Search Results (773)

Peanut (Arachis hypogaea L.) is a globally important oilseed and food legume, yet its productivity is persistently constrained by devastating diseases and insect pests that thrive under changing climates. This review aims to provide a comprehensive synthesis of advances in precision breeding and molecular approaches for enhancing disease and pest resistance in peanut. Traditional control measures ranging from crop rotation and cultural practices to chemical protection have delivered only partial and often unsustainable relief. The narrow genetic base of cultivated peanut and its complex allotetraploid genome further hinder the introgression of durable resistance. Recent advances in precision breeding are redefining the possibilities for resilient peanut improvement. Multi-omics platforms genomics, transcriptomics, proteomics, and metabolomics have accelerated the identification of resistance loci, effector-triggered immune components, and molecular cross-talk between pathogen, pest, and host responses. Genome editing tools such as CRISPR-Cas systems now enable the precise modification of susceptibility genes and defense regulators, overcoming barriers of conventional breeding. Integration of these molecular innovations with phenomics, machine learning, and remote sensing has transformed resistance screening from manual assessment to real-time, data-driven prediction. Such AI-assisted breeding pipelines promise enhanced selection accuracy and faster deployment of multi-stress-tolerant cultivars. This review outlines current progress, technological frontiers, and persisting gaps in leveraging precision breeding for disease and pest resistance in peanut, outlining a roadmap toward climate-resilient, sustainable production systems. Full article

Fusarium head blight (FHB) is a devastating disease of wheat (Triticum aestivum) globally. Utilizing resistance genes from wild relatives like Thinopyrum elongatum offers a promising approach for genetic improvement. We introgressed FHB resistance from Th. elongatum chromosome 1E into common wheat by inducing homoeologous recombination with wheat chromosome 1B using the ph1b mutant. From a population of 376 BC₁F₂ individuals, we identified 19 independent 1E-1B recombinant lines using KASP markers and fluorescence genomic in situ hybridization (FGISH). High-resolution genotyping with a 130K SNP array precisely mapped recombination breakpoints, revealing a hotspot in the distal long arm. Further phenotypic evaluation revealed that 11 recombinants exhibited significantly enhanced FHB resistance compared to the susceptible Chinese Spring (CS) control. Cytogenetic and physical mapping localized the resistance to a ~48 Mb subtelomeric interval on the long arm of chromosome 1E. This study provides novel wheat germplasm with improved FHB resistance, delineates the physical location of the resistance gene(s) on chromosome 1E, and demonstrates an efficient strategy for precise introgression of valuable genes from wild relatives into cultivated wheat. Full article

Breeding for disease-resistant varieties is a sustainable solution to reduce substantial production losses caused by pathogenic infestations in Brassica vegetables, bypassing environmentally risky disease management practices. Host-resistant genetic mechanisms aid breeders to identify resistance loci and linked markers for the clubroot, Fusarium yellows, downy mildew, black rot, stem rot, soft rot, white rust, and turnip mosaic virus diseases in Brassica vegetables. Introgression of the resistance (R) genes by marker-assisted selection (MAS) breeding strategies allow the development of disease-resilient varieties. Brassica rapa clubroot-resistant genes (CRa, CRc, CRd, CRk, and Crr5) have been introgressed into Chinese cabbage, while CR genes (CRa, CRb, CRc, Crr1, Crr2, and Crr3) from B. rapa were also introgressed into B. oleracea. Beyond MAS, R genes can be precisely engineered by CRISPR-based technologies into precise and durable resistant varieties. The involvement of DNA methylation and histone modifications epigenetically regulate resistance mechanisms, often via ethylene/salicylic acid/jasmonic acid signaling pathways. DNA methylation mediates systemic acquired resistance by the differential expression of genes such as JAZ1, PR3, and NDR1. Future progress will depend on identifying epiQTLs and epi-markers linked to R genes. Epigenetic insights with genetic knowledge will facilitate breeding of biotic stress-resilient Brassica vegetables. This review synthesizes current molecular understanding of biotic stressors and provides future directions for disease resistance breeding of Brassica vegetable plants. Full article

The objectives of this study were to select Thai rice that are tolerant at the seedling stage and investigate their growth, physiological and yield responses at the reproductive stage in comparison with the standard salt-tolerant Pokkali (PK). Twenty-two local, commercial and improved Thai rice genotypes along with PK and salt-susceptible IR29 were evaluated at the seedling stage for salt tolerance using a 15 dS m⁻¹ saline solution with five replications. Ten selected genotypes were grown in pots with four replications and exposed to a 15 dS m⁻¹ saline level from early booting to the flowering stage. During the grain-filling stage, salt treatments decreased from 15 to 12 dS m⁻¹ and were sustained at this level until harvest. The experimental design for both experiments was a randomized complete block design (RCBD). Based on the physiology of flag leaves, almost all genotypes exceled in the protection of chlorophyll, relative water content (RWC), membrane integrity and lipid peroxidation. In contrast, the photosynthesis, growth and grain yield of all were dramatically reduced. The rice genotypes exhibited varying degrees of osmotic adjustment (OA), ranging from 1.598 to 2.541 MPa. The cultivar RD73 and line TSKC1–144, which were genetically improved from KDML105 by the introgression of a salt-tolerant QTL/gene from PK, showed the least reduction in grain yield (60 and 53% reduction, respectively) along with PK (60%). Among the five Thai local rice varieties, Go Main Surin (GMS) showed the least reduction in grain weight (58%), total plant dry weight (28%) and green leaf dry weight (1%), while Khao Gaew (KG) and Leuang Puang Tawng (LPT) were the most reduced. PK and RD73 showed a high level of tolerance at both the seedling and reproductive stages. In contrast, KG and LPT, which exhibited high tolerance at the seedling stage, showed high susceptibility in growth, yield and most physiological traits. On the other hand, TSKC1–144 was sensitive at the seedling stage but showed increased tolerance at the reproductive stage. This result implies that suitable cultural practices should be performed to obtain the best field conditions for growing rice genotypes having different levels of salt tolerance at the seedling and reproductive stages. Future research should focus on molecular characterization of tolerance mechanisms of the promising local genotypes and the potential to use them as tolerance gene donors. Full article

Pepino mosaic virus (PepMV) is a highly infectious potexvirus that poses a significant threat to tomato cultivation in greenhouses worldwide. The threat posed by this virus is attributed to by its genetic complexity, characterized by the presence of multiple genotypes in circulation, mixed infections, and ongoing genotype turnover. Surveys of wild Solanum species have identified promising sources of resistance; however, this resistance is often incomplete, manifesting as symptomless, yet virus-positive, plants. When resistance is identified, introgressing of these traits into elite backgrounds is frequently impeded by reproductive barriers and linkage drag. Consequently, there are currently no commercially available cultivars with durable resistance to PepMV. Current control measures rely on stringent hygiene practices, seed health protocols, and the use of mild isolate cross-protection, which can mitigate fruit symptoms when carefully genotype-matched and closely monitored. Looking forward, achieving durable control will likely require host-centered strategies. Loss-of-susceptibility mutations and RNA interference-based approaches have demonstrated strong potential in experimental studies. Future solutions may involve the integration of genome editing with RNA-based technologies, supported by regulatory harmonization and socioeconomic viability considerations. Full article

To recast Theodosius Dobzhansky’s famous 1973 quote: ‘nothing in coral taxonomy makes sense except in light of reticulate evolution’. Coral species evolve through the continual intermixing of ancestral lineages forming a network of changing genetic interconnections rather than stable hierarchical trees. Most species are not discrete units but rather are components of continua with variable genetic, morphological, and geographic boundaries. Hybridisation and introgression are key processes maintaining reticulated networks, making polyphyletic species (those with mixed evolutionary origins) potentially the norm. This creates grey zones of speciation where taxonomic divisions are uncertain and gene flow is ongoing. With this understanding, we critically review: (1) Sources of information for taxonomic decisions, including biology, population dynamics and the need for comprehensive field and foundational molecular studies capturing environment-correlated and geographic variations; (2) Nomenclature (a human construct) and taxonomy (which endeavours to reflect nature’s organisation): (3) Synonymy, including serial errors stemming from historical publications; (4) Type specimens, their use and misuse as a basis for taxonomic decisions; (5) Genus and species level agreements and disagreements between morphological and molecular taxonomies; (6) Use of the terms ‘cryptic species’, ‘cryptic variant’ and ‘cryptic lineage’; (7) Taxonomic decisions based on inferences beyond the scope of individual studies, creating nomenclatural instability and concern, not least among those working to address the impacts of climate change. This review also provides context for an extensive array of Factsheets and linked documentation about each of the species included in CoralsOfTheWorld.org (2026 in prep.). Full article

Triticale, a man-made cereal, has been grown worldwide since the 1980s in order to replace established cereals in difficult areas, at least partially. The present cultivars are mostly hexaploid genotypes with 42 chromosomes, of genomic structure AA BB RR. Their agricultural performance does not meet all breeding requirements. In particular, some technological characteristics are inadequate compared to tetraploid (durum) and hexaploid (soft) wheats. Therefore, we aimed to find ways to improve modern triticale varieties by targeted introgression with genes and even chromosomes from wheat, in particular, from the D genome. Through appropriate bridge crossings and embryo culture technique and under cytogenetic control, a series of new stable hexaploid lines with reasonable agronomic stability were finally produced. All of them carried a complete D sub-genome, a complete R sub-genome, plus a mixed genome consisting of various combinations of chromosomes derived from the A and B genomes representing the seven homoeologous groups. It is clear that such mixed genomes can be of genetic and breeding significance. These large introgression lines demonstrate the flexibility of genome organization and offer the opportunity for further regulatory and genetic optimization. Full article

The American lobster (Homarus americanus) is a non-native species to Europe, but is imported as live seafood and has been identified in European waters. These introductions threaten native populations of the European lobster (Homarus gammarus) via disease introduction, competition, direct predation, and genetic introgression. Differentiating the two species and their hybrids based solely on morphological criteria can be difficult and unreliable. This study presents a real-time PCR assay targeting the cytochrome c oxidase gene 1 (cox1) for rapid detection and identification of H. americanus and H. gammarus. We have also designed a conventional duplex PCR from a previously described nuclear marker (Hgam98), which was sequenced and revealed the presence of a specific H. americanus insert downstream from a variable number tandem repeat region. The combination of these assays resulted in the accurate identification of the two lobster species and F1 hybrid specimens. Full article

Tomato (Solanum lycopersicum) is the most important vegetable crop globally; however, its production is often hindered by soil-borne biotic and abiotic stresses. The use of rootstocks provides an effective strategy to mitigate these soil-related challenges. Hence, the development of new rootstock cultivars remains crucial to meet the demands of rapidly changing environmental conditions. Wild tomato species represent valuable genetic resources for rootstock improvement and are increasingly utilized in rootstock breeding programs. Nevertheless, the genetic mechanisms, particularly quantitative trait loci (QTL), underlying rootstock–scion interaction, remain poorly understood. In this study, 38 introgression lines (ILs) derived from S. lycopersicoides were used as rootstock and grafted with the commercial cultivar ‘Torry F₁’ to evaluate their effects on morphological and fruit quality traits under greenhouse conditions. The evaluations included assessments of morphological and fruit quality traits for QTL analysis. A total of 19 QTLs were identified, associated with 11 traits such as yield, antioxidant capacity, flavonoid content, and fruit color parameters (L*, a*, b*, C*, h°), with the phenotypic variance explained ranging from 12% to 61%. Of these QTLs, seven favorable alleles originated from S. lycopersicoides, notably including a major yield-associated locus (Fy5.1). In addition, the identification of a QTL for scion stem thickness (Tsc3.1) highlights the genetic contribution of the rootstock to scion development. This study represents the first evaluation of the rootstock potential of S. lycopersicoides ILs and provides novel insights into the genetic basis of rootstock–scion interaction in tomato. The identified QTLs offer valuable information for future breeding efforts aimed at developing improved rootstock cultivars for sustainable tomato production. Full article

Background: Human chromosome 3p21.31 variants introgressed from Neanderthals have been associated with a higher risk of developing a severe form of COVID-19. These Neanderthal DNA variants would regulate the expression of several genes, including LZTFL1 (implicated in the epithelial–mesenchymal transition) and proinflammatory chemokine receptors. Methods: We studied three introgressed haplotypes in patients who developed critical COVID-19 (N = 446; 82 deaths), less severe non-critical COVID-19 (N = 552), and population controls (N = 500) from the region of Asturias, Northern Spain. All the participants were genotyped for six single nucleotide polymorphisms that defined the three 3p21.31 haplotypes. Results: For the haplotype in the LZTFL1 gene, the total patients were significantly higher frequency carriers of the Neanderthal variant compared to controls (24% vs. 17%; p < 0.05, OR = 1.53, 95% CI = 1.16–2.01). Multiple logistic regression showed that critical COVID-19 was independently associated with male sex, hypertension, dyslipaemia, and the introgressed LZTFL1 haplotype (p = 0.006). The frequency of these introgressed genotypes did not differ between normotensives and normolipaemics in the two patient groups but was significantly increased among hypertensives (p = 0.003) and dyslipaemics (p = 0.001). Conclusions: In our population, the 3p21.31 haplotypes introgressed from Neanderthals were associated with increased risk of critical COVID-19, and the risk effect was higher among patients with hypertension and dyslipaemia. Full article

Polyploid crops such as wheat, Brassica, and cotton are critical in the global agricultural and economic system. However, their productivity is threatened increasingly by biotic stresses such as disease, and abiotic stresses such as heat, both exacerbated by climate change. Understanding the molecular basis of stress responses in these crops is crucial but remains challenging due to their complex genetic makeup—characterized by large sizes, multiple genomes, and limited annotation resources. Proteomics is a powerful approach to elucidate molecular mechanisms, enabling the identification of stress-responsive proteins; cellular localization; physiological, biochemical, and metabolic pathways; protein–protein interaction; and post-translational modifications. It also sheds light on the evolutionary consequences of genome duplication and hybridization. Breeders can improve stress tolerance and yield traits by characterizing the proteome of polyploid crops. Functional and subcellular proteomics, and identification and introgression of stress-responsive protein biomarkers, are promising for crop improvement. Nevertheless, several challenges remain, including inefficient protein extraction methods, limited organelle-specific data, insufficient protein annotations, low proteoform coverage, reproducibility, and a lack of target-specific antibodies. This review explores the genomic complexity of three key allopolyploid crops (wheat, oilseed Brassica, and cotton), summarizes recent proteomic insights into heat stress and pathogen response, and discusses current challenges and future directions for advancing proteomics in polyploid crop improvement through proteomics. Full article

The Rural Development Administration (RDA) of the Republic of Korea, in collaboration with International Rice Research Institute (IRRI), developed six temperate japonica rice varieties—MS11, Japonica 1, 2, 6, 7, and Cordillera 4—which were officially approved for release in tropical environments. These varieties offer improved eating quality, enhanced lodging resistance, and increased market value. Although initial evaluations indicated that the varieties were resistant to moderately resistant to major biotic stresses, recent field trials revealed a gradual increase in susceptibility over time. To address this, we conducted comprehensive evaluations of these varieties against rice blast under both greenhouse and field conditions and assessed their responses to bacterial leaf blight (BLB), rice tungro spherical virus (RTSV), and brown planthopper (BPH) under controlled environments. Additionally, whole-genome sequencing was employed to confirm the presence of known resistance alleles. Our findings revealed variable resistance profiles across the six varieties. Japonica 1 exhibited the most stable resistance to blast, supported by the presence of the Pi5 allele. Japonica 7 showed strong resistance to key BLB isolates and moderate resistance to a broader range of Xoo races, supported by the resistant Xa25/OsSWEET13 haplotype. In addition, Japonica 7, along with Japonica 6, carried the tsv1 gene for RTSV resistance. However, none of the six varieties possessed other major resistance genes for BPH. These results highlight the urgent need to introgress durable resistance genes into tropical japonica rice to enhance resilience and broaden the spectrum of biotic stress resistance—critical traits for sustainable rice production in tropical environments. Full article

The aim of this research was to characterize the genetic structure of brown trout species complex populations in nine river basins in the Aosta Valley and neighbouring regions in northern Italy. We used a combined analysis of nuclear lactate dehydrogenase (LDH-C1*), mitochondrial DNA-CR (control region) (mtDNA-CR) sequences and ddRAD-seq-generated single-nucleotide polymorphism. In this way, we estimated the degree of hybridization of wild populations with the Atlantic-derived hatchery lineage. The results of the genetic analyses showed a complex genetic structure with different levels of introgression at the respective sampling sites. The mitochondrial lineages (Atlantic (AT), Mediterranean (ME), Adriatic (AD), and Marmoratus (MA)) were present with varying percentages across the sampling sites. Data analysis using the Admixture v.1.3.0 software allowed the identification of four distinctive cluster units in the Aosta Valley. For the Vertosan River, we identified a distinct native population and a level of hybridization close to zero. In terms of conservation, this population with a distinct native lineage represents a high priority for protection and serves as a reservoir for the entire western north Italian alpine zone. Some interventions to support conservation actions within the study area can be envisaged. Full article

The Red-legged Partridge (Alectoris rufa, Phasianidae) is a non-migrant gamebird endemic to southwestern Europe that was introduced into Mediterranean and Atlantic islands in historical times. This is the case for Madeira, Portugal, where a population morphologically assigned to A. r. hispanica has been present since the XV century. We assessed its genetic identity using 2248 (Cytochrome-b, Cyt-b + Control Region, CR) and 297 bp-long (CR) mitochondrial DNA sequences obtained from modern and archival (1900–1964, including Caccabis rufa maderensis syntypes) partridges, respectively. These sequences were compared against an already published dataset covering the entire Iberian A. rufa range. We found that all the haplotypes of modern birds from Madeira were private to this island. The putative subspecies was confirmed, and northern Portugal with northwestern Spain turned out to host the closest mainland populations. This result was in line with the origin of the first human settlers of Madeira from, among other historical provinces, Douro Litoral and Minho, the latter neighboring Galicia. Despite relatively recent A. rufa importations from continental Europe, we did not find any significant change over time in the haplotypic pattern of Madeiran partridges as well as any evidence for maternal introgression from species such as the congeneric Chukar Partridge (A. chukar). Studies relying on genome-wide markers and including the only captive-bred population of Madeira are needed to gain more comprehensive information for the management of the local A. rufa. Full article

The genetic diversity of cultivated crops is limited, largely as a result of domestication bottlenecks and the selective pressures imposed during modern breeding. An introgression cross was initiated by mating bitter apple (Citrullus colocynthis), as a wild founder parent, with ‘Charleston Grey’ watermelon (Citrullus lanatus) commercial cultivar, focused on identifying and utilizing trait-enhancing alleles from crop wild relative (CWR). Successful crosses resulted in diverse families, including F₁ hybrids, F₂ population, and backcross (BC) progenies. The study revealed substantial variation among the founder parents and their derived progeny in plant growth and major agronomic fruit traits, highlighting the value of this genetic diversity for breeding programs and demonstrating the potential of Citrullus introgression lines to enhance desired traits in cultivated watermelon. Morphological analysis demonstrated that F₁ progeny resembled the maternal parent for the majority of investigated fruit traits. A considerable proportion of the introgression progeny in the F₂ generation outperformed both parents in total soluble solids and lycopene content, suggesting that crop wild relatives hold strong breeding value through beneficial allelic recombination. BC₁ siblings were closer to the wild watermelon, which is presumably maternally controlled through plastome and mitogenome in crosses between cultivated watermelon and wild bitter apple, which is expected to be retained in successive backcrosses. The study uncovers novel alleles of CWR that preserve extensive genetic variation that is essential for enhancing resilience traits in current breeding lines. These introgression-derived resources provide a critical platform for advancing genetic studies and enhancing crop resilience. Full article