeding. Full article

Clostridium perfringens is a major livestock pathogen responsible for histotoxic diseases and intestinal infections, posing serious threats to public health and the poultry and breeding industry. Overreliance on antibiotics has driven the emergence of drug-resistant strains and disruption of gut microbiota homeostasis, underscoring the urgent need for alternative control strategies. In this study, a lytic phage designated vB_CppII_Hohhot was isolated from wastewater samples collected from large-scale dairy farms in Inner Mongolia. The optimal multiplicity of infection was determined to be 0.1. pH stability was assessed. The phage was found to remain stable across pH 3 to 11, but no viable phage was detected at pH 12 (detection limit: <1 PFU/mL). Temperature adaptability was also assessed. Peak titers were achieved between 37°C and 40°C, and the titer was observed to fall below the detection limit at temperatures above 45°C. At a constant temperature of 37 °C, the phage rapidly reached the plateau phase within 40 min, with bacterial counts significantly reduced by 14 h. Whole-genome sequencing revealed that the phage genome consisted of 76 open reading frames, with no detectable antibiotic resistance or virulence genes; an endolysin gene potentially responsible for its lytic activity was also identified. In a prophylactic mouse model, phage administration significantly reduced pathological damage. Collectively, these findings provide a newly isolated candidate agent and a theoretical basis for the prophylactic application of phages against C. perfringens-associated infections. Full article

Background: Local goat resources have unique meat quality and phenotypic advantages over cultivated breeds. Clarifying breed-specific metabolic differences in meat helps understand meat quality formation and resource utilization. Methods: the study used ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) technology to perform untargeted metabolomic analysis on the longissimus dorsi meat of Beichuan White goats (BCWG) and Tianfu goats (TMG). Results: A total of 452 differential metabolites were identified between the two breeds, including 100 lipids and lipid-like molecules, 74 organic acids and their derivatives, 12 nucleosides, nucleotides, and analogues, 204 organic compounds, and 62 unclassified metabolites. Among them, 132 metabolites exhibited higher abundance in Beichuan White goats and 320 metabolites showed significantly higher abundance in Tianfu goats. Metabolomic profiling revealed that differential metabolites of lipids and amino acids (e.g., valine and glutamate) might be correlated with interbreed disparities in meat sensory quality and flavor, as indicated by metabolomic profiling. BCWG displayed relatively higher abundances of nucleoside and nucleotide metabolites, which might hint at a possible link to variations in disease-resistance capacity. Among the 12 nucleoside and nucleotide differential metabolites, UDP-N-acetylglucosamine, 1-methyllinosine, 1-methylguanosine, 3-methylcytidine, and N-(2-Furanylmethyl) adenosine could serve as candidate molecular indicators for studying immune-related traits in goats. Conclusions: The study clarifies the breed-specific metabolic characteristics of the longissimus dorsi meat in BCWG and TMG at the metabolite level, provides novel molecular markers for chevon quality evaluation and immune trait selection, and lays a theoretical foundation for the rational development and utilization of local goat resources and improvement of cultivated meat goat breeds. Full article

Background: Rice breeding requires faster development of high-yielding, climate-resilient, resource-efficient, and high-quality cultivars for production systems exposed to environmental variability and increasing input constraints. Genomic selection offers an opportunity to predict breeding value before extensive field evaluation, although its effectiveness depends on the integration of genomic, phenotypic, and environmental information. Methods: This narrative review critically examines recent advances in genomic selection for rice and its integration with high-throughput genotyping, high-throughput phenotyping, machine learning, multi-environment prediction, and speed breeding. Results: Genome-wide marker data can support early ranking of breeding materials for grain yield, grain quality, disease resistance, drought tolerance, salinity tolerance, and nutrient-use efficiency. Prediction performance is influenced by trait architecture, marker density, training-population size, genetic relatedness between training and candidate populations, phenotypic data quality, and genotype-by-environment interaction. Red-green-blue, multispectral, hyperspectral, thermal, and light detection and ranging platforms can generate temporal traits associated with plant architecture, biomass, water status, nutrient status, and stress responses, which may improve prediction under suitable population and validation designs. Speed-breeding systems shorten generation intervals and facilitate rapid advancement, recurrent selection, and recycling of superior parental lines. Conclusions: Integrated breeding pipelines that combine genomic prediction, high-throughput phenotyping, environmental data, and speed breeding can improve selection efficiency and shorten rice improvement cycles. Wider adoption will require affordable technology platforms, standardized data systems, multi-environment validation, breeder capacity development, and collaborative data-sharing frameworks for smart and greener agriculture. Full article

Background: This study aimed to investigate the molecular mechanisms underlying the response of Codonopsis pilosula roots to Fusarium oxysporum infection, which causes root rot and significant economic losses, and to provide a theoretical basis for breeding resistant varieties and developing effective control strategies. Methods: Root samples of C. pilosula were inoculated with F. oxysporum and harvested across five distinct intervals (0, 6, 24, 72, and 120 h after inoculation). Transcriptome sequencing was performed on 15 samples, generating 171.65 GB of clean data. De novo assembly was used to construct unigenes, followed by functional annotation and differential expression analysis. In addition, CpMAPK9 was transiently overexpressed in C. pilosula leaves to evaluate its role in jasmonic acid (JA) biosynthesis and disease resistance. Results: A total of 94,896 unigenes were obtained. Functional analysis showed that genes involved in hormone signal transduction, the MAPK signaling pathway, and plant–pathogen interactions were consistently activated in response to infection. Among the MAPK gene family, CpMAPK9 showed significant expression changes. Transient overexpression of CpMAPK9 significantly increased JA accumulation, indicating that CpMAPK9 positively regulates JA biosynthesis and may enhance resistance to root rot. Conclusions: In conclusion, our findings indicate that CpMAPK9 actively modulates JA-mediated defense pathways in C. pilosula during F. oxysporum invasion. Our findings shed light on the intricate molecular networks that drive disease defense, offering valuable theoretical insights to guide subsequent crop improvement initiatives. Full article

Potato early blight is a fungal disease caused by Alternaria solani that seriously affects potato production. Catalase (CAT), an important antioxidant enzyme in plants, regulates the basal immune response to necrotrophic pathogens by decomposing hydrogen peroxide (H₂O₂); however, its role in potato early blight remains unclear. The results revealed that using a H₂O₂ biosensor for transient overexpression in Nicotiana benthamiana, we found that A. solani infection significantly induced sustained H₂O₂ accumulation in tobacco leaves. Exogenous application of H₂O₂ to potato leaves followed by inoculation with A. solani showed that elevated H₂O₂ levels promoted infection by the pathogen. StCAT1 expression was upregulated upon A. solani infection. Silencing StCAT1 in potato reduced antioxidant enzyme activities (SOD, PAL, CAT) and disease resistance, accompanied by elevated H₂O₂ accumulation. Overexpression of StCAT1 enhanced antioxidant enzyme activities and disease resistance while decreasing H₂O₂ levels. Additionally, StABI5 was identified as an upstream transcription factor that activates StCAT1 expression, and silencing StABI5 compromised potato resistance to early blight. In conclusion, this study confirms that StCAT1 acts as a positive regulatory factor and mediates potato resistance to early blight through the StABI5-StCAT1 signaling pathway, providing scientific basis and genetic resources for disease-resistant breeding. Full article

Clubroot, caused by the obligate biotrophic protist Plasmodiophora brassicae (P. brassicae), is a destructive soil-borne disease that severely threatens the production of radish (Raphanus sativus L.). Although chitinases are known to execute critical defense functions by degrading pathogen chitin, a comprehensive genome-wide characterization of the radish chitinase (RsChi) gene family and its specific role in clubroot resistance remains lacking. Here, we systematically identified 24 RsChi genes in the radish genome, characterizing their chromosomal distribution, structural organization, and promoter regulatory networks. These genes are unevenly distributed across seven chromosomes and cluster into four subfamilies, with tandem duplication driving family expansion, particularly on Chromosome 3. Promoter analysis revealed a significant enrichment of jasmonic acid- and abscisic acid-responsive cis-elements, implicating RsChi genes in hormone-mediated defense signaling. Using qRT-PCR to profile expression dynamics during P. brassicae infection across contrasting radish lines, we identified strong genotype- and stage-specific transcriptional responses. Notably, TRs0x1c000780 remained transcriptionally silent prior to infection but was specifically induced over 10-fold in the resistant line at 28 days post-inoculation. This infection-triggered induction positions TRs0x1c000780 as a promising candidate defense gene. Together, these findings provide structural and functional insights into the RsChi family and highlight candidate targets for breeding clubroot-resistant radish cultivars. Full article

Mastitis remains the most economically damaging disease in the global dairy industry, and conventional genetic selection based on somatic cell score (SCS) has produced only limited gains in resistance. Epigenetic mechanisms—mitotically heritable yet environmentally responsive and largely reversible modifications that regulate gene expression without altering the DNA sequence—are now emerging as a complementary layer of biological information that can sharpen the prediction of disease susceptibility. This review summarizes current evidence on three classes of epigenetic markers associated with bovine mastitis resistance: DNA methylation, non-coding RNAs (with emphasis on microRNAs, long non-coding RNAs, circular RNAs, and small nucleolar RNAs), and histone modifications, alongside the increasingly important epitranscriptomic layer of N6-methyladenosine (m6A) RNA modification. Particular attention is given to differentially methylated regions and discriminant methylation haplotype blocks in immune-related genes, circulating and milk-derived non-coding RNA biomarkers, m6A-mediated regulation of inflammatory transcripts, and histone-mark dynamics in mammary epithelial cells challenged with Staphylococcus aureus and Escherichia coli. We conclude with current limitations and perspectives on translating these markers into selection tools and therapeutic targets. Across all marker classes, current evidence remains constrained by small cohort sizes, breed-specific study designs, a scarcity of longitudinal and multi-generational data, and limited functional validation, so most candidate markers are still at the discovery stage and require cautious interpretation before deployment. Full article

Fusarium wilt, caused by Fusarium oxysporum f. sp. melonis (FOM), is a main disease of melon (Cucumis melo L.). FOM 1.2 is the most widespread and detrimental variant of FOM, causing substantial economic losses under severe disease conditions. Current information suggests that resistance to race 1.2 (FOM 1.2) is controlled by multiple recessive genes and is strongly influenced by the environment. Therefore, identifying genetic polymorphisms within diverse melon populations is essential to elucidate the loci and putative candidate genes associated with resistance. The objective of this investigation was to identify single-nucleotide polymorphism (SNP) and structural variant (SV) markers associated with FOM 1.2 resistance utilizing a panel of 160 genotypes through a genome-wide association study (GWAS). Phenotypic evaluation was performed two weeks after sowing, at the first-true-leaf stage, on 2400 individual plants inoculated by the root dip method with a concentration of about 10⁶ spores/mL. Biochemical and disease-related traits, including area under disease progress curve (AUDPC), disease severity index (DSI), standardized AUDPC (SAUDPC), latent period (LP), catalase, peroxidase activity, and ascorbate peroxidase activity were measured 35 days after inoculation. PCA identified eighty-three individual melon plants with a broad range of disease-response variation. Genotyping-by-sequencing (GBS) was conducted on these plants, resulting in the identification of 737,435 SNPs and 75,133 SVs. Evaluation of the population structure outlined four genetic groups, including one associated with germplasm highly resistant to FOM 1.2. We used SNP data to describe linkage disequilibrium (LD), which was estimated to decay at 14 kb, on average. A GWAS was performed using the Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK) method, which revealed nine SNPs significantly associated with several disease indices, namely ascorbate peroxidase activity, AUDPC, catalase, peroxidase activity, rAUDPC, and SAUDPC. Also, eight SVs were associated with AUDPC and relative area under disease progress curve (rAUDPC), including translocation and deletion types. In addition, GWAS using the fixed and random model circulating probability unification (FarmCPU) method unveiled thirteen SVs associated with rAUDPC, peroxidase activity and ascorbate peroxidase activity, including translocation and inversion types. According to the performed models of GWAS, several significant SNPs and SVs, associated with putative candidate genes, including multidrug resistance-associated protein 6 (MRP6), LOB domain-containing protein 15 (LBD15), phosphomannomutase, and NADH-ubiquinone oxidoreductase B8 subunit, which may be involved in FOM 1.2 resistance. However, these findings represent a preliminary genome-wide survey and require further validation using high-coverage or long-read sequencing approaches. The results provide remarkable insights into the genetic control of FOM 1.2 resistance and valuable information for the implementation of the putative molecular markers identified in this study in melon breeding programs. Full article

Porcine reproductive and respiratory syndrome (PRRS), caused by PRRSV, causes substantial economic losses in the swine industry. Because viral variability and host genetic complexity limit conventional control, identifying host genetic factors associated with PRRS resistance through genomic approaches is important for disease-resistant breeding. In this study, 699 pigs were immunized with a PRRSV vaccine, 135 were selected for PRRSV infection experiments, and 133 were retained for whole-genome resequencing after two-stage phenotypic screening based on post-immunization and post-infection profiles. Genome-wide selection-signal analysis identified 12 highly differentiated regions (F_st > 0.15), annotated to 11 candidate genes: NFXL1, NIPAL1, CHIC2, LOC100623351, LOC100513671, LOC100513484, CENPC, STAP1, UBA6, GNRHR, and LOC100512727. The original exploratory GWAS identified candidate association signals, including signals annotated to PYGM, NFXL1, KIAA1324L, and FLNC; after PC1/PC2 adjustment, NFXL1 retained exploratory support, and additional exploratory signals were observed. Public PRRSV-related transcriptomic datasets provided additional expression-level evidence, with NIPAL1 and PYGM showing increased expression in PRRSV-infected porcine alveolar macrophages. Functional enrichment and variant-level analyses supported the biological relevance of the prioritized candidate gene set, particularly the chromosome 8 NFXL1 region, where the A-C-G haplotype was more frequent in resistant pigs. These findings provide useful genetic clues for further validation and PRRS resistance breeding. Full article

Kazakhstan ruminant genomics is expanding through targeted diagnostic testing, SNP-array studies, whole-genome sequencing, runs of homozygosity, candidate-gene analyses, transcriptomic studies and pathogen molecular diagnostics. However, these evidence types differ substantially in their relevance for breeding decisions. This structured narrative review evaluates molecular evidence for inherited disorders, deleterious alleles, disease-resistance loci, reproductive genes and genomic-health indicators in Kazakhstan cattle, sheep and goats. We define actionable evidence as evidence that can directly inform breeding management because it involves a validated pathogenic variant, risk variant or fertility haplotype detected or excluded in breeding-relevant animals or germplasm. Under this definition, cattle currently provide the strongest immediately actionable evidence, mainly because targeted studies have screened validated defects and fertility-related loci in artificial-insemination bulls, imported germplasm or breed-relevant populations. Evidence includes Kazakhstan-associated screening for BLAD (Bovine leukocyte adhesion deficiency), DUMPS (Deficiency of uridine monophosphate synthase), hypotrichosis, OH1-associated achromatopsia, fertility haplotypes and several beef- or dairy-breed recessive defects. In sheep, evidence is broader but less directly actionable, consisting mainly of prion protein gene preparedness, MHC (Major histocompatibility complex)-related immune hypotheses, reproductive candidate loci, runs of homozygosity, genome wide associated data and pathogen-exposure context. In goats, current evidence is mostly population-genomic and adaptation-oriented, while hereditary-disease surveillance and phenotype-linked resistance studies remain sparse. We propose an author-defined staged genomic-health framework that separates validated carrier-screening evidence from candidate genomic signals and international evidence requiring local validation. Priority actions include carrier-aware management of high-impact cattle germplasm, representative prion protein gene and runs of homozygosity baselines in small ruminants, phenotype-first surveillance, biobanking and national genotype–phenotype databases. Full article

Rust, caused by the fungus Uromyces pisi, is the most harmful disease of peas in temperate regions. It is necessary to search for sources of resistance with different defense mechanisms in the pea gene pool. A set of 38 Pisum sativum accessions of various origin was studied in Western Siberia in 2021–2024. The aim of the research was to assess the accessions in the field and under controlled conditions using seedlings and adult plants, as well as to study the interaction of U. pisi with resistant varieties, and to determine genetic control of rust resistance. All accessions showed partial (incomplete) resistance to rust in the field. A set of 10 resistant varieties was used for studying U. pisi interaction with peas using cytological methods. The protective mechanisms of Russian varieties led to the inhibition of 50–90% spores on leaf surfaces before penetration into the stomata, and a part of the small colonies died without hypersensitive reaction in the tissues. Hydrogen peroxide and phenolic compounds with red and green autofluorescence appeared by the stage of sporogenesis. Five varieties showed adult resistance to rust. A hybridological analysis revealed monogenic dominant control of resistance in two varieties, and digenic control in two others. The information obtained expands the understanding of the partners’ interaction in the pathosystem ‘U. pisi–P. sativum’, and can also be used for breeding pea varieties with different resistance mechanisms. Full article