Search Results (1,272)

The population size of black poplar (Populus nigra L.), once an important part of floodplain forests in the Czech Republic, has greatly declined due to human activity. In this study, we applied microsatellite (SSR) markers to identify species and assess genetic diversity, with the aim of supporting conservation of this endangered species. A total of 378 poplar trees were analyzed following field surveys. Five diagnostic SSR markers with species-specific alleles for P. deltoides Bartr. ex Marsh. enabled the identification of 39 interspecific hybrids, which were distinguished from native P. nigra. Thirteen SSR loci were used to evaluate genetic diversity among confirmed P. nigra individuals. The results revealed high genetic variation, with 66% of pairwise genotype comparisons differing at all loci. After excluding 45 genetically similar individuals, 292 genetically verified and polymorphic P. nigra trees were selected as potential sources of reproductive material. Genetic differentiation (Fst) was highest between P. nigra and P. deltoides (0.27), and lowest between reference Populus ×euroamericana clones and detected hybrid poplars (0.05) from natural localities. Distinct genetic structures were identified among P. nigra, P. deltoides, and hybrid individuals. These findings provide essential data for the protection, reproduction, and planting of black poplar. Full article

Background: Host genetic factors significantly influence individual susceptibility to severe COVID-19, potentially explaining the observed disparities in clinical outcomes across populations. One of the key effectors in innate immunity and antiviral defense is the CD209 gene. This study explored the potential correlation of the CD209 gene SNP rs2287886 with diverse COVID-19 patient outcomes. Materials and Methods: A total of 176 patients (87 in the moderate group and 89 in the severe/critical/death group) were included in the study. Genotyping of patients was performed using the qPCR methodology, through the TAQMAN system. The results were analyzed adopting a significance level of p < 0.05. Results: The GG genotype (compared to AG + AA) and the G allele (compared to the A allele) of the rs2287886 SNP were significantly associated with an increased severity of COVID-19 (p = 0.0005 and p < 0.0001, respectively). The G allele was more frequent in individuals with more severe clinical outcomes (49.43% vs. 25.28%). Furthermore, expression quantitative trait loci (eQTL) analysis indicated that the GG genotype of rs2287886 is associated with higher CD209 gene expression. Furthermore, the observed interaction analysis suggests that the interactions between CD209 and its associated proteins may play a role in modulating the immune response. Conclusions: Our findings suggest that Brazilian patients homozygous for the GG genotype of the rs2287886 polymorphism in the CD209 gene may be at increased risk of severe COVID-19 in the Brazilian population and may act as a potential prognostic marker of disease severity. Full article

Myriophyllum spicatum is a globally distributed aquatic plant capable of sexual and clonal reproduction. Despite its ecological importance and biochemical potential, studies on its genetic and clonal structure in freshwater systems throughout South Korea remain limited. We investigated the genetic and clonal diversity of M. spicatum using 30 newly developed microsatellite markers across 120 individuals from six freshwater systems in South Korea. Overall, 148 alleles were identified, with an average polymorphism information content value of 0.530. Clonal diversity differed among populations, with the genotypes to individuals (G/N) ratio ranging from 0.200 to 1.000. Bottlenecks and clonal dominance were observed in riverine populations. High genetic differentiation (mean F_ST = 0.556) indicated limited gene flow, and STRUCTURE analysis revealed six distinct genetic clusters. No significant correlation was found between genetic and geographic distance, suggesting possible seed dispersal by waterfowl, particularly between adjacent populations. Genetic structure was shaped by habitat type, disturbance intensity, and reproductive strategy. Stable reservoir habitats favored sexual reproduction and higher genetic diversity, whereas disturbed river systems showed clonal dominance and reduced variation. These findings provide essential genetic insights for conservation planning and sustainable management of aquatic plant resources. Full article

Background/Objectives: Y-chromosomal short tandem repeats (Y-STR) are genetic markers widely used in forensic and population genetics. However, despite their importance, many populations remain under-represented in published studies and genetic databases. One such population is the Cape Verdean, which, despite its unique history of admixture between European and sub-Saharan African populations, continues to be under-represented in global Y-STR reference databases. This study aims to characterize the Y-STR haplotype diversity and paternal lineage composition of the Cape Verdean population using a high-resolution STR panel. Methods: A total of 143 unrelated Cape Verdean men were analyzed using a set of 26 Y-STR loci, including rapidly mutating markers. Allele and haplotype frequencies were calculated, along with standard forensic parameters such as gene and haplotype diversity. Paternal lineages were inferred, and genetic relationships with other populations were evaluated using distance-based and graphical methods. Results: A total of 135 haplotypes were detected, with 88.8% being unique, yielding a haplotype diversity of 0.999. The most common haplogroups reflected both West African and European ancestry. Genetic distance analysis positioned the Cape Verdean population between African and European groups, supporting its intermediate and admixed genetic background. Conclusions: This study provides the first high-resolution Y-STR dataset for Cape Verdeans, contributing valuable reference data for forensic casework and population genetic studies. The results highlight the utility of extended Y-STR panels in admixed populations and underscore the need to enhance the representation of admixed populations in international forensic reference databases. Full article

The Naozhou stock of large yellow croakers (Larimichthys crocea) exhibits unique phenotypic traits and high genetic diversity, making it a valuable resource for selective breeding and genetic conservation in aquaculture. Despite its importance, simple sequence repeat (SSR) markers have not been developed for this stock, which limits efforts in genetic evaluation, breeding optimization, and sustainable utilization of this commercially important species. In this study, 195,263 SSRs were identified from the genome of the Naozhou stock of large yellow croaker, covering a total length of 16,578,990 bp with a density of 288 bp/Mb. Dinucleotide repeats were the most common, with the AC motif being the most prevalent. The frequency of SSR markers ranged from 245.63 to 346.60 per Mb. A total of 30 primer pairs were synthesized, of which 28 pairs (93.3%) successfully amplified clear and reproducible bands in PCR assays. Among these, 28 SSR markers exhibited distinct and reproducible bands following gel electrophoresis. For eight SSR loci, the number of alleles (Na) ranged from 4 to 22 (mean = 11.375), while the effective number of alleles (Ne) ranged from 1.5401 to 10.4727 (mean = 5.6475). The assembled mitochondrial genome (mtDNA) was 16,467 bp in length and comprised 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The total sequence length of the PCGs was 11,431 bp, accounting for 69.4% of the mtDNA. A large portion of the PCGs (5) used incomplete stop codons (e.g., nad2, nad3, cox2), while others used TAA stop codons (e.g., nad6, nad5, TrnT). The mtDNA encoded a total of 3808 codons, with UAA showing the highest relative synonymous codon usage value. The SSR markers and mtDNA data generated in this study provide valuable tools for future genetic breeding and genomic research on the Naozhou stock of large yellow croakers. Full article

This study utilized SRAP molecular markers to analyze the genetic basis of 106 multigerm sugar beet germplasm accessions. By revealing the genetic diversity, population structure, and differentiation patterns, it aimed to tap into the germplasm potential, guide core germplasm construction and hybrid combination optimization, and ultimately design a molecular breeding route to break through bottlenecks in sugar beet genetic breeding. In total, 24 core primer combinations were screened from 546 initial primer pairs for genomic DNA amplification. The results demonstrated that each primer combination amplified an average of five alleles. Genetic parameter calculations revealed moderate variation potential. Population structure analysis divided the germplasm into four genetic groups (G1–G4), highly consistent with cluster analysis and DAPC analysis results. Its reliability was jointly confirmed by STRUCTURE convergence verification (LnP(K) standard deviation) and cluster goodness-of-fit testing (r = 0.63166, p < 0.0001). Key findings indicated that Group G4 possesses a unique genetic background, and the maximum genetic distance exists between Group G1 and the other three groups, indicating its significant genetic differentiation characteristics. Gene exchange exists between the G3 and G4 populations. Genetic variation primarily originated from within populations (93%, F_ST = 0.1283). Genetic distances spanned from 0.385 (between accessions 66 and 71 within a group) to 0.836 (between accessions 47 and 85 across groups). Concurrently, gene flow analysis (Nm = 3.3977) indicated moderate genetic exchange among populations. This achievement established the first SRAP marker-based genetic architecture for multigerm sugar beet germplasm resources. It provides a quantitative population genetics basis for formulating targeted strategies for germplasm resource conservation and utilization, and lays the foundation for constructing an innovation system for sugar beet germplasm resources. Full article

The Shagya Arabian horse breed was created to address the need of Imperial Hussars (Hungarian light horsemen) for a horse with the intelligence, essential characteristics, and endurance of the Arabian breed, but also of a bigger size and having a better weight-carrying capacity and jumping ability. The present study aimed to explore the genetic variability and population structure of the uninvestigated Shagya Arabian horse population in Bulgaria based on genotyping at 15 equine microsatellite markers. A total of 140 horses belonging to six genealogical lines (Dahoman, Gazal, Ibrahim, Kuhailan Zaid, O’Bajan, and Shagya) were included in the survey. Genetic distances, analysis of molecular variance, principal coordinates analysis, and a Bayesian method were applied. The mean number of alleles in the individual subpopulations ranged from 3.67 in the Shagya to 5.13 in the Ibrahim sire line. The F_IS index was negative or close to 0 for the entire population and was −0.202. The overall F_ST was 0.014, indicating a low level of genetic differentiation between the subpopulations. The results of the principal components and the STRUCTURE analysis showed some level of admixture among the subpopulations in almost all genealogical lines. However, structural analysis also indicated a genetic similarity between the Ibrahim, Kuhailan Zaid, and Shagya lineages, while it showed a completely different genetic profile regarding the other three sire lines. Due to the higher admixture and the discovery of more distinct genetic clusters, it can be assumed that there is a higher gene flow from one lineage to another in the Shagya Arabian horse population in Bulgaria and that there is sufficient genetic variability and diversity to suggest adequate measures for preserving this rare breed. In addition, this study may highlight the risk of the loss of gene diversity in this population and help to implement suitable breeding programs to preserve genetic diversity. Full article

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), represents a major global threat to wheat (Triticum aestivum. L). Planting varieties with adult-plant resistance (APR) is an effective approach for long-term management of this disease. The Chinese winter wheat variety Lantian 25 exhibits moderate-to-high APR against stripe rust under field conditions. To investigate the genetic basis of APR in Lantian 25, a set of 219 F₆ recombinant inbred lines (RILs) was created from a cross between Lantian 25 (resistant parent) and Huixianhong (susceptible parent). These RILs were assessed for maximum disease severity (MDS) in Pixian of Sichuan and Qingshui of Gansu over the 2020–2021 and 2021–2022 growing seasons, resulting in data from four different environments. Genotyping was performed on these lines and their parents using the wheat Illumina 50K single-nucleotide polymorphism (SNP) arrays. Composite interval mapping (CIM) identified six quantitative trait loci (QTL), named QYr.gaas-2BS, QYr.gaas-2BL, QYr.gaas-2DS, QYr.gaas-2DL, QYr.gaas-3BS and QYr.gaas-4BL, which were consistently found across two or more environments and explained 4.8–12.0% of the phenotypic variation. Of these, QYr.gaas-2BL, QYr.gaas-2DS, and QYr.gaas-3BS overlapped with previous studies, whereas QYr.gaas-2BS, QYr.gaas-2DS, and QYr.gaas-4BL might be novel. All the resistance alleles for these QTL originated from Lantian 25. Furthermore, four kompetitive allele-specific PCR (KASP) markers, Kasp_2BS_YR (QYr.gaas-2BS), Kasp_2BL_YR (QYr.gaas-2BL), Kasp_2DS_YR (QYr.gaas-2DS) and Kasp_2DL_YR (QYr.gaas-2DL), were developed and validated in 110 wheat diverse accessions. Additionally, we identified seven candidate genes linked to stripe rust resistance, including disease resistance protein RGA2, serine/threonine-protein kinase, F-box family proteins, leucine-rich repeat family proteins, and E3 ubiquitin-protein ligases. These QTL, along with their associated KASP markers, hold promise for enhancing stripe rust resistance in wheat breeding programs. Full article

A necessary step towards the development of genetic diversity is the protection of the valuable genetic resources of farm animals that are at risk of extinction. We analyzed 375 individuals of nine local sheep breeds bred in Central Europe (Carpathia area) from Czech Republic, Slovakia, Poland, Ukraine, and Romania using a panel of 13 microsatellite markers to investigate genetic differences and evaluate the genetic structure among and within breeds, thereby improving future breeding and conservation strategies. The mean number of alleles was 8.84, the mean number of effective alleles was 4.76, and the polymorphism information content (PIC) was 0.79. Diversity was measured using principal coordinate analysis (PCoA) as well as genetic structure, which revealed two main clusters. The first cluster was the Czech Wallachian sheep (CVA) and the Świniarka (SWI). The second cluster consisted the Improved Wallachian sheep (IVA), the Šumava sheep (SUM), the Slovak Wallachian sheep (SVA), the Polish Mountain sheep (POG), the Uhruska sheep (UHR), the Ukrainian sheep (UKR) and the Tsurcana sheep (TUR). The values of genetic distance and the fixation coefficient indicate sufficient differences between the analyzed breeds (Gst = 0.052 and Fst = 0.063). Negative values of the inbreeding coefficient also confirmed the predominance of outbreeding (Fis = −0.015). The results obtained may be helpful in breeding programs and conservation plans for local sheep breeds, as their genetic resources must be preserved to maintain an adequate level of biodiversity in animal husbandry. Full article

Myriophyllum heterophyllum is an aquatic macrophyte that is invasive to the northeastern United States and several western European countries. Spreading by vegetative clonal propagation, especially fragmentation, extensive resources are devoted to limiting its growth and spread; however, genetic assessments are not typically included in management strategies. Reduction in genetic (clonal) diversity should accompany biomass reduction, yet without genetic assessment, the efficacy of plant removal remains unclear. This paper is the first to describe a microsatellite marker library and its use in the characterization of Myriophyllum heterophyllum. Eighty-seven tissue samples were collected across the invasive distribution of Myriophyllum heterophyllum in Maine, USA. DNA was extracted, and PCR amplification was employed to screen 13 published microsatellites. Sequencing of the amplified loci was performed to characterize repeat motifs and confirm primer binding sites. Fragment sizing of PCR amplicons was employed to determine microsatellite lengths across the 87 samples. A total of 7 of the 13 tested markers were amplified, with six of those seven found to be variable. Polyploidy was evident from allelic diversity within individuals, although precise ploidy could not be determined. Observed heterozygosity ranged from 0.16 to 1.00 across variable markers. This seven-marker library was effective in characterizing the genetic diversity of both newly discovered (<5 years) and older (>50 years) infestations and is expected to be suitable for assessment of genetic diversity in populations within the native range of M. heterophyllum. The marker library also shows potential for use in several other Myriophyllum species. Full article

Chili peppers, a staple spice in global cuisine, hold substantial economic value due to their diverse pungency levels and distinctive aromatic profiles. In addition to their sensory attributes, Capsicum fruits exhibit notable morphological diversity and potential health benefits. While contemporary Capsicum breeding efforts have focused on the yield, shelf life, and resistance to biotic and abiotic stresses, comparatively less emphasis has been placed on the fruit quality and flavor traits increasingly valued by consumers seeking novel flavors and functional foods. We evaluated seven underutilized Capsicum landraces collected from Peru, Myanmar, and Japan and conducted an integrative analysis of their morphological traits, nutritional composition, pungency, and volatile compounds. Our findings highlight C. chinense from Myanmar and Peru as a particularly diverse species, encompassing accessions with mild to very highly pungent, elevated antioxidant content, and significant contributions to fruity aromatic notes. These findings support the development of flavor-driven chili-pepper-based food products with enhanced nutritional value and tailored pungency. Our identification of beneficial alleles also offers opportunities for interspecific breeding to produce novel cultivars aligned with evolving consumer preferences, thereby supporting the commercialization of traditional varieties, conserving genetic resources, and expanding the market potential of new cultivars. Full article

The objective of this work was to analyse the genetic diversity of a population of Citrus spp. in the south of the State of Espírito Santo, Brazil, for pre-breeding studies. For that, a total of sixty genotypes were analysed, including ten citrus varieties from four species of the Citrus genus. The methodology involved DNA extraction, amplification via polymerase chain reaction, and the use of a set of 16 Simple Sequence Repeat markers. These markers identified 42 alleles, with a variation of one to four alleles per locus, an average heterozygosity value of 0.53, and an average polymorphic information content of up to 0.29 per species. After the analysis, a dissimilarity matrix was generated using Jaccard distance and a dendrogram, revealing the formation of two groups: Group I, comprising Citrus sinensis varieties, and Group II, comprising varieties of Citrus latifolia, Citrus aurantifolia, and Citrus reticulata. Our study demonstrated that the combination of these markers allowed for the differentiation of genotypes within the collection. The results obtained are valuable for the future management of the collection and the efficient use of genetic diversity estimation in Citrus spp. Full article

Background/Objectives: Loss and fragmentation of habitat from agricultural conversion led to the near extirpation of the pygmy rabbit (Brachylagus idahoensis Merriam, 1891) population in the Columbia Basin (CB) of Washington, USA. Recovery efforts began in 2002 and included captive breeding, translocations from other regions for genetic rescue, and reintroduction into native habitat in three sites: Sagebrush Flat (SBF), Beezley Hills (BH), and Chester Butte (CHB). Methods: We used noninvasive and invasive genetic sampling to evaluate demographic and population genetic parameters on three translocated populations of pygmy rabbits over eight years (2011–2020). For each population, our goal was to use fecal DNA sampling and 19 microsatellite loci to monitor spatial distribution, apparent survival rates, genetic diversity, reproduction, effective population size, and the persistence of CB ancestry. Over the course of this study, 1978 rabbits were reintroduced as part of a cooperative conservation effort between state and federal agencies. Results: Through winter and summer monitoring surveys, we detected 168 released rabbits and 420 wild-born rabbits in SBF, 13 released rabbits and 2 wild-born in BH, and 16 released rabbits in CHB. Observed heterozygosity (H_o) values ranged from 0.62–0.84 (SBF), 0.59–0.80 (BH), and 0.73–0.77 (CHB). Allelic richness (AR) ranged from 4.67–5.35 (SBF), 3.71–5.41 (BH), and 3.69–4.65 (CHB). Effective population (N_e) within SBF varied from 12.3 (2012) to 44.3 (2017). CB ancestry persisted in all three wild populations, ranging from 15 to 27%. CB ancestry persisted in 99% of wild-born juveniles identified in SBF. Apparent survival of juvenile rabbits differed across years (1–39%) and was positively associated with release date, release weight, and genetic diversity. Survival of adults (0–43%) was positively influenced by release day, with some evidence that genetic diversity also positively influenced adult apparent survival. Conclusions: Noninvasive genetic sampling has proven to be an effective and efficient tool in monitoring this reintroduced population, assessing both demographic and genetic factors. This data has helped managers address the goals of the Columbia Basin recovery program of establishing multiple sustainable wild populations within the sagebrush steppe habitat of Washington. Full article

Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating capacity of the cytotoxin and plays a key role in the bacterium’s pathogenic potential. This study investigated the allelic diversity of the vacA among H. pylori strains infecting patients in Jordan with various gastric conditions and examined potential associations between vacA s-and m- genotypes, histopathological and endoscopic findings, and the development of gastric diseases. Gastric biopsies were collected from 106 patients at two hospitals in Jordan who underwent endoscopic examination. The collected biopsies for each patient were subjected to histopathological assessment, urease detection using the Rapid Urease Test (RUT), a diagnostic test for H. pylori, and molecular detection of the vacA gene and its s and m alleles. The histopathology reports indicated that 83 of 106 patients exhibited gastric disorders, of which 81 samples showed features associated with H. pylori infection. The RUT was positive in 76 of 106 with an accuracy of 93.8%. Real-time polymerase chain reaction (RT-PCR) targeting the 16S rRNA gene confirmed the presence of H. pylori in 79 of 81 histologically diagnosed cases as infected (97.5%), while the vacA gene was detected only in 75 samples (~95%). To explore genetic diversity, PCR-amplified fragments underwent sequence analysis of the vacA gene. The m-allele was detected in 58 samples (73%), the s-allele was detected in 45 (57%), while both alleles were not detected in 13% of samples. The predominant genotype combination among Jordanians was vacA s2/m2 (50%), significantly linked to mild chronic gastritis, followed by s1/m2 (35%) and s1/m1 (11.8%) which are linked to severe gastric conditions including malignancies. Age-and gender-related differences in vacA genotype were observed with less virulent s2m2 and s1m2 genotypes predominating in younger adults specially males, while the more virulent m1 genotypes were found exclusively in females and middle-aged patients. Genomic sequencing revealed extensive diversity within H. pylori, likely reflecting its long-standing co-evolution with human hosts in Jordan. This genetic variability plays a key role in modulating virulence and influencing clinical outcomes. Comprehensive characterization of vacA genotypic variations through whole-genome sequencing is essential to enhance diagnostic precision, strengthen epidemiological surveillance, and inform targeted therapeutic strategies. While this study highlights the significance of the vacA m and s alleles, future research is recommended in order to investigate the other vacA allelic variations, such as the i, d, and c alleles, to achieve a more comprehensive understanding of H. pylori pathogenicity and associated disease severity across different strains. These investigations will be crucial for improving diagnostic accuracy and guiding the development of targeted therapeutic strategies. Full article

The P1104A variant in the TYK2 gene is recognized as the first common monogenic cause of tuberculosis, and recent studies also suggest a potential role in COVID-19 severity. However, its frequency and impact in admixed Latin American populations remain underexplored. Therefore, we investigated the P1104A/TYK2 variant in a cohort comprising 1826 RT-PCR-confirmed COVID-19 patients from Southern Brazil. Cases were stratified by severity into non-severe (n = 1190) and severe (n = 636). Three homozygous individuals were identified—one non-severe and two severe cases—although no statistically significant association with disease severity was observed. The frequency of the C allele in the COVID-19 cohort (2.85%) was significantly higher than in Brazilian population databases, including “DNA do Brasil” (1.81%, p < 0.001) and ABraOM (2.34%, p = 0.03), but lower than in the multi-ancestry gnomAD database (3.71%, p = 0.01), possibly reflecting ancestry bias. We also observed associations between COVID-19 severity and sex (p = 0.003), age (p < 0.001), obesity (p < 0.001), diabetes (p < 0.001), and hypertension (p < 0.001). Future studies in larger and more diverse cohorts are needed to characterize the prevalence of the variant in admixed populations and assess its contribution to COVID-19 susceptibility. Full article