Search Results (823)

Background/Objectives: Closely related species provide an opportunity to study evolutionary processes that underpin new species formation. Speciation driven by adaptation to distinct environments, such as adaptation to high and low elevation in Senecio aethnensis and Senecio chrysanthemifolius, respectively, on Mount Etna, Sicily, is particularly informative about the interplay between natural selection and ongoing interspecific gene flow. Methods: In this study, we analysed the relative contribution of adaptive introgression and local adaptation in these Senecio species. We used genome resequencing with short read sequence data, and analysed patterns of polymorphism within and between the two Senecio species. Results: Genome-wide scans for selection identified numerous putative selective sweep regions, many of which overlap with selected regions detected in cline-based analysis in the same system. Our results indicate the prevalence of local over introgressive sweeps, consistent with local adaptation to contrasting environments driving divergence of these species. However, many putative introgressive sweeps were also detected, possibly driven by shared selective forces, such as adaptation to volcanic soils and disease resistance, as indicated by GO terms linked to defence responses for some of the introgressive sweeps. Conclusions: The results suggest that even though the two species are now adapted to different environments, introgression has facilitated their adaptation by sharing adaptive alleles between species, which is likely an important factor for adaptation in closely related species. Full article

Soybean seeds have long been regarded as “storehouses of high-quality proteins”. The breakdown of dietary proteins by digestive proteases is essential for achieving adequate protein digestibility in animals and humans. However, plants have evolved a diverse array of protease inhibitors that regulate or restrict protease activity. In soybean, these inhibitors are concentrated primarily within the 2S protein fraction. Trypsin inhibitors (TIs) of Kunitz trypsin inhibitor (KTI) and Bowman–Birk inhibitor (BBI) are the most impactful due to their strong anti-tryptic activity, which interferes with digestive proteases in humans and animals. Elevated TI levels render raw soybeans unsuitable for direct food or feed use unless thermal or processing inactivation treatments are applied. Elimination or reduction in KTI and BBI using classical and biotechnology-based breeding efforts is a promising strategy. Soybean germplasm harboring BBI null alleles has not been reported. Breeding only for low or null KTI content in soybean would not be sufficient for practical applications. Hybridizing IT105782 × PI 547656 and using the reported Kompetitive Allele-Specific PCR (KASP) markers represents an effective classical breeding strategy. Simultaneous CRISPR/Cas9-mediated knockout of key KTI and BBI genes is expected to enable the development of soybean lines with substantially reduced TI levels, an outcome that cannot be readily achieved through classical introgression of null alleles, as naturally occurring null BBI alleles have not yet been identified. Moreover, this approach avoids the linkage drag associated with donor-derived null KTI alleles. However, this approach remains challenging due to functional redundancy and compensatory effects among KTI and BBI family members, extensive sequence homology among KTI and BBI genes that complicates the minimization of off-target effects, and the genotype dependency of Agrobacterium-mediated soybean transformation. Microtiter plate AACCI/AOCS could be one practical option for measuring TIA in breeding programs in terms of precision. Potential trade-offs associated with reduced trypsin inhibitor levels, including possible effects on plant defense and stress resistance, should be investigated in future studies, as these aspects have received little attention in previous research. Full article

Knowledge of the biology of the genus Vitis has undergone a profound transformation, evolving from the morphological descriptions of classical ampelography to the high-resolution analyses enabled by modern phylogenomics. This review explores the “Paradox of the Vine”—the remarkable phenotypic plasticity that historically complicated botanical nomenclature—and examines how genomic tools have helped resolve many of these long-standing taxonomic challenges. We trace the development of grapevine genomics from the first near-homozygous reference genome (PN40024) to the current era of telomere-to-telomere (T2T) assemblies and phased diploid genomes. Attention is given to the genomic “dark matter” represented by transposable elements and structural variation, which contribute substantially to varietal identity and species-specific adaptation to changing environmental conditions. Advances in bioinformatic methodologies, including pangenome graph construction and machine learning-based variant detection, now enable clonal discrimination and complex parentage analysis with unprecedented precision. The definition of genuine wild grapevines (Vitis vinifera subsp. sylvestris) remains a critical issue in studies of grapevine evolution, domestication, and genome structure. The traditional concept of wild populations free from introgression by cultivated grapevines has been increasingly challenged by ecological observations and molecular evidence. Distinguishing truly wild populations from feral lineages is therefore essential for reconstructing the history of grapevine domestication and understanding patterns of gene flow between cultivated and wild compartments. Future progress in Vitis systematics will depend on the integration of genomic, ecological, and morphometric approaches. We propose that the next generation of grapevine taxonomy will combine the historical insights of ampelography with high-throughput phenotyping and comprehensive pangenomic resources, leading to a predictive and evolutionarily informed framework for the classification of Vitis species and cultivars. Full article

Background/Objectives: The common quail (Coturnix coturnix) is a game species facing conservation challenges, particularly hybridization with the Japanese quail (Coturnix japonica). To address this issue, one proposed measure is the urgent prohibition of releasing farmed quails into the wild. If authorized, mechanisms should be established to guarantee their genetic origin and prevent contamination of native populations. This work focuses on the development of a genetic tool based on Single-Nucleotide Polymorphism (SNP) markers that can differentiate between the two species and their hybrids. Our goal was to incorporate the selected markers into an OpenArray^® platform, to allow efficient, rapid, and cost-effective analysis. Methods: We tested two mitochondrial DNA SNPs (previously described in the literature) as diagnostic markers for species differentiation. We also assessed 24 nuclear DNA SNPs for compatibility with the OpenArray^® platform. Results: Of the 26 total SNPs, eight were excluded due to their limited utility. The remaining 18 SNPs achieved an overall genotyping success rate of 96.21%. Using the OpenArray^® platform with these 18 SNPs in a trial with samples from diverse Spanish field populations, we found 1.00% of C. japonica alleles (affecting 15.63% of individuals), suggesting introgression in the field. Population genetic analyses revealed strong differentiation between species and confirmed the presence of admixed individuals in field populations. Conclusions: This paper presents a new tool to differentiate between quail species and to identify foreign alleles in stocks and populations, by using an open platform system that optimizes the practical application of the diagnostic procedure based on the to-date most-reliable SNP markers for this goal. Full article

Traditional Mediterranean grapevine landraces represent irreplaceable reservoirs of adaptive diversity, yet many regional germplasm pools remain poorly characterized, limiting conservation strategies and climate-resilient breeding. This study presents the first comparative genetic assessment of 154 local Vitis accessions from three historically interconnected but genomically underrepresented Mediterranean regions: Greece, Morocco, and Slovenia. Using 12 highly polymorphic nuclear SSR markers, we detected substantial genetic diversity (168 alleles; mean heterozygosity He = 0.881) with distinct regional signatures. Moroccan accessions exhibited the highest allelic richness and 11 private alleles, reflecting diverse agroecological adaptation. Slovenian germplasm formed a cohesive, genetically stable cluster with high effective allele numbers. Greek accessions exhibited the highest observed heterozygosity and 14 private alleles, consistent with the Aegean’s role as a major diversification hotspot. Despite >90% of variance occurring within individuals, AMOVA and pairwise FST (0.050–0.061) revealed low to moderate but significant geographic differentiation. Multivariate analyses (PCA, UPGMA) and Bayesian clustering (sNMF, K = 3) consistently resolved three regional genetic groups with varying admixture levels, consistent with a mosaic domestication model, as previously proposed for the Mediterranean basin, shaped by recurrent introductions, wild introgression, and region-specific selection. Our results show that peripheral Mediterranean germplasm harbors meaningful, regionally distinctive, substantial, non-redundant diversity not fully represented in surveys focused on climate adaptation, disease resistance breeding, and long-term genetic resource conservation. These findings challenge simplistic diffusion models and emphasize the strategic importance of geographically comprehensive sampling in grapevine conservation programs. Full article

Introduction: Brown trout (Salmo trutta L.) is a salmonid fish considered a genetically and geographically highly structured species. The species is catalogued as vulnerable in the Spanish Red List since 1992. Based on morphological differentiation, some authors have proposed splitting Salmo trutta into many taxa and in recent years, several binomials involving morphologically differentiated Western Mediterranean brown trout morphs have regained relevance as distinct species and are now assessed in the IUCN Red List. However, Spanish legislation still considers a single species, S. trutta, inhabiting Atlantic and Mediterranean rivers. Analyses of mitochondrial DNA variation across the species’ native range have revealed numerous matrilineal lineages and helped disentangle the phylogenetic relationships and biogeographic history of brown trout. Four largely distant evolutionary lineages defined by sequencing the mitochondrial control region (Adriatic, AD, Mediterranean, ME, Atlantic, AT and Duero, DU) are native among the Iberian brown trout populations. Stocking activities have resulted in introgressive hybridization of these native populations with non-native northern Atlantic stocks throughout the Iberian rivers and compromise the evolutionary singularities of brown trout in the Iberian Peninsula. Methodology: In this study, we compare complete mitogenomes from Iberian brown trout specimens with those from other regions, using both newly sequenced samples and whole mitogenomes from the GenBank database and estimate their divergence times relative to those observed among species of other Salmoninae genera, such as Oncorhynchus and Salvelinus, to assess patterns of species-specific divergence among Iberian brown trout populations. Results: The evolutionary relationships of the specimens using their mitogenomes fitted with previous analyses using partial mitochondrial sequences and confirmed the strong differentiation among the Iberian lineages. All the branches involving distant Iberian mitogenomes are sister branches with taxa historically described under different binomials (such as Salmo macrostigma, S. multipunctatus, S. pallaryi). Conclusions: The results provide evidence supporting the existence of potentially distinct and undescribed native Salmo species in the Iberian rivers. Full article

The einkorn wheat group, comprising ancient diploid species (2n = 14, AA), including Triticum monococcum, Triticum boeoticum, and Triticum urartu, represents a valuable source of genetic variation for improving disease resistance in wheat. To develop a practical platform for introgressing powdery mildew resistance into bread wheat, we screened 21 einkorn accessions with Blumeria graminis f. sp. tritici (Bgt) race E09 and identified seven resistant donors. Because direct hybridization between diploid einkorn (AA) and hexaploid wheat (AABBDD) is constrained by genomic divergence and poor cross-compatibility, we crossed resistant einkorn accessions with susceptible durum wheat and induced chromosome doubling in the F₁ hybrids to generate synthetic durum–einkorn amphiploids. Nine amphiploids were obtained. Chromosome counts and genomic in situ hybridization confirmed the expected genomic constitution (AABBAA) in most lines, with limited variation in chromosome number in two amphiploids. Phenotyping against Bgt race E09 showed that three amphiploids retained high resistance, four showed moderate resistance, and two were moderately susceptible. Marker analysis identified five einkorn accessions contain known Pm genes such as Pm60, Pm60b, and PmNCA6/Pm37, as well as their derived amphipliods. Two einkorn accessions and their derived amphiploids may harbor novel Pm genes. Field evaluation of the agronomic traits of these amphiploids indicated some improvement in tillering, spike length, and seed weight. Moreover, these amphiploids had better seed-setting rates in crosses and backcrosses with common wheat. These synthetic durum–einkorn amphiploids thus offer a new bridging platform for transferring alien genes from diploid einkorn to hexaploid common wheat, providing valuable genetic resources for wheat-breeding programs. Full article

In the Iberian Peninsula, the rapid expansion of the invasive species Alburnus alburnus (bleak) has intensified its contact with several endemic cyprinid species, raising concerns about hybridization, introgression, and the loss of genetic diversity. Despite increasing evidence of hybridization, data remain limited for many Iberian River basins, where endemic species persist in fragmented and vulnerable habitats. The aim of this study is to assess the extent and spatial distribution of hybridization between the bleak and the following native cyprinid species, Anaecypris hispanica (jarabugo), Iberochondrostoma lemmingii (pardilla), Pseudochondrostoma willkommii (Guadiana nase), and Squalius alburnoides (calandino), across several rivers within the Guadalquivir Basin. To this end, Sanger sequencing will be performed on the mitochondrial cytochrome b gene (maternal lineage; approximately 1000 base pairs (bp)) and the nuclear β-actin gene (paternal lineage; approximately 950 bp) from individuals of all endemic species and the bleak. Parental species and putative hybrids were initially identified in the field using diagnostic morphological and meristic characters, including number of rays in the anal fin morphology, mouth position, and the number of lateral line scales. Molecular analyses will include haplotype network reconstruction and phylogenetic tree inference to evaluate relationships among individuals from different species and to assess lineage divergence. The results will allow us to: (1) detect hybrids between the bleak and endemic cyprinids, (2) identify hybridization events among endemic cyprinid species, and (3) evaluate the correspondence between diagnostic morphological and meristic traits and the molecular identification of hybrid individuals. Overall, these findings will provide key information for the conservation management of endangered Iberian freshwater fishes in the context of invasive species expansion and global change. Full article

A total of 159 wheat–Thinopyrum intermedium derivatives, originating from six Zhong partial amphiploids, were evaluated for resistance to powdery mildew (Blumeria graminis f. sp. tritici) at both seedling and adult-plant stages, as well as for field resistance to wheat aphids, together with key agronomic traits. Adult-plant resistance to powdery mildew was common across three years: 34 lines (21.4%) exhibited stable resistance, and 27 (17.0%) were moderately resistant. Resistance frequencies differed among pedigree backgrounds, with Zhong 2 & 5 derivatives showing the highest proportion of stable resistant lines (35.7%). Seedling resistance was detected in 63 lines (39.6%). Aphid resistance was less frequent, with 61 lines (38.4%) classified as resistant, including two highly resistant lines derived from Zhong 3 and Zhong 1 & 3 backgrounds. Combined resistance traits were comparatively rare. Thirty-two lines exhibited resistance to powdery mildew at both seedling and adult-plant stages, while nine lines displayed combined resistance to seedling mildew, adult mildew, and aphids. Analysis of agronomic traits indicated that environmental effects accounted for a substantial proportion of the observed phenotypic variation, whereas pedigree background and resistance responses contributed comparatively little. Correlation analyses revealed generally weak associations between resistance responses and agronomic traits, suggesting that resistance was not a major determinant of agronomic performance within the evaluated population. The identified resistant materials, therefore, represent valuable pre-breeding resources for the incorporation of resistance to multiple biotic stresses in wheat. Further genetic characterization and multi-environment evaluation will facilitate their effective utilization in wheat improvement programs. Full article

Introduction: The upper Arlanza River (Duero Basin, Burgos, Spain) hosts a genetically distinct local lineage of brown trout (Salmo trutta fario), the “Arlanza strain”, largely free from hatchery-derived introgression, alongside other native cyprinids of conservation concern, including the Iberian chub (Achondrostoma arcasii, Vulnerable—IUCN). The river also supports the Iberian desman (Galemys pyrenaicus, Endangered—IUCN) and Eurasian otter (Lutra lutra). Despite these values, the study reach presents multiple transverse obstacles limiting longitudinal connectivity and degraded riparian cover in critical sections due to livestock erosion, compromising habitat quality for all species. Objective: This study aimed to design engineering interventions to improve fluvial and riparian habitat in a 4 km reach of the upper Arlanza River, restoring longitudinal connectivity and thermal refuge availability while strictly preserving the genetic integrity of the native Arlanza trout strain. Methodology: The reach was characterised through electrofishing surveys, riparian quality assessment (modified RQI index), hydraulic refuge evaluation (IR index), and hydrological analysis based on a 30-year flow record. Brown trout population dynamics were modelled using dimP 1.0 software, with a comparative analysis between upstream (Quintanar de la Sierra village) and downstream (Vilviestre del Pinar village) sampling points to identify connectivity bottlenecks. Engineering works were scheduled to avoid reproductive periods of all target species. Results: The upstream population showed a rejuvenated age structure (density: ~1.40 ind/m; mean length: 12.0 cm), consistent with good spawning conditions but limited growth capacity due to cold temperatures and low summer flows. The downstream point exhibited a severely reduced population (~0.10 ind/m), indicating marked loss of connectivity and habitat degradation. Priority intervention zones were identified in the Camping and lower Prado Mayor sub-reaches. Proposed measures included weir notching to restore fish passage, livestock watering points to reduce bank erosion, and riparian restoration by planting native species (Populus tremula, Betula alba, Salix spp.) protected with fences. Conclusions: Restoring longitudinal connectivity and riparian cover in the upper Arlanza River are essential to protect the genetically valuable Arlanza trout strain, the endangered G. pyrenaicus, and other native fish species, providing a transferable framework for headwater fluvial restoration that jointly addresses biodiversity conservation and genetic resource protection. Full article

Cowpea (Vigna unguiculata (L.) Walp.) is a legume valued in several countries for its nutritional quality, low input requirements, and economic profitability. However, cowpea productivity is significantly constrained by anthracnose disease caused by Colletotrichum species. Enhancing host resistance through the introgression of resistance alleles from landraces and wild relatives offers a promising strategy for durable disease management. This study evaluated 20 cowpea landraces and 18 V. unguiculata ssp. dekindtiana accessions for resistance to anthracnose under natural field infection. The cultivars Ife Brown and V. vexillata line TVNu-428 were included as susceptible and resistant checks, respectively. The experiment was laid in an alpha lattice design (8 × 5) with three replications arranged. Anthracnose symptoms characterized by enlarged light-brown lesions surrounded by reddish-brown halos were produced on all the accessions and the symptoms progressed throughout the assessment period. Five V. unguiculata ssp. dekindtiana accessions (TVNu-113, TVNu-1506, TVNu-1222, TVNu-420, and TVNu-136) and three cowpea landrace accessions (TVu-14076, TVu-17556, and TVu-17567) were identified as promising sources of anthracnose resistance. These accessions represent valuable genetic resources for broadening the cowpea resistance gene pool and support the strategic utilization of wild cowpea germplasm in breeding programs. Full article

Wheat powdery mildew and stripe rust, caused by Blumeria graminis f. sp. tritici (Bgt) and Puccinia striiformis f. sp. tritici (Pst), respectively, are two devastating diseases that threaten global wheat production. Long-term reliance on a limited number of resistance genes can accelerate resistance breakdown. Triticum urartu (2n = 14, A^uA^u), the progenitor of the wheat A subgenome, serves as a valuable gene pool for disease resistance. In this study, we identified three T. urartu accessions exhibiting high resistance to Bgt and Pst. Molecular marker analysis indicated that PI 428215 and PI 428315 carry Pm60b, whereas CITR 17664 carries both Pm60 and YrU1. Durum–T. urartu amphiploids (AABBA^uA^u) displayed resistance responses identical to their T. urartu parent and were used as bridges to transfer these resistance genes into a common wheat (AABBDD) background. Using marker-assisted selection (MAS), recurrent backcrossing, selfing, and phenotypic screening, we developed wheat lines carrying Pm60, Pm60b, YrU1, or Pm60 + YrU1. Segregation analysis in backcross-derived populations supported the functionality of these genes in the common wheat background. The selected introgression lines have high resistance to Bgt and Pst and showed no obvious adverse agronomic effects, providing useful germplasm for wheat disease resistance breeding. This study used a “multi-resistance, multi-combination” pyramiding strategy by MAS to introduce resistance genes from wild wheat into common wheat. Full article

Hybridization between sugarcane (Saccharum spp.) and its wild relative Erianthus rockii offers a promising route to broadening the narrow genetic base of modern cultivars, but the authenticity and chromosome inheritance patterns of such hybrids remain poorly understood. In this study, we combined molecular marker (tetra-primer ARMS-PCR) and cytogenetic (genomic in situ hybridization, GISH) approaches to verify hybridity and track chromosome transmission in 24 F₁ and 12 BC₁ progeny. The F₁ hybrids exhibited a strict n + n transmission pattern, receiving exactly 15 chromosomes from E. rockii. When F₁ plants were used as the male parent in backcrosses, no BC₁ seeds were obtained due to complete pollen sterility. Remarkably, when F₁ plants served as the female parent, all 12 BC₁ clones retained the entire set of 15 E. rockii chromosomes intact, following an unconventional 2n + n pattern. These findings reveal a strong parent-of-origin effect and, for the first time, demonstrate that the whole E. rockii chromosome complement can be stably transmitted into backcross progeny without loss or recombination. This opens a direct route for introgressing complete wild genomes into sugarcane breeding lines, preserving complex polygenic traits and guiding rational crossing strategies. Full article

Early and late leaf spot (ELS and LLS), caused by Passalora arachidicola and Nothopassalora personata, are major constraints to peanut (Arachis hypogaea L.) production. Durable resistance in cultivated germplasm remains limited due to the crop’s narrow genetic base. Wild Arachis species represent an important but underutilized source of resistance. This study aimed to identify and prioritize wild introgressions associated with foliar disease resistance in advanced peanut backcross lines derived from the induced allotetraploid BatSten1 (Arachis batizocoi × A. stenosperma)^4x. A population of advanced backcross lines carrying reduced wild genome content (~5% to ~1% across advancement) was evaluated through four years of field trials for LLS severity and yield, complemented by detached-leaf bioassays to dissect resistance components for both ELS and LLS. Genome-wide SNP genotyping, combined with mixed-model analysis and association mapping, identified introgressed regions influencing disease response. Genome-wide association studies (GWAS) detected loci on chromosomes A06 and A09 associated with LLS resistance, explaining approximately 25% and 11% of phenotypic variation, respectively, with evidence of additive effects between loci. Component-level analyses further revealed both resistance- and susceptibility-associated introgressions. Although tomato spotted wilt virus (TSWV) incidence was evaluated in field trials, exploratory GWAS did not detect significant marker–trait associations, indicating that genetic components associated with this trait were not resolved under the conditions tested. Overall, these results expand the understanding of the genetic architecture of leaf spot resistance beyond traditional donor sources and provide a framework for prioritizing beneficial wild introgressions while minimizing linkage drag in peanut pre-breeding programs. Full article

The spongy moth (Lymantria dispar) is a significant defoliator of broadleaf forests and fruit trees, but its population genetic structure in Central Asia remains poorly defined. We analyzed 153 specimens collected from ten populations across Kazakhstan between 2023 and 2024, using a combination of diagnostic real-time PCR, RAPD genotyping, and mitochondrial COI sequencing. Subspecies identification and Asian introgression were initially assessed with the COI/FS1 TaqMan assay. All samples carried the European mitochondrial type L. dispar dispar, while the nuclear FS1 locus indicated Asian introgression in 92.8% of specimens, including eleven heterozygotes for the Asian allele. RAPD amplification with five polymorphic primers produced 107 variable bands, which we converted into a presence/absence matrix for population genetics analysis. Principal coordinate analysis showed weak but detectable population structure, and Bayesian clustering (STRUCTURE) supported the presence of two primary nuclear clusters. Populations from Ketpentau, Sumbe, Kazachka, Butakovka, and Pavlodar were assigned predominantly to one cluster, whereas most individuals from Almaty, Ile-Alatau, Koksu, North Kazakhstan, and Tekeli were assigned predominantly to the other, with limited admixture in several localities. COI sequences formed a single, minimally differentiated L. dispar clade, with no evidence of distinct mitochondrial lineages. Overall, these findings reveal extensive Asian nuclear introgression in populations retaining European mitochondrial haplotypes, supporting the interpretation of Kazakhstan as part of a broad contact zone within the larger dispar–asiatica gradient. The observed mito-nuclear discordance has important implications for quarantine diagnostics and highlights the need for multilocus molecular assays in regional biosurveillance. Full article