High Genetic Diversity Research Articles

Climatic factors, but not geographic distance, promote genetic structure and differentiation of Cleistogenes squarrosa (Trin.) Keng populations

Climate can shape plant genetic diversity and genetic structure, and genetic diversity and genetic structure can reflect the adaptation of plants to climate change. We used rbcl and trnL-trnF sequences to analyze the genetic diversity and genetic structure of C. squarrosa under the influence of different environmental factors in Inner Mongolia grassland. The results showed that the genetic diversity of this species was low. (The trnL-trnF sequences have higher genetic diversity than rbcl sequences.) C. squarrosa had low genetic diversity compared to other prairie plants, but had a more pronounced genetic structure. The haplotype network diagram of the combined sequences could be divided into two categories, and the results of the NJ, MP, and ML trees also showed that the haplotypes were divided into two branches. The results of genetic structure analysis showed that that the populations located in the desert steppe fall into exactly one cluster, and the populations located in the typical steppe fall into exactly another cluster. The neutrality tests were all negative and the mismatch distribution also showed a single peak across the population, suggesting that C. squarrosa had undergone population expansion and was well adapted to the local environment. The results of the mantel test showed that climate had a greater influence on the genetic distance of C. squarrosa, with annual precipitation having a higher influence than mean annual temperature. This study provided basic genetic information on the genetic structure of C. squarrosa and contributes to the study of genetic adaptation mechanisms in grassland plants.

Assessment of genetic biodiversity and association of micronutrients and agronomic traits using microsatellites and staining methods which accelerates high-micronutrients variety selections within different wheat groups

Evaluation of genetic biodiversity for micronutrients is crucial for breeding high-quality crops and addressing the negative impacts of mineral deficiencies. The objectives of this research were to assess genetic variation and the relationship between grain Fe and Zn levels and agronomic traits in a diverse collection of wheat varieties. Additionally, the study aimed to determine the correlation between microsatellite markers (SSR) and micronutrient quantities. A total of 42 genotypes (Iranian commercial cultivars, landraces, and Afghan and Swiss varieties) were evaluated over a two-year period. Fe and Zn levels were measured using two semi quantitative staining assays and atomic absorption spectrophotometry (AAS) facility. Semi-quantitative staining methods and AAS showed high correlations for micronutrient contents. Landraces exhibited higher Fe (63.79 mg/kg) and Zn (44.76 mg/kg) but lower grain yield compared with commercial cultivars. Heritability estimates ranged 53%-79.43%, suggesting that genetic variance played a higher contribution in the phenotypic variation of traits than environmental factors. Notably, Fe content displayed significant correlations with days to maturity. Canonical correlation analysis (CCA) revealed that Zn content was correlated with four agronomic traits. Evaluation of genetic diversity using SSR markers demonstrated high genetic variation among the genotypes tested. The analysis of polymorphism information content (PIC) indicated that SSR primers had an average PIC of 0.75, with the Xgwm192 primer exhibiting higher PIC than others. Several SSR markers revealed association with micronutrient content that can be used in marker-assisted selection (MAS) programs aimed at selection of high micronutrient genotypes. In conclusion, the findings underscored the substantial genetic diversity present in micronutrient levels among global wheat genotypes, the potential of landraces for micronutrients biofortification of wheat cultivars through cross hybridization, the utility of staining methods for screening high/low micronutrient genotypes, and use of microsatellite markers for marker-assisted breeding aiming to micronutrient improvement in breeding programs.

Does Every Strain of Pseudomonas aeruginosa Attack the Same? Results of a Study of the Prevalence of Virulence Factors of Strains Obtained from Different Animal Species in Northeastern Poland

Background: Pseudomonas aeruginosa is a pathogen that causes infections in animals and humans, with veterinary implications including ear infections in dogs, respiratory diseases in cats, and mastitis in ruminants. In humans, it causes severe hospital-acquired infections, particularly in immunosuppressed patients. This study aimed to identify and assess the prevalence of specific virulence factors in Pseudomonas aeruginosa isolates. Methods: We analyzed 98 Pseudomonas aeruginosa isolates from various animal samples (dogs, cats, ruminants, fowl) from northeastern Poland in 2019–2022 for virulence-related genes (toxA, exoU, exoT, exoS, lasB, plcN, plcH, pldA, aprA, gacA, algD, pelA, endA, and oprF) by PCR and assessed biofilm formation at 48 and 72 h. Genomic diversity was assessed by ERIC-PCR. Results: The obtained results showed that all strains harbored the pelA gene (100%), while the lowest prevalence was found for pldA (24%) and exoU (36%). Regardless of the animal species, strong biofilm forming ability was prevalent among the strains after both 48 h (75%) and 72 h (74%). We obtained as many as 87 different genotyping profiles, where the dominant one was profile ERIC-48, observed in four strains. Conclusions: No correlation was found between presence or absence of determined genes and the nature of infection. Similarly, no correlation was found between biofilm-forming genes and biofilm strength. The high genetic diversity indicates challenges for effective prevention, emphasizing the need for ongoing monitoring and research.

The genome landscape of the Xinglong buffalo

BackgroundXinglong buffalo, as an indigenous breed in Hainan province of China, possesses characteristics such as high humidity tolerance, disease resistance and high reproductive capacity. Combined with whole genome sequencing technology, comprehensive investigation can be undertaken to elucidate the genomic characteristics, functions and genetic variation of Xinglong buffalo population.ResultsXinglong buffalo has the highest genetic diversity, lowest runs of homozygosity average length, and fasted decay of linkage disequilibrium in our study population. Phylogenetic tree results revealed that Xinglong buffalo was gathered together with Fuzhong buffalo firstly. The population genetic structure analysis indicates that at K = 3, the Xinglong buffalo for the first time showed a distinct ancestral origin from other water buffalo. Furthermore, compared to different populations, candidate genes displaying significantly distinct patterns of single nucleotide polymorphisms (SNPs) (e.g., RYR2, COX15, PCDH9, DTWD2, FCRL5) distribution have been identified in the Xinglong buffalo.ConclusionsBased on the whole genome sequencing data, this study identified a substantial number of SNPs and assessed the genetic diversity and selection signatures within the Xinglong buffalo population. These results contribute to understanding the genomic characteristics of Xinglong buffalo and their genetic evolutionary status. However, the practical significance of these signatures for genetic enhancement still requires confirmation through additional samples and further experimental validation.

Whole-Genome Analysis of Porcine Epidemic Diarrhea Virus from Yunnan, China

Porcine epidemic diarrhea virus (PEDV) is a member of the genus α-coronavirus and causes severe diarrhea in piglets, leading to enormous economic losses in the pig industry. To understand the epidemic variation of PEDV strains in Yunnan province, three PEDV strains (YN2021, YNLP 2022, and YNBS 2022) and one commercially available attenuated vaccine strain (Attenuated AJ1102-R) that were previously isolated were sequenced and compared with the representative PEDV strains. NJ phylogenetic analysis showed that YN2021 strain and Attenuated CV777 strain were clustered into GI-b subtype, while YNLP 2022 and YNBS 2022 belong to GII-b subtype, accompanying ZJCZ4 and Attenuated AJ1102-R. RDP analysis revealed that YNLP 2022 was a genome recombination from both GII-b strain PEDV-7C and GII-a strain YN1, of which the recombination region is in the range nt4994–7605. YNBS 2022 strain was another recombination originated from GII-b subtype strain 17GXZC-1ORF3c and GII-a subtype strain PEDV-CHZ, of which the counterpart is in the range nt16399–22326. The Yunnan strain of PEDV was analyzed for the first time from the whole-genome perspective, and comprehensive analysis showed that the Yunnan strains have high genetic variation. This study may shed new light on the current PEDV infections in Yunnan and pave the way toward further control of PEDV infections.

Genetic Diversity Analysis of Rice (Oryza sativa L.) Genotypes for Yield and Sheath Blight Screening

Sheath blight disease, caused by Rhizoctonia solani Kühn, is considered the second most important disease affecting rice, causing yield reduction globally. In the present study thirty diverse rice genotypes were inoculated with fungal mycelia during the maximum tillering stage to assess the genetic diversity of rice genotypes for sheath blight reactions. Mahalanobis D2 statistics was performed for grain yield and yield contributing features under sheath blight stress to calculate the genetic divergence between the genotypes. Four clusters were formed from the genotypes. Cluster III has the highest number of genotypes (nine). The highest inter-cluster distance was noticed between cluster I and cluster IV (11.41) and minimum between cluster III and cluster IV (6.50). The intra-cluster distances were lower, indicating the homogeneity of the genotypes within the clusters. Maximum intra-cluster D2 value was recorded in cluster IV (6.32) and minimum in cluster II (5.36). Cluster I showed high genetic divergence from all other clusters. Hence, the genotypes from cluster I could be used for hybridization with the genotypes of other clusters to develop high yielding sheath blight resistant rice varieties.

Genetic Diversity and Selection Signatures of Lvliang Black Goat Using Genome-Wide SNP Data

Lvliang black goat (LBG) is an excellent local breed resource in China that is known for its black fur, excellent meat quality, and strong adaptability. Studying the genetic mechanism and germplasm characteristics of LBG can provide theoretical and practical basis for the protection of the genetic resources of this breed and help implement conservation and breeding. In this study, the genetic diversity of the LBG population was evaluated using whole-genome SNP data. It was found that the LBG population had a high genetic diversity and a low degree of inbreeding. According to the clustering results of male goats and the relationship between individuals, the LBG population was divided into 13 families. Then, through population structure analysis, it was found that LBG had a close genetic relationship with the Nanjiang goat and Qinggoda goat populations, and they may have the same ancestors. The LBG population has retained some ancient genetic characteristics and is a special population that integrates local genetic characteristics and foreign gene flow. Through four selection signal analyses, we detected multiple candidate genes related to economic traits (CFL2, SCD, NLRP14, etc.) and adaptability (C4BPA, FUT8, PRNP, etc.) in the LBG population. In addition, in a comparative analysis with three commercial breeds (Saanen goat, Boer goat and Angora goat) we also found multiple genes related to physical characteristics (ERG, NRG3, EDN3, etc.). Finally, we performed functional enrichment analysis on these genes and explored their genetic mechanisms. This study provides important data support for the protection and breeding of LBG and provides a new perspective for enriching the genetic diversity of goat populations.

Long live the cat: Ocelot population viability in a planned reintroduced population in Texas, USA

AbstractReintroductions are often needed to recover carnivore populations and restore ecological processes. Felids are common subjects of reintroduction efforts, but published population models informing felid reintroduction plans are uncommon, and poor planning has sometimes caused issues in felid reintroduction programs. In the United States, ocelots (Leopardus pardalis pardalis) are classified as endangered, and recovery requires population expansion into historic habitat. A multi‐organization effort is underway to establish a new ocelot population in Texas by releasing ocelots into an area of 478 km2 of suitable habitat in ocelots' historic but now unoccupied range. In this study, we used population viability analyses to compare different ocelot reintroduction strategies for the identified reintroduction area. Based on a potential ocelot breeding program's limitations, we modeled reintroduction using a founding population of no more than six ocelots and no more than four ocelots released per year for no more than 15 subsequent years. Within these limitations, we assessed projected population abundances and extinction risks after 30 years for 20 different reintroduction strategies. We found that long‐term releases are necessary to establish a viable population; under conservative model assumptions, releasing six ocelots in the initial year and then releasing four individuals annually for an additional 10–15 years is necessary for attaining a projected population greater than 36.62 ocelots (baseline) with <6% extinction risk. We also found that ocelot population abundance is about equally sensitive to post‐release mortality and inbreeding depression. This highlights the importance of not only supporting reintroduced ocelots' survival but also managing for high genetic diversity in the reintroduction program. Further, we found that realistic but more liberal assumptions on the carrying capacity of the reintroduction area and the age of first reproduction for ocelots increase projected population abundances (53.95 individuals and 61.26 individuals, respectively), and thus reintroduction success. The model's sensitivity to carrying capacity suggests that long‐term habitat protection and expansion are among the most important management actions to support ocelot reintroduction. Our study establishes the first population viability model for an ocelot reintroduction plan anywhere across the species' wide geographic range, and it reinforces several key considerations for wildlife reintroduction efforts worldwide.

Genetic Diversity and Population Structure Analysis of Pinus elliottii Germplasm Resources in Jiangxi Province

This study aimed to compare and assess the genetic diversity and trends among the introduced family provenance, first-cycle superior trees breeding provenance, and improved-generation superior trees breeding provenance of Pinus elliottii using EST-SSR markers. The goal was to provide a foundation for advanced genetic improvement and sustainable utilization of P. elliottii in Jiangxi Province. A total of 417 individuals were analyzed for their genetic diversity and population structure using 19 pairs of SSR markers. The analysis identified 103 alleles across all the samples, with an average of 5.421 alleles per locus. Compared to other coniferous species, P. elliottii exhibited a moderate to high level of genetic diversity (I = 0.862, He = 0.457). Analysis of the molecular variance (AMOVA) revealed that 97.90% of the genetic variation occurred within provenances, consistent with a low genetic differentiation coefficient (Fst = 0.016 < 0.05) and high gene flow (Nm = 15.715) among provenances. In addition, analysis using STRUCTURE v. 2.3.4 software divided the 417 germplasm samples into two distinct groups, corroborating the results of the principal coordinates analysis (PCoA) and the unweighted pair group method with arithmetic (UPGMA) clustering analysis. Overall, the germplasm resources of P. elliottii exhibited rich genetic diversity, with the majority of the genetic variation occurring within provenances. For the genetic improvement of high-resin-yielding slash pines, breeding programs should prioritize populations with high genetic diversity while carefully selecting superior individuals from within those populations. These findings provide a solid foundation for breeding high-resin-yielding varieties and for future research on the sustainable utilization of these valuable resources.

Population Structure and Selection Signatures in Chinese Indigenous Zhaotong Pigs Revealed by Whole-Genome Resequencing

Zhaotong pig (ZTP) is a Chinese indigenous pig breed in Yunnan Province, known for its unique body shape and appearance, good meat quality, strong foraging ability, and adaptability. However, there is still a lack of research on its genome. In order to investigate the genetic diversity, population structure, and selection signatures of the breed, we conducted a comprehensive analysis by resequencing on 30 ZTPs and comparing them with genomic data from 10 Asian wild boars (AWBs). A total of 45,514,452 autosomal SNPs were detected in the 40 pigs, and 23,649,650 SNPs were retained for further analysis after filtering. The HE, HO, PN, MAF, π, and Fis values were calculated to evaluate the genetic diversity, and the results showed that ZTPs had higher genetic diversity and lower inbreeding coefficient compared with AWBs. Population structure was analyzed using NJ tree, PCA, ADMIXTURE, and LD methods. It was found that ZTPs were population independent of AWBs and had a lower LD decay compared to AWBs. Moreover, the results of the IBS genetic distance and G matrix showed that most of the individuals had large genetic distances and distant genetic relationships in ZTPs. Selection signatures were detected between ZTPs and AWBs by using two methods, FST and π ratio. Totals of 1104 selected regions and 275 candidate genes were identified. Finally, functional enrichment analysis identified some annotated genes that might affect fat deposition (NPY1R, NPY5R, and NMU), reproduction (COL3A1, COL5A2, GLRB, TAC3, and MAP3K12), growth (STAT6 and SQOR), tooth development (AMBN, ENAM, and ODAM), and immune response (MBL2, IL1A, and DNAJA3). Our results will provide a valuable basis for the future effective protection, breeding, and utilization of ZTPs.

The Influence of Altitude on the Polyphenols Content and Antioxidant Capacity of Northern Moroccan 'Dellahia' Prickly Pear Juice

Moroccan cactus exhibits high genetic variability with several cultivars. The 'Dellahia' prickly pear variety, prevalent in northern Morocco and noted for its green pulp, is among the least valued cactus varieties, primarily consumed fresh. This study aimed to assess the impact of altitude on total phenolic acids and flavonoid content (TPC and TFC) and the antioxidant activity of 'Dellahia' prickly pear juice from northern Morocco. Significant differences in TPC ranged from 91.29 to 130.45 mg GAE/Kg of juice from the Mestassa and Wahran sites (at 119 m and 482 m altitude, respectively). TFC also varied slightly, from 18.8 to 19.1 mg RE/Kg of juice. Variations in antioxidant activity were evident in both DPPH• and ABTS+ assays, with DPPH• inhibition percentages ranging from 8.85% to 19.14% and ABTS+ inhibition from 41.07% to 54.35%. However, the influence of altitude on these parameters was inconclusive, as samples from higher altitudes did not consistently yield lower or higher values. Other factors such as soil composition, sunlight, and farming practices may influence these results.

Genotyping-by-sequencing shows high genetic diversity in Corylus avellana germplasm resistant to eastern filbert blight

European hazelnut (Corylus avellana) is an anemophilous, dichogamous, self-incompatible tree nut species. It is native to a large portion of Europe, Turkey, and the Caucasus region, across which a wealth of plant genetic resources is present. The objective of this study was to evaluate the genetic diversity of a core set of C. avellana representing the world’s germplasm using genotyping-by-sequencing derived single nucleotide polymorphism (SNP) markers and to classify novel eastern filbert blight (EFB) resistant or tolerant accessions. Two-hundred-twenty-two accessions underwent next-generation sequencing (NGS) to generate SNP markers. From this, 1,250 SNP markers were used to construct a neighbor-joining (NJ) dendrogram and perform a STRUCTURE and discriminant analysis of principal coordinates (DAPC) analyses. In the dendrogram, five major groups were established, which generally corresponded to geographic origins of the plant materials studied. In STRUCTURE, support was found for groupings at (K) = 3, (K) = 6, and (K) = 10 populations, with the greatest Δ-(K) value occurring at (K) = 10. Although the three different analyses indicated slightly different solutions, the overall results were generally consistent from the standpoint of identifying similar accession groupings. For many of the accessions, recorded origins tended to correspond with their genetic grouping, although there was also evidence of intermixing and likely movement of plant materials. Interestingly, in all three analyses, a vast majority of the new accessions from the Republic of Georgia formed their own distinct group, highlighting this geographic region as a unique pool of C. avellana genetic resources. Overall, EFB resistant/tolerant accessions were placed across a wide range of genetic backgrounds. Thus, our results indicate EFB resistance/tolerance is present across a wide spectrum of C. avellana genetic resources, with the Georgian accessions representing a new and relatively unique germplasm pool that can be incorporated into hazelnut breeding programs.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

Genetic diversity and molecular evolution of the internal transcribed spacer regions (ITS1–5.8S–ITS2) of Babesia vogeli

Canine babesiosis, a severe haemoparasitic disease caused by Babesia species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of B. vogeli on the basis of the internal transcribed spacer regions (ITS1–5.8S–ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (n = 62) exhibited 92.5–100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5–93.8 % between them. Notably, the newly generated Indian sequences (n = 21) demonstrated a high degree of homology, with 98.3–100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different B. vogeli populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2–25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The B. vogeli populations between Thailand and Tunisia exhibited the highest genetic differentiation (FST = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of B. vogeli indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-term molecular surveillance program. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of B. vogeli were observed on the basis of internal transcribed spacer regions (ITS1–5.8S–ITS2).

Genetic diversity of Bartonella species in small mammals in the Qinghai Menyuan section of Qilian Mountain National Park, China

Bartonella are vector-borne gram-negative facultative intracellular bacteria that can infect a wide spectrum of mammals, and are recognized as emerging human pathogens. This study aimed to investigate the prevalence and molecular characteristics of Bartonella infections in small mammals within the Qinghai Menyuan section of Qilian Mountain National Park, China. Small mammals were captured, and the liver, spleen and kidney were collected for Bartonella detection and identification using a combination of real-time PCR targeting the transfer-mRNA (ssrA) gene and followed by sequencing of the citrate synthase (gltA) gene. A total of 52 rodents were captured, and 36 rodents were positive for Bartonella, with a positivity rate of 69.23% (36/52). Bartonella was detected in Cricetulus longicaudatus, Microtus oeconomus, Mus musculus, and Ochotona cansus. The positivity rate was significantly different in the different habitats. Two Bartonella species were observed, including Bartonella grahamii and Bartonella heixiaziensis, and B. grahamii was the dominant epidemic strain in this area. Phylogenetic analysis showed that B. grahamii mainly clustered into two clusters, which were closely related to the Apodemus isolates from China and Japan and the local plateau pika isolates, respectively. In addition, genetic polymorphism analysis showed that B. grahamii had high genetic diversity, and its haplotype had certain regional differences and host specificity. Overall, high prevalence of Bartonella in small mammals in the Qinghai Menyuan section of Qilian Mountain National Park. B. grahamii is the dominant strain with high genetic diversity and potential pathogenicity to humans, and corresponding control measures should be considered.

Development and Application of Microsatellite Markers for Genetic Diversity Assessment and Construction of a Core Collection of Myrciaria dubia (Kunth) McVaugh Germplasm from the Peruvian Amazon

The Amazonian shrub Myrciaria dubia (camu-camu) produces vitamin C-rich fruits of growing commercial interest. However, sustainable utilization requires assessment and protection of the genetic diversity of the available germplasm. This study aimed to develop and apply microsatellite markers to assess genetic diversity and construct a core collection of M. dubia germplasm from the Peruvian Amazon. Sixteen polymorphic microsatellite loci were developed using an enrichment approach. The evaluation of 336 genotypes from 43 accessions of the germplasm bank, originating from eight river basins, was conducted using these newly developed markers. Genetic diversity parameters, including observed and expected heterozygosity, were calculated. Analysis of molecular variance (AMOVA) was performed to assess the distribution of genetic variation within and among accessions and river basins. Bayesian clustering analysis was employed to infer population structure. A core collection was constructed to maximize allelic richness. High genetic diversity was observed, with heterozygosity values ranging from 0.468 to 0.644 (observed) and 0.684 to 0.817 (expected) at the river basin level. AMOVA indicated significant genetic variation within (73–86%) compared to among (14–27%) accessions and river basins. Bayesian clustering detected ten genetic clusters, with several degrees of admixture among river basins, except for the genetically homogeneous Putumayo River basin. A core collection comprising 84 plant genotypes (25% of the full collection) was established, representing 90.82% of the overall allelic diversity. These results have important implications for M. dubia conservation strategies and breeding programs, in demonstrating a need for genetic connectivity between populations but preserving unique genetic resources in isolated basins. These results validate the expected levels of diversity and population subdivision in a crop and stress the need to secure genetically diverse germplasms, underscoring the importance of thorough genetic characterization for ex situ germplasm management.

Temporal and inter-specific population genetics analyses of Sebastiscus marmoratus and S. tertius provide novel implications for fishery management

ABSTRACT Understanding population genetic diversity and evolutionary dynamics of marine fish species can provide theoretical bases for fishery management and germplasm conservation, especially facing a changing environment. The rockfish species in genus Sebastiscus are economically important species for farming and sport fisheries in China, Japan and Korea. In this study, inter-annual and inter-specific comparisons on genetic diversity, population differentiation and historical demography of S. marmoratus and S. tertius collected from coastal waters of Zhangzhou, China were conducted using mitochondrial control region sequences. High levels of genetic diversity were observed in both species, indicating high adaptive potential to environmental changes. Demographic analyses detected recent population expansion in population S. tertius (Ste-2020) and population S. marmoratus collected in 2020 (Sma-2020), yet failed in population collected in 2016 (Sma-2016). Moreover, in population Sma-2020, novel haplotypes were detected and grouped into a separate sub-branch, revealed by neighbour-joining topology. Detected recent population expansion and novel haplotypes might be considered as a response to environmental changes. Besides, results of genetic differentiation analysis suggested high intra-specific genetic variation in both species. These genetic data and information will provide novel implications for strengthening the management of S. marmoratus and S. tertius fisheries in climate change scenarios.

Prevalence and genetic characterization of linezolid resistance gene reservoirs in hospital sewage from Zhejiang Province, China

Hospital sewage represented important hotspots for the aggregation and dissemination of clinically relevant pathogens and antimicrobial resistance genes. To investigate the prevalence and molecular epidemiology of linezolid resistance genes in hospital sewage, both influent and effluent samples from 11 hospitals in Zhejiang Province, China, were collected and analyzed for linezolid resistance gene carriers. Thirty colonies of putative isolates that grew on the selective media with 10 mg/L florfenicol were randomly picked per sample. A total of 420 Gram-positive isolates, including 330 from 11 influent samples and 90 from three effluent samples, were obtained. Each isolate carried at least one of the linezolid resistance genes, including optrA, poxtA, cfr, and cfr(D), and the optrA gene was highly dominant (388/420). Enterococci displayed predominance among the linezolid resistance gene carriers in the hospital sewage, exhibiting a resistance rate to linezolid of 77.8 %. The wild-type OptrA and OptrA variants KLDP, RDK, and KLDK, all associated with high linezolid MICs, were most frequently detected. Phylogenetic analysis revealed the multispecies and polyclonal distribution of linezolid-resistant bacteria in hospital sewage, while Enterococcus faecalis sequence types (STs) 16 and 179 demonstrated the widest dissemination across different hospitals. Despite generally high genetic diversity, phylogenetic analysis showed that 87 isolates, assigned to ten STs from both sewage and other sources, were genetically related. Moreover, the genetic environment of linezolid resistance genes in isolates from sewage was similar to that from animals, humans, or the environment, with “Tn554-fexA-optrA” as the most common structure. These findings revealed the potential risk of the transmission of linezolid resistance genes through hospital sewage to other environments.

Clade I mpox virus genomic diversity in the Democratic Republic of the Congo, 2018–2024: Predominance of zoonotic transmission

Recent reports raise concerns on the changing epidemiology of mpox in the Democratic Republic of the Congo (DRC). High-quality genomes were generated for 337 patients from 14/26 provinces to document whether the increase in number of cases is due to zoonotic spillover events or viral evolution, with enrichment of APOBEC3 mutations linked to human adaptation. Our study highlights two patterns of transmission contributing to the source of human cases. All new sequences from the eastern South Kivu province (n= 17; 4.8%) corresponded to the recently described clade Ib, associated with sexual contact and sustainedhuman-to-human transmission. By contrast, all other genomes are clade Ia, which exhibits high genetic diversity with low numbers of APOBEC3 mutations compared with clade Ib, suggesting multiplezoonotic introductions. The presence of multiple clade I variants in urban areas highlights the need for coordinated international response efforts and more studies on the transmission and the reservoir of mpox.

Assessment of genetic parameters and heritability of Dendrobium species section Spatulata native to Indonesia

Being one of the most abundant genera of orchids, Dendrobium presents a valuable genetic resource for hybridization programs. Morphological characterization and assessment of genetic parameters plays a crucial role in establishing genetic connections among orchid species within the same genus. The study aims to discern the morphological traits of five Indonesian Dendrobium species, intending to evaluate their potential as candidates for crossbreeding programs. The materials used in this study were D. antennatum, D. discolor, D. stratiotes, D. lineale, D. gouldii, and D. sylvanum. This research examines 21 quantitative traits and 21 qualitative morphological traits of the studied Dendrobium. The findings reveal variations in characters related to flowers, leaves, and pseudobulbs. The analysis of genetic parameters indicates the presence of genetic diversity in traits such as flower stalk length, length of inflorescence, flower series length, flower length, flower width, dorsal sepal width, lateral sepal width, petal length, petal width, labellum length, labellum width, and the number of florets. All observed traits demonstrate high heritability. So, the characters that have high genetic variability and heritability are valuable in selection criteria for plant breeding.