Search Results (229)

Potato virus Y (PVY) is a major threat to global potato production, causing yield losses of nearly 90%. This emphasizes the urgent need to explore the genetic factors underlying resistance mechanisms. Developments in transcriptomics and plant genomes have shed significant light on the genetic underpinnings of PVY resistance. This review summarizes current knowledge on PVY biology and structure, its impacts, key hypersensitive resistance (HR) and extreme resistance (ER) genes and their associated molecular markers, genomic strategies for discovering resistance genes and improving resistance breeding, and challenges. Genetic resistance is a key strategy for controlling PVY, primarily through HR and ER, which are governed by specific genes: the Ny gene for HR and the Ry gene for ER. Our understanding of the molecular mechanisms underlying this resistance has increased significantly due to the advancement of high-throughput sequencing methods, including RNA and whole-genome sequencing. More than 10 PVY resistance genes have been identified in potato, including well-characterized ER genes such as Ry_sto, Ry-f_sto, Ry_adg, Ry_chc, and Ry(o)_phu, as well as HR genes such as Ny-1, Ny-2, and Ny-Smira, which are discussed in this review. Transcriptomic analyses have revealed the involvement of small RNAs and other regulatory molecules in modulating resistance responses. Transcriptomic studies have also identified 6071 differentially expressed genes (DEGs) in potato cultivars infected with PVY, highlighting strong defense responses influenced by strain, cultivar, and environmental conditions. The identification of these resistance genes facilitates the development of PVY-resistant cultivars through marker-assisted selection and gene pyramiding, offering significant opportunities to enhance PVY management and promote sustainable potato production under the challenges posed by climate change. Full article

Kernel row number (KRN) is a pivotal determinant for yield in maize breeding programs. However, the genetic basis underlying KRN remains largely elusive. To identify candidate genes regulating KRN, a population of 318 BC₄F₄ chromosomal segment substitution lines (CSSLs) was developed via backcrossing, with Baimaya (BMY) as the donor parent and B73 as the recurrent parent. Furthermore, a high-density genetic linkage map containing 2859 high-quality single-nucleotide polymorphism (SNP) markers was constructed for quantitative trait locus (QTL) mapping of KRN. Notably, 19 QTLs controlling KRN were detected across three environments and in the Best Linear Unbiased Prediction (BLUP) values; among these, a major-effect QTL (qKRN4.09-1) was consistently identified across all three environments and BLUP. Then, the integration of linkage mapping and transcriptome analysis of 5 mm immature ears from near-isogenic lines (NILs) uncovered a candidate gene, Zm00001eb205550. This gene exhibited significant downregulation in qKRN4.09-1^BMY, and two missense variants were detected between qKRN4.09-1^BMY and qKRN4.09-1^B73. Zm00001eb205550 exhibited preferential expression in developing ears. Moreover, the pyramiding of favorable alleles from the five stable QTLs significantly increased KRN in maize. These findings advance our genetic understanding of maize ear development and provide valuable genetic targets for improving KRN in maize breeding. Full article

The Pheophorbide a oxygenase (PaO) is a key enzyme in chlorophyll degradation and plays an important role in plant senescence. However, the PaO gene’s function in sorghum remains underexplored. In this study, we identified five SbPaO gene family members in the sorghum genome through bioinformatics analysis. Analyses of gene structure, phylogeny, and collinearity revealed high conservation of this gene family among grass crops, suggesting similar functions. Subcellular localization and protein network predictions indicated that SbPaOs may participate in chlorophyll catabolism and regulate leaf senescence. Expression pattern analysis showed that SbPaO1, SbPaO3, SbPaO4, and SbPaO5 were highly expressed in leaves and significantly upregulated during senescence. Haplotype analysis found three SbPaO genes significantly linked to thousand-grain weight (TGW); superior haplotypes SbPaO1-hap4, SbPaO3-hap5, and SbPaO4-hap4 notably increased this trait. Single-gene improvements increased TGW by 10.57–17.20%, dual-gene aggregation by 18.78–24.75%, and three-gene aggregation by 29.09%. The study also developed Kompetitive Allele-Specific PCR (KASP) markers that identify superior haplotypes with 100% accuracy. In summary, this study’s results provide a theoretical basis and genetic resources for further exploration of haplotype pyramiding strategies to breed new high-yielding sorghum varieties and delineate a clear research direction for subsequent functional validation and breeding practices. Full article

Despite the recognized social and economic importance of common beans (Phaseolus vulgaris L.), the average grain yield is far below the productive potential of cultivars. This situation is explained by several factors, such as the large number of diseases and pests that affect the crop, some of which cause significant damage. It is estimated that approximately 200 diseases can significantly affect common beans. These can be bacterial, viral, fungal, and nematode-induced. The main bean fungal diseases include anthracnose, angular leaf spot, powdery mildew, gray mold, Fusarium wilt, dry root rot, Pythium root rot, southern blight, white mold, charcoal rot and rust. This review provides a comprehensive overview of eleven major fungal diseases affecting common bean, describing their associated damage, characteristic symptomatology, and the epidemiological factors that favor disease development. It further synthesizes current knowledge on host resistance mechanisms that can be exploited to develop molecularly informed resistant genotypes. The compilation includes characterized resistance genes and mapped quantitative trait loci (QTLs), with details on their chromosomal locations, genetic effects, and potential for use in breeding. Moreover, the review highlights successful applications of molecular breeding approaches targeting fungal resistance. Finally, it discusses conclusions and future perspectives for integrating advanced genetic improvement strategies—such as marker-assisted selection, genomic selection, gene editing, and pyramiding—to enhance durable resistance to fungal pathogens in common bean. This work serves as both a reference for forthcoming resistance-mapping studies and a guide for the strategic selection of resistance loci in breeding programs aimed at developing cultivars with stable and long-lasting fungal resistance. Full article

Tourette Disorder (TD) is a prevalent neurodevelopmental condition characterized by chronic motor and vocal tics. A mechanistic understanding of both the genetic etiology and brain pathophysiology remains poor. To gain insight into the molecular underpinnings of TD, we have generated a novel mouse model expressing an orthologous human mutation in CELSR3, a high-confidence TD risk gene. This putative damaging de novo variant, R774H, causes an amino acid substitution within the fifth cadherin repeat. Unlike previous Celsr3 TD models and Celsr3 constitutive null mice, mice homozygous for the R774H amino acid substitution are viable. They have grossly normal forebrain development and no changes to the density of cortical and striatal interneuron subpopulations. However, 3D geometric analysis of cortical pyramidal neurons revealed changes to dendritic patterning and the types and distributions of spines. Furthermore, patch clamp recordings in cholinergic interneurons located within the sensorimotor striatum uncovered mild intrinsic hyperexcitability and changes to spine density. Despite these changes, Celsr3^R774H homozygous mice do not show repetitive motor behaviors at baseline nor motor learning impairments. However, Celsr3^R774H homozygous males have sensorimotor gating deficits, a behavioral phenotype observed in both humans with TD and previously reported mouse models. Our findings suggest human mutations in CELSR3 may affect dendritic patterning, spine formation and/or turnover, and the firing properties of neurons within cortico-striatal circuits. Full article

Submergence during germination (SG) is a major constraint during sowing, severely limiting the promotion and application of direct-seeded rice. Recent studies have revealed the adaptive mechanisms by which rice responds to SG. At the physiological level, flood-tolerant varieties effectively maintain energy supply and cellular homeostasis by enhancing amylase activity, improving glycolysis and ethanolic fermentation efficiency, promoting embryo sheath elongation, and activating antioxidant enzyme systems; at the molecular level, multiple key genes and signalling pathways have been identified, including SUB1A, OsTPP7, OsGF14h, etc., participating in hypoxia perception, metabolic reprogramming, and hormone signal integration to regulate SG under flooding. In addition, the interactions among plant hormones, such as ethylene, gibberellin, abscisic acid, and cytokinin, also play key roles in the SG process. Future research should prioritize breeding strategies that pyramid multiple genes by integrating gene editing, whole-genome selection, and high-throughput phenotyping to improve seed germination under flood stress. Full article

Wheat blast, caused by Magnaporthe oryzae pathotype Triticum (MoT), poses a major threat to wheat (Triticum aestivum) cultivation, particularly in South America and Bangladesh. The rapid evolution and spread of the pathogen necessitate the development of durable and broad-spectrum resistance in wheat cultivars. This review summarizes current insights into the multi-layered defense mechanisms of wheat, encompassing resistance (R) genes, pattern-triggered immunity (PTI), and effector-triggered immunity (ETI) against MoT. The R-genes provide race-specific resistance through ETI, while both ETI and PTI are required to form integral layers of the plant immune system that synergistically reinforce host defense network. Recent advances in genomics, transcriptomics, and molecular breeding have facilitated the discovery and deployment of key R-genes and signaling components involved in PTI and ETI pathways. Integrating these immune strategies through gene pyramiding, marker-assisted selection (MAS), and genome editing offers a promising route towards enhanced and durable resistance in hosts. Harnessing and optimizing these multilayered immune systems will be pivotal to securing wheat productivity amid the growing threat of wheat blast. Full article

Saccharum spontaneum L. (wild sugarcane) possesses advantages such as strong perenniality, high stress resistance, and broad adaptability, making it the most successfully utilized wild species in sugarcane hybrid breeding. However, previous exploitation of S. spontaneum has been limited. To further explore its breeding potential, this study employed recurrent selection to improve the population of S. spontaneum (S0) before its application in germplasm innovation. Subsequently, S1 (containing two S. spontaneum bloodlines) were developed and optimized. Using S1 as dual parents, S2 (containing three or more S. spontaneum bloodlines) were further created and selected. Genetic diversity among 199 materials from seven populations (S0, S1 and S2) was evaluated using simple sequence repeat (SSR) markers. The results showed that an unweighted pair-group method with arithmetic means (UPGMA) cluster analysis based on genetic distance classified the 199 S. spontaneum materials into seven groups, largely consistent with their original population divisions. Compared to their parents, the S1 population generated an average of 18.79 novel loci (mutation rate: 25.00%), while the S2 population produced an average of 15.40 novel loci (mutation rate: 19.00%). The polymer of S. spontaneum exhibited rich genetic diversity, with Nei’s gene diversity index of 0.3390 and Shannon information index of 0.5082. Due to the increased number of original parents and trait pyramiding, the polymer of S. spontaneum demonstrated expanded genetic backgrounds and enhanced heterogeneity. Furthermore, hybridization and recombination generated novel elite loci compared to their parents, further enriching the overall genetic background and diversity of the polymer of S. spontaneum. Full article

Hereditary spastic paraplegia (HSP) and hereditary ataxias (HA) are clinically and genetically heterogeneous neurodegenerative disorders that primarily affect motor coordination and neural integrity. Despite distinct pathological features, such as pyramidal tract degeneration in HSP and spinocerebellar pathway involvement in HA, these conditions share overlapping genetic pathways and mechanisms. The fruit fly Drosophila melanogaster has emerged as a powerful model organism for investigating the molecular basis of rare diseases, including HSP and HA. Its genetic tractability, rapid life cycle, and high degree of gene conservation with humans make it a cost-effective and ethically viable platform for disease modelling. In this review, we provide a comprehensive overview of Drosophila-based models for HSP and HA. We highlight the use of advanced genetic tools, including RNA interference, CRISPR/Cas9, and the GAL4/UAS system, as well as behavioral and neuroanatomical assays to model disease features. Furthermore, we discuss the application of genetic “avatars” and high-throughput drug screening platforms to test therapeutic candidates. Collectively, these models have deepened our understanding of the pathophysiology of HSP and HA, offering valuable insights for the development of targeted therapies and approaches to personalized medicine. Full article

Oat (Avena sativa L.) is a widely cultivated cereal crop valued for both its nutritional benefits and agricultural versatility. However, oat production is increasingly challenged by powdery mildew, which is caused by Blumeria graminis f. sp. avenae (Bga) and can lead to considerable yield losses. Genetic resistance remains the most sustainable and environmentally friendly method of disease control. This study aimed to evaluate the effectiveness of 14 oat genotypes carrying known resistance genes (Pm1–Pm12) and Avena strigosa accessions against Bga populations collected across four regions of Poland between 2021 and 2023. Host–pathogen assays were used to assess resistance levels, virulence frequency, and pathotype diversity. Resistance genes were categorized into three groups based on performance: highly effective (Pm2, Pm4, Pm5, Pm7 in APR122 and A. strigosa), variably effective (Pm7 in ‘Canyon’ and Pm9–Pm12), and moderately effective (Pm1, Pm3, Pm6 and Pm3+8). Pathogen populations exhibited decreasing virulence complexity and diversity over time, with substantial regional variation. There were few dominant pathotypes, but most were rare and transient. This study confirms the long-term effectiveness of several resistance genes and the necessity of continuous resistance monitoring. It supports the use of gene pyramiding to ensure durable, regionally adapted protection. These results highlight the importance of combining resistance breeding with integrated disease management to ensure sustainable oat production under changing environmental conditions. Full article

Background: The COX20 gene encodes a critical assembly factor for cytochrome C oxidase (complex IV), and biallelic loss-of-function variants in this gene cause mitochondrial complex IV deficiency, typically presenting in infancy or childhood with hypotonia, ataxia, neuropathy, or dystonia. Methods: This study describes an adult male patient with a broad clinical spectrum of central and peripheral nervous system involvement. Different medical genetic tests were performed for the patient, and only whole-genome trio sequencing identified pathogenic variants in the COX20 gene. A review of previously reported cases was conducted to compare clinical and imaging findings. Results: Two compound heterozygous COX20 variants in were identified: a known missense variant (c.41A>G; p.Lys14Arg) disrupting splicing, and a novel start-loss variant (c.2T>C; p.Met1?). The patient exhibited progressive ataxia, pyramidal signs, and peripheral neuropathy, accompanied by cervical spinal cord atrophy on spinal cord MRI and lower leg muscle fat infiltration on muscle MRI, an imaging feature not previously emphasized in COX20-related disease. Conclusions: A review of previously reported cases underscores broad clinical variability of the COX20-associated disorder, which may contribute to a prolonged diagnostic odyssey. Full article

Knowledge of the genetic diversity and resistance genes of Coffea canephora genotypes is essential to identify genetic resources that are better adapted to current climate conditions. This study aimed to molecularly characterize and evaluate the genetic diversity of coffee plants cultivated in Rondônia (Amazonia), Brazil, using SNP molecular markers, and to identify plants carrying resistance genes to two major coffee diseases: rust (Hemileia vastatrix) and coffee berry disease (CBD; Colletotrichum kahawae). Genetic diversity analysis revealed five main groups: Group II included 33 genotypes, primarily of the Robusta botanical variety; Group III contained 18 genotypes of the Conilon variety; Group V, the largest, comprised 85 genotypes, mostly hybrids between Robusta and Conilon. Groups I and IV showed fewer, more divergent genotypes. Molecular markers linked to resistance genes enabled the identification of clones with pyramided resistance alleles for both diseases. Three genotypes exhibited a complete pyramided configuration, while others showed different combinations of resistance loci. Marker patterns also allowed classification of genotypes based on origin, variety, and genealogy. These findings provide a valuable foundation for guiding crosses in breeding programs aiming to develop disease-resistant and climate-resilient clones and hybrids, while also supporting cultivar and clone traceability. Full article

Xiangwanxian 13 (XWX13), an elite fragrant indica rice, is highly susceptible to rice blast and accumulates cadmium (Cd) in grain above the food safety limit in Cd-contaminated paddies, severely constraining its commercial use. Despite these shortcomings, the variety is widely grown for its high yield and superior grain quality. To overcome these limitations, we conducted marker-assisted backcrossing (MABC) complemented by genome-wide background selection. Four major genes, namely Pi1, Pi2, OsHMA3, and OsNramp5, were precisely introduced into XWX13. Two preferable BC₃MF₅ improved lines iXWX13-1 (stacking Pi1 + Pi2 + OsHMA3) and iXWX13-2 (stacking Pi1 + Pi2 + OsNramp5) were obtained with genomic background recovery rates of 94.44% and 94.63%, evaluated by using the RICE 1K SNP array, respectively. Seedling resistance spectrum assays demonstrated more than a 97% blast resistance rate against 39 Magnaporthe oryzae isolates, and both lines showed enhanced leaf and panicle neck blast resistance in natural nurseries. Multi-site field trials revealed grain Cd concentrations of 0.009–0.077 mg kg⁻¹ in iXWX13-2, 90.98–98.87% lower than those in XWX13. Importantly, yield, major agronomic traits, and grain quality remained indistinguishable from the original variety. This study provides the first demonstration that MABC coupled with SNP array background selection can simultaneously enhance blast resistance and reduce grain Cd in XWX13 without yield or quality penalties, offering a robust strategy for pyramiding multiple desirable genes into elite cultivars. Full article

Background/Objectives: Hereditary spastic paraplegias (HSPs) comprise a heterogenous spectrum of rare neurogenetic disorders predominantly characterized by progressive spasticity and weakness of the lower extremities. Among autosomal-dominant forms of HSP, molecular defects in the SPAST gene—particularly those associated with the SPG4 subtype—represent the most frequent genetic cause. SPAST encodes spastin, a microtubule-severing ATPase, crucial for cytoskeletal remodeling, neuronal connectivity, and intracellular trafficking. Disruption of spastin function can impair neurite outgrowth and synaptic formation, processes increasingly implicated in neurodevelopmental disorders (NDDs). Methods: We conducted a comprehensive clinical, neurological, and dysmorphological evaluation of a 4-year-old male. Standardized neuropsychological assessments were administered. Whole-exome sequencing (WES) was performed to identify underlying genetic causes. EEG and 3T-brain MRI were also acquired. Results: The proband harbored two novel de novo heterozygous missense variants in cis of the SPAST gene, displaying the typical features of early-onset and complex HSP, in addition to global developmental delay and severe autism spectrum disorder (ASD), an underexplored manifestation in this rare genetic disorder. Conclusions: These findings broaden the clinical and mutational spectrum of SPG4, underscoring the importance of considering SPAST gene analysis in patients with ASD in the early years of life and early motor delay, even in the presence of only subtle pyramidal signs. We advocate for comprehensive neuropsychiatric assessment in the diagnostic pathway of early-onset complex HSP presentations and support further investigation into the role of spastin in neuronal connectivity. Full article

Bacterial spot of the pepper (BSP) and the tomato (BST) caused by multiple Xanthomonas spp. remains a major constraint to production of both crops worldwide. The widespread breakdown of dominant resistance genes, such as Bs2, due to the emergence of virulent races, like Xanthomonas euvesicatoria P6, has underscored the need for more durable, non-race-specific resistance. The recessive genes, bs5; bs6; and bs8, have emerged as promising alternatives, conferring broad-spectrum resistance without triggering a hypersensitive response. In this study, we systematically evaluated the individual and combinatorial effects of these three recessive resistance genes against three Xanthomonas species, X. euvesicatoria (Xe), X. hortorum pv. gardneri (Xhg), and X. perforans (Xp). Using near-isogenic lines (NILs) developed in the susceptible Early Calwonder (ECW) background, we assessed the in planta bacterial population growth and symptom development across a panel of eight genotypes carrying different gene combinations. Our results demonstrate that bs5, particularly when combined with either bs6 or bs8, significantly reduces bacterial growth and disease severity across all three Xanthomonas species. The triple-stacked line (ECW568 (i.e., bs5, bs6, and bs8)) consistently displayed the strongest suppression of pathogen proliferation and symptom development. By contrast, bs6 and bs8, alone or in combination, were largely ineffective. In some cases, combining bs6 with bs8 was less effective than bs8 alone. These findings reinforce the central role of bs5 in conferring quantitative resistance and highlight the additive benefit of pyramiding recessive resistance genes. Furthermore, we have demonstrated that these recessive resistance genes are effective in limiting the ability of the emerging pathogen, X. perforans, to grow in planta, and thus are predicted to offer a high level of resistance in the field. Our work provides key insights for breeding durable, broad-spectrum resistance into commercial pepper cultivars and offers a framework for integrated disease management strategies in the face of rapidly evolving bacterial pathogens Full article