Search Results (80)

Pear (Pyrus communis L.) is a widely cultivated fruit tree species, valued for its significant economic impact and cultural relevance. The rise in commercial cultivars, characterized by genetic uniformity and high yield, is increasingly displacing traditional landraces. However, traditional varieties are highly adapted to local environmental conditions, having resulted from centuries of selection. In this study, 51 pear (Pyrus communis L.) accessions conserved in the Greek national germplasm collection were genotyped using eight SSR markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR). A total of 44 alleles were detected, including several private alleles, indicative of localized adaptation or potential genetic isolation. Analyses of population structure and genetic diversity, using Principal Coordinate Analysis (PCoA), UPGMA clustering, and Bayesian inference via STRUCTURE, uncovered distinct genetic groupings within the collection. The results revealed moderate genetic variability among the 51 accessions and identified some accessions with significant genetic divergence. These findings underscore the importance of conserving Greek pear germplasm, as it represents an ideal source of desirable traits, such as stress tolerance and fruit quality, which can be utilized in breeding programs. Full article

Maintaining genetic diversity is vital for biodiversity and livestock sustainability, with monitoring serving as a prerequisite for conservation strategies. As an initial step for developing future strategies, we analysed the genetic diversity and conservation priorities of 16 chicken breeds managed by a government institute in this study. The breeds were classified as native or locally adapted per FAO definitions and grouped by origin (i.e., governmental or private farms). Genetic diversity, assessed through observed and expected heterozygosity, inbreeding coefficients, and linkage disequilibrium, was high in native breeds from government institutions, such as Chungnam White Korean Native (CNW) and Gangwon Black Korean Native (GWL). Private farm breeds, including Hoeungseong-Yakdak (HYD), exhibited lower diversity. Conservation priorities based on contributions to total genetic diversity (HT) and allelic diversity (AT) revealed that locally adapted breeds, such as Cornish (S) and White Leghorn, significantly contributed to HT. Native breeds, such as CNW and Hyuin black, had higher contributions to AT. Combined assessments indicated that S, CNW, and GWL have the highest conservation priorities. Despite lower rankings, unique breeds such as HYD require targeted conservation owing to their distinctiveness. In conclusion, Korean chicken breeds such as S, CNW, and GWL are vital for maintaining genetic diversity among government-managed breeds. Full article

The mountain pine beetle Dendroctonus ponderosae (Curculionidae: Scolytinae) (MPB) is one component of an intensively studied co-evolved insect–host system. We investigated the spatial genetic structure of the MPB within its historic and recent geographic range expansion as it relates to host use in western North America using 13 pre-selected microsatellite loci. Analysis of molecular variation (AMOVA) indicates that genetic structure is not correlated with the host tree species and therefore does not support the hypothesis of the formation of a host race within this species. STRUCTURE analysis delineates four main clusters in western North America: (1) northern: northern British Columbia/northern Alberta; (2) central: southern British Columbia/southern Alberta/Washington/Idaho/Montana; (3) southwestern: Oregon/California/Nevada; and (4) southeastern: Utah/Wyoming/Arizona/Colorado/South Dakota. Heterozygosity, allelic richness, and the number of private alleles are greatest in the Southwest cluster. This cluster correlates with one of the three refugia hypothesized from a recent analysis of neo-Y haplotypes and represents an important reservoir of MPBs’ genetic diversity. Full article

Muskellunge (Esox masquinongy) are a recreationally and ecologically important apex predator found throughout North America. In West Virginia, the genetic structuring and diversity of native muskellunge is poorly understood. The supplementary stocking of non-native muskellunge has further complicated the issue, as the introgression of non-native alleles and prevalence of non-native muskellunge post stocking remains unclear as well. Using ddRAD sequencing, several datasets were generated to investigate the population structure and genomic diversity of muskellunge in West Virginia. Populations stocked with New York-strain muskellunge exhibited significant introgression, with genetic composition diverging from unstocked native West Virginia populations. However, one population showed greater genetic similarity to native and unstocked populations despite New York-strain prevalence, suggesting resilience against genetic alteration. Fixed SNPs between the New York and West Virginia strains were identified that can be used for broodstock screening and the enhancement of native populations. A genetically distinct population was identified in the Little Kanawha River system, with this population having the highest levels of genomic diversity among native populations as well as a high number of private alleles. However, elevated inbreeding coefficients highlight potential conservation concerns for this unique population. This study establishes a genomic baseline for muskellunge in West Virginia and underscores the importance of preserving native genomic diversity while balancing the demands of recreational fishing programs. Full article

The genetic diversity of tomato in Italy and the growing interest in high-quality food products highlight the importance of establishing varietal distinctiveness through molecular strategies to ensure agrifood product quality and traceability. In this study, four Italian potato-like leaf (PL) landraces were analyzed: “Spagnoletta di Formia e di Gaeta” (SPA) from southern Lazio, “Giagiù” (GIA) and “Patanara” (PTN) from Campania, and “Pomodoro di Mola” (MOL) from Apulia. These landraces were genotyped for the potato leaf gene (C), with two PL American genotypes and a non-allelic PL mutant line included as outgroups. Nagcarlang served as control. An allelism test confirmed C as determinant gene. The SCAR marker for C revealed that the Italian landraces presented determinants other than the most representative one responsible for PL. Whole-genome sequencing of SPA identified a private novel nonsense SNP variant allele, confirmed through dCAPS marker analysis. Additionally, two novel PL alleles responsible for missense variations were identified in GIA/PTN and MOL. In silico protein analysis suggested that novel C alleles could be functional determinants for the protein activity. Overall, PL mutations identified for the first time could serve as molecular tools for agrifood chain traceability, enabling early differentiation and recognition of genotypically similar varieties. Full article

Polyploidy is a powerful mechanism driving genetic, physiological, and phenotypic changes among cytotypes of the same species across both large and small geographic scales. These changes can significantly shape population structure and increase the evolutionary and adaptation potential of cytotypes. Alyssum moellendorfianum, an edaphic steno-endemic species with a narrow distribution in the Balkan Peninsula, serves as an intriguing case study. We conducted a comprehensive analysis of genetic diversity and population structure across the species’ range, employing an array of genetic techniques (nuclear microsatellites, amplified fragment length polymorphisms, and plastid DNA sequences), flow cytometry (FCM), morphometry, and pollen analysis. The study reveals two genetic lineages: spatially distributed diploid and tetraploid cytotypes. Clear divergence between diploids and tetraploids was shown by AFLP, while plastid DNA sequences confirmed private haplotypes in each of the studied populations. Higher genetic diversity and allelic richness following the north-south pattern were documented in tetraploids compared to diploids, as indicated by nuclear microsatellites. Morphometric analysis via principal component analysis (PCA) and canonical discriminant analysis (CDA) did not reveal any divergence between diploid and tetraploid cytotypes. Nonetheless, a distinction in pollen size was clearly observed. The results suggest an autopolyploid origin of tetraploids from diploid ancestors. Despite the population fragmentation in a very small geographic range, these populations harbour high genetic diversity, which would allow them to remain stable if natural processes remain undisturbed. Full article

Background/Objectives: Lebanon, one of the oldest centers of grapevine (Vitis vinifera L.) cultivation, is home to a rich diversity of local grape varieties. This biodiversity is linked to the country’s unique topography and millennia of cultural history. However, the wine industry primarily utilizes international varieties, putting many local varieties at risk of extinction. Methods: In this study, we analyzed 202 samples from old vineyards, home gardens, and private collections using 21 microsatellite markers to assess their identity and genetic diversity. Results: A total of 67 different genotypes were identified, with 34 not matching any existing profiles in the consulted databases, based on comparisons with the European Vitis Database, the Vitis International Variety Catalogue (VIVC), and the databases established in two previous studies conducted in Armenia and Lebanon. Cluster analyses revealed Lebanon’s rich diversity of local grape varieties, highlighting cases of synonymy, homonymy, and misnaming. All loci were polymorphic, with 228 alleles and an average of 11.4 alleles being detected. The highest number of alleles was observed at the VVIV67 locus (19 alleles), while the lowest was found at the VVIQ52 and VVIN73 loci (5 alleles). The observed heterozygosity was 0.732, slightly below the expected value of 0.757, with gene diversity varying among the markers. Conclusions: Of the 67 genetic profiles identified, 34 are absent from national and international databases, underscoring Lebanon as a hotspot for grapevine genetic diversity. This unique genetic variation, which includes several synonyms due to geographic isolation, could provide valuable opportunities for producing distinctive wines and emphasizes the need for further research and documentation. Full article

Naked barley (Hordeum vulgare var. nudum) is a staple food crop, contributing significantly to global food security. Understanding genetic diversity will facilitate its effective conservation and utilization. To determine genetic diversity and its distribution within and among varieties, we characterized 30 naked barley varieties from Tibet, representing the traditional, modern, and germplasm-resources-bank gene pools, by analyzing SSR molecular fingerprints. The results demonstrate abundant genetic diversity in Tibetan naked barley varieties, particularly those in the traditional gene pool that holds much more private (unique) alleles. Principal coordinates and STRUCTURE analyses indicate substantial deviation of the modern varieties from the traditional and germplasm-resources-bank varieties. A considerable amount of seed mixture is detected in the modern varieties, suggesting the practices of using mixed seeds in modern-variety cultivation. Cluster analyses further indicate the narrow genetic background of the modern varieties, likely due to the limited number of traditional/germplasm-resources-bank varieties applied in breeding. Relationships between increases in genetic diversity and sample sizes within naked barley varieties highlight the importance of effective sampling strategies for field collections. The findings from this study have important implications for the sustainable utilization and effective conservation of different types of naked barley germplasm, both in Tibet and in other regions around the world. Full article

Phylogeographic studies have been conducted on many different mammal species in order to track their recent demographic histories. The climatic fluctuations associated with the Last Glacial Maximum (LGM) appear to have had a profound influence on the geographic patterning of genetic diversity in mammals. However, most phylogenetic studies have focused on single species. Few have used a holistic approach covering multiple taxa to explore common patterns. Here, we conducted meta-analyses of mitochondrial DNA control region sequences, identifying haplotype diversity and private allelic richness patterns in a geographic context. Four general patterns emerged among European mammals: an east–west decline in variation, a Western-Central belt of the highest diversity, southern richness, and homogeneity with no geographic pattern. These patterns likely reflect the refugial origins of modern populations. The east–west variation decline suggests species with eastern LGM refugia; the Western-Central belt of the highest diversity may harbor taxa with cryptic northern refugia, while southern richness may correspond to traditional southern refugia. Species with homogeneity and no geographic pattern may have been panmictic without a specific refugium or may reflect the occurrence of both southern and cryptic northern refugia. Surprisingly, the “no pattern” phenomenon is seldom discussed and may frequently have been discounted. Our study emphasizes the importance of considering multiple taxa, providing valuable insights into the responses of European mammals to past climatic changes. Full article

Helichrysum italicum (Roth) G. Don is a Mediterranean medicinal plant with great potential in the cosmetics, culinary and pharmaceutical fields due to its unique bioactive compounds. Its recent introduction into agroecosystems has enhanced the exploitation of genetic diversity in natural populations, although limited molecular markers have made this challenging. In the present study, primers were designed for all 43 SSRs (72.1% mononucleotide, 21% dinucleotide and 6.9% trinucleotide repeats) identified in the chloroplast genome. Populations from Cape Kamenjak (Croatia) and Corsica (France) were analyzed with ten carefully selected cpSSR markers. From the initial set of 16 cpSSRs amplified in all samples, 6 cpSSR markers were removed due to low-length polymorphisms, size homoplasy and nucleotide polymorphisms that could not be detected with allele length. Of the 38 haplotypes detected, 32 were unique to their geographic origin. The highest number of private haplotypes was observed in the Cape Kamenjak population (seven out of nine detected). Based on clustering analyses, the Kamenjak population was the most similar to the Capo Pertusato (south Corsica) population, although only one sub-haplotype was shared. Other Corsican populations were more similar to each other. A cross-species transferability test with Helichrysum litoreum Guss. and Helichrysum arenarium (L.) Moench was successfully conducted and private alleles were identified. Full article

Thyroid gland carcinoma (TGC), though only 1% of all carcinomas, is the most common endocrine neoplasm with an increasing incidence since the 1990s. Of the TGC types, papillary thyroid carcinoma (PTC) is the most common and has the best overall prognosis. Although primarily studied in various neural spectrum disorders, monoamine oxidase A (MAOA) may also contribute to cancer occurrence. This case control study assessed the prevalence of MAOA uVNTR polymorphism in PTC patients, compared its frequency with a healthy control, and assessed the variant’s impact on clinical features. The research participants consisted of 30 PTC patients (20 female, 10 male) over 18 years old who underwent thyroidectomy and radioiodine therapy at a Federal District private clinic and 30 paired and unrelated healthy volunteers (18 female, 12 male). The most frequent MAOA uVNTR alleles were 3R and 4R. Although no significant difference was detected in the genotypic distribution nor the PTC patients’ thyroglobulin, thyroid-stimulating hormone, and antithyroglobulin levels; body mass indexes; administered radiopharmaceutical (131I) doses; or biological sex, the presence of at least one 3R allele was associated with a larger tumor size (T3 + T4 staging). Thus, the 3R allele seems to be associated with PTC pathogenesis severity. Full article

Turnip rape is a multi-purpose crop cultivated in temperate regions. Due to its ability to fit into crop rotation systems and its role as a food and feed source, spring-type turnip rape cultivation is on the rise. To improve the crop’s productivity and nutritional value, it is essential to understand its genetic diversity. In this study, 188 spring-type accessions were genotyped using SeqSNP, a targeted genotyping-by-sequencing method to determine genetic relationships between various groups and assess the potential effects of mutations within genes regulating major desirable traits. Single nucleotide polymorphism (SNP) alleles at six loci were predicted to have high effects on their corresponding genes’ functions, whereas nine loci had country/region-specific alleles. A neighbor-joining cluster analysis revealed three major clusters (I to III). About 72% of cluster-I accessions were of Asian origin, whereas 88.5% of European accessions and all North American accessions were placed in cluster-II or cluster-III. A principal coordinate analysis explained 65.3% of the total genetic variation. An analysis of molecular variance revealed significant differentiation among different groups of accessions. Compared to Asian cultivars, European and North American cultivars share more genetic similarities. Hence, crossbreeding Asian and European cultivars may result in improved cultivars due to desirable allele recombination. Compared to landraces and wild populations, the cultivars had more genetic variation, indicating that breeding had not caused genetic erosion. There were no significant differences between Swedish turnip rape cultivars and the NordGen collection. Hence, crossbreeding with genetically distinct cultivars could enhance the gene pool’s genetic diversity and facilitate superior cultivar development. Full article

Extra virgin olive oil (EVOO) is a precious and healthy ingredient of Mediterranean cuisine. Due to its high nutritional value, the interest of consumers in the composition of EVOO is constantly increasing, making it a product particularly exposed to fraud. Therefore, there is a need to properly valorize high-quality EVOO and protect it from fraudulent manipulations to safeguard consumer choices. In our study, we used a straightforward and easy method to assess the molecular traceability of 28 commercial EVOO samples based on the use of SSR molecular markers. A lack of correspondence between the declared origin of the samples and the actual origin of the detected varieties was observed, suggesting possible adulteration. This result was supported by the identification of private alleles based on a large collection of national and international olive varieties and the search for them in the molecular profile of the analyzed samples. We demonstrated that the proposed method is a rapid and straightforward approach for identifying the composition of an oil sample and verifying the correspondence between the origin of olives declared on the label and that of the actual detected varieties, allowing the detection of possible adulterations. Full article

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (H_obs) and the expected heterozygosity (H_exp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (N_a), the average effective number of alleles at the locus (N_e), the F_ST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ²-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering. Full article

An 8-month-old female Lagotto Romagnolo dog was presented for a 1-month history of an initial severe reluctance to move, rapidly progressing to a marked stiff gait and progressive muscular weakness and evolving to tetraparesis, which persuaded the owner to request euthanasia. A primary muscle pathology was supported by necropsy and histopathological findings. Macroscopically, the muscles were moderately atrophic, except for the diaphragm and the neck muscles, which were markedly thickened. Histologically, all the skeletal muscles examined showed atrophy, hypertrophy, necrosis with calcification of the fibers, and mild fibrosis and inflammation. On immunohistochemistry, all three dystrophin domains and sarcoglycan proteins were absent. On Western blot analysis, no band was present for delta sarcoglycan. We sequenced the genome of the affected dog and compared the data to more than 900 control genomes of different dog breeds. Genetic analysis revealed a homozygous private protein-changing variant in the SGCD gene encoding delta- sarcoglycan in the affected dog. The variant was predicted to induce a SGCD:p.(Leu242Pro) change in the protein. In silico tools predicted the change to be deleterious. Other 770 Lagotto Romagnolo dogs were genotyped for the variant and all found to be homozygous wild type. Based on current knowledge of gene function in other mammalian species, including humans, hamsters, and dogs, we propose the SGCD missense variant as the causative variant of the observed form of muscular dystrophy in the index case. The absence of the variant allele in the Lagotto Romagnolo breeding population indicates a rare allele that has appeared recently. Full article