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Background: In malaria endemic regions, Plasmodium falciparum infection is characterized by variable genetic diversity at different settings. The parasite's various forms are found at varied frequency in different geographic areas. Understanding malaria parasite diversity and transmission is vital to evaluate control interventions. The aim of this study was under taken to determine the status of P. falciparum genetic diversity and MOI in different regions of Ethiopia. Methods: Relevant publications were identified from electronic databases such as; PubMed, EMBASE, Google scholar and Google. Besides, an online search was done using the above databases for all articles published in English on genetic diversity of P. falciparum in Ethiopia. STATA software was used for data analysis. The pooled estimates were calculated using random effect model. The summary estimates were presented using forest plots and tables. Results: A total of 11 studies were included in the systematic review. However, only 8, 10 and 2 studies were included for Pfmsp-1, Pfmsp-2 and glurp gene meta-analysis, respectively. However, the meta-analysis result showed that the pooled prevalence of Pfmsp-1, msp-2 and glurp gene were 84% for both msp-1/2% and 51%, respectively. The pooled prevalence of msp-1 gene was higher in Amhara followed by Oromia region and lower in SNNPR while, for msp-2 gene the pooled prevalence was higher in Benshangul gumez region. Among the allelic family of msp-1 and msp-2 genes, MAD20 (34%) and FC27 (44%) were the most predominant respectively. Conclusion: Based on the review, there is evidence of the presence of high genetic diversity of P. falciparum parasites in Ethiopia, suggesting that malaria transmission remain high and that strengthened control efforts are needed. The approaches and methods used for investigation of diversified parasites have similarity between studies and should use advanced molecular techniques, like microsatellite, to assess the genetic diversity of P. falciparum for better results.

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Objective: Characterization studies of the phenotypic and genetic diversity of Mongolian goats are limited, despite several goat breeds being registered in the country. This study aimed to evaluate the phenotypic and genetic diversity of 14 cashmere goat populations in Mongolia, consisting largely of identified goat breeds. Methods: Body weight, cashmere quality, and coat color were the phenotypic traits considered in this study. A linear model was used to fit body weight and cashmere traits, and least squares means (LSMs) were estimated for the region and location classes. Genetic diversity and structure were assessed using a goat 50K SNP array. Results: The studied populations exhibited greater phenotypic diversity at the regional level. A very small overall differentiation index (Fst: 0.017) was revealed by Wright's Fst and a very small overall inbreeding index (F ROH1 :0.019) was revealed based on runs of homozygosity. Genetic clustering of populations by principal components showed large variances for the two goat populations of the Russian admixture (Gobi Gurvan Saikhan and Uuliin Bor), and smaller but differentiated clusters for the remaining populations. Similar results were observed in the admixture analysis, which identified populations with the highest (Govi Gurvan Saikhan and Uuliin Bor) and lowest (Tsagaan Ovoo Khar) exotic admixtures. A genomewide association study (GWAS) of body weight and cashmere traits identified a few significant variants on chromosomes 2, 4, 5, 9, and 15, with the strongest variant for cashmere yield on chromosome 4. The GWAS on coat color yielded nine significant variants, with the strongest variants located on chromosomes 6, 13, and 18 and potential associations with KIT, ASIP, and MC1R genes. These signals were also found in other studies on coat color and patterns in goats. Conclusion: Mongolian cashmere goats showed relatively low genetic differentiation and low inbreeding levels, possibly caused by the traditional pastoral livestock management system and the practice of trading breeding bucks across provinces, along with a recent increase in the goat population. Further investigation of cashmere traits using larger samples and alternative methods may help identify the genes or genomic regions underlying cashmere quality in goats.

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Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5-5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P < 0.001), more total variants (P < 0.001), and lower individual inbreeding (FROH; P < 0.001) than horses in Group 2. However, the distribution of numbers of variants, allele frequency, and extent of ROH overlapped among all horses such that it was not possible to identify the group of origin of any single horse using these measures. Consequently, the Thoroughbred population would be better monitored by investigating changes in specific variants, rather than relying on broad measures of diversity. The WGS for these 185 horses is publicly available for comparison to other populations and as a foundation for modeling changes in population structure, breeding practices, or the appearance of deleterious variants.

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Candida krusei, also known as Pichia kudriavzevii, is an emerging non-albicans Candida (NAC) species causing both superficial and deep-seated infections in humans. This fungal pathogen is inherently resistant to the first-line antifungal drug, fluconazole, and is widely distributed in natural environments such as soil, foods, vegetables, and fruits. In this study, we collected 86 C. krusei strains from clinical settings and traditional fermented vegetables from different areas of China. Compared to C. krusei strains from fermented vegetables, clinical isolates exhibited a higher ability to undergo filamentation and biofilm development, which could facilitate its host colonization and infections. Isolates from fermented vegetables showed higher resistance to several antifungal drugs including fluconazole, voriconazole, itraconazole, amphotericin B, and caspofungin, than clinical strains, while they were more susceptible to posaconazole than clinical strains. Although C. krusei has been thought to be a diploid organism, we found that one-fourth of clinical strains and the majority of isolates from fermented vegetables (87.5%) are triploid. Whole-genome sequencing and population genetic analyses demonstrated that isolates from clinical settings and fermented food are genetically associated, and distributed across a wide range of genetic clusters. Additionally, we found that six nucleotide substitutions at the promoter region of the ABC11 gene, encoding a multidrug efflux pump, could play a critical role in antifungal resistance in this species. Given the ubiquitous distribution of C. krusei strains in fermented vegetables and their genetic association with clinical strains, a One Health approach will be necessary to control the prevalence of this pathogen.

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Host genetic variability can modulate infection resistance, although its role in infection clearance remains unclear. Hookworm disease (Uncinaria sp.) is the leading cause of pup mortality in several otariid species, although the parasite can be cleared through immune-mediated processes. We evaluated the association of host genetic diversity, body condition and immune response with hookworm resistance and/or clearance in the South American fur seal (Arctocephalus australis). Uninfected pups had higher heterozygosity than parasitized individuals, indicating a negative relationship between heterozygosity and the chances of infection. Likewise, pups that died of hookworm infection had lower heterozygosity than those that died of non-infectious causes. Interestingly, once infected, pups that survived hookworm infection had heterozygosities similar to pups that died of hookworm disease. However, pups that cleared the infection had a higher body mass and parasite-specific immunoglobulin G levels than those that did not recover or died of hookworm disease. Thus, although heterozygosity predicted resistance to and mortality from hookworm infections, it did not affect parasite clearance, which was facilitated by better body condition and adaptive immune responses. This demonstrates that host genetic variability and host-environment interactions influence disease dynamics, acting at different, well-defined stages of infection.

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Bacterial leaf spot (BLS) of lettuce (Lactuca sativa L.) is caused by the bacterium Xanthomonas hortorum pv. vitians which is hypothesized to have at least three races of the pathogen present in North America as defined by their differential resistance phenotypes in lettuce cultivars/accessions. Though resistance to X. hortorum pv. vitians race 1 has been identified in cultivated lettuce, numerous other X. hortorum pv. vitians strains cause disease on cultivars carrying this resistance locus. Thus far, resistance to these 'additional' X. hortorum pv. vitians strains has not been adequately described in L. sativa or in any other wild Lactuca species sexually compatible with cultivated lettuce. We have performed an extensive screening of approximately 500 Lactuca accessions from L. sativa, L. serriola, L. saligna, L. virosa, L. aculeata, L. altaica, and L. perennis species to identify accessions resistant to these additional X. hortorum pv. vitians races. Following the initial screenings, greenhouse tests confirmed that X. hortorum pv. vitians race 2 and race 3 could be defined using Lactuca sativa accessions. Race 2 strain BS3217 had an incompatible response (hypersensitive response) on ten Lactuca serriola accessions including PI491114 and PI491108, while race 1 (BS0347) and race 3 (BS2861) strains of X. hortorum pv. vitians showed a compatible response (disease) on these genotypes. L. serriola accession ARM09-161 (and selections derived from it) was the only genotype resistant to the race 3 strain BS2861. L. serriola accessions identified in this study to be resistant to race 2 and race 3 of X. hortorum pv. vitians, together with race 1 resistant cultivars, can be used for pyramiding resistance loci against the three races of the BLS-causing pathogen.

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Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to "listing" decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data-deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD-based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities.

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Sago plant (Metroxylon sagu Rottb.) is one of the most carbohydrate-producing plants in the world. Microsatellites or simple sequence repeats (SSRs) play an important role in the genome and are used extensively compared to other molecular markers. For the first time, we are exploiting data expressed sequence tags (EST) of sago plants to identify and characterise markers in this species. EST data about sago plants are obtained through the EST database on the National Center for Biotechnology Information (NCBI) website. We obtained data of 458 Kb (412 contig) with a maximum and minimum length of 1,138 and 124 nucleotides, respectively. We successfully identified 820 perfectly patterned SSR using Phobos 3.3.12 software. The type characterisation of EST-SSR was dominated by tri-nucleotides 36% (294), followed by hexa-nucleotides 24% (202), tetra-nucleotides 15% (120), penta-nucleotides 13% (108) and di-nucleotides 12% (96). The most frequency of SSR motifs in each type is AG, AAG and AAAG. Analysis of synteny on the EST sequence with the online application Phytozome found that sequences were distributed on 12 Oryza sativa chromosomes with a likeness percentage between 63% to 100% and e-value between 0 to 0.094. We developed the primer and generated 19 primers. Furthermore, we validated 7 primers that all generated polymorphic alleles. To our knowledge, this report is the first identification and characterisation of EST-SSR for sago species and these markers can be used for genetic diversity analysis, marker assisted selection (MAS), cultivar identification, kinship analysis and genetic mapping analysis.

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This study aims to analyse the genetic diversity of Siganus canaliculatus in the Inner Ambon Bay (IAB) waters. DNA of S. canaliculatus specimens collected from IAB was extracted from tissues using a Tissue Genomic DNA Mini Kit, and partial CO1 genes were amplified using pair of universal primers. Genetic distances were determined by Kimura 2-parameter, and phylogenetic trees were constructed using the neighbour-joining method in MEGA 10.2.2 software. Arlequin software was used to analyse Fixation Index (Fst) and Analysis of Molecular Variance (AMOVA). There are three SNPs of S. canaliculatus from IAB that distinguish GenBank sequence data from S. canaliculatus. In Tanjung Tiram population group, contained three specific 677 (A), 679 (G), 703 (T) sites and two 693 (G), 714 (A) sites for the Nania population. Haplotype and nucleotide diversity of each population range from 0.000 to 1,000 and 0.000 to 0.004. Intra- and inter-population genetic differentiation were 21.19% dan 78.81%, respectively. Intra- and inter-population genetic distances were in range of 0.40-1.13 and 0.00-0.37, respectively. The pattern and direction of tidal currents as a link or barrier to spatial distribution and connectivity of S. canaliculatus larvae between seagrass habitats, as well as the presence of different anthropogenic pressures in each seagrass habitat, are thought to influence the genetic characteristics (genetic diversity, genetic variation, genetic differentiation and genetic distance) of S. canaliculatus populations in IAB waters. The results of this study provide information about the urgency of habitat-based fisheries management to support sustainable utiliation.s.

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BACKGROUND: Trueperella pyogenes is an opportunistic pathogen that causes suppurative infections in various animal species, including goats. So far, only limited knowledge of phenotypic and genotypic properties of T. pyogenes isolates from goats has been gathered. In our study, we characterized the phenotypic and genotypic properties of caprine T. pyogenes isolates and established their relationship by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR). RESULTS: From 2015 to 2023, 104 T. pyogenes isolates were obtained from 1146 clinical materials. In addition, two T. pyogenes isolates were obtained from 306 swabs collected from healthy goats. A total of 51 T. pyogenes isolates were subjected to detailed phenotypic and genotypic characterization. The virulence genotype plo/nanH/nanP/fimA/fimC/luxS was predominant. All of the tested isolates showed the ability to form a biofilm but with different intensities, whereby most of them were classified as strong biofilm formers (72.5%). The high level of genetic diversity among tested caprine T. pyogenes isolates (19 different RAPD profiles) was observed. The same RAPD profiles were found for isolates obtained from one individual, as well as from other animals in the same herd, but also in various herds. CONCLUSIONS: This study provided important data on the occurrence of T. pyogenes infections in goats. The assessment of virulence properties and genetic relationships of caprine T. pyogenes isolates contributed to the knowledge of the epidemiology of infections caused by this pathogen in small ruminants. Nevertheless, further investigations are warranted to clarify the routes of transmission and dissemination of the pathogen.

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Garlic, an asexually propagated bulbous crop, displays a wide diversity based on its morphological traits and biochemical compositions. This study investigated the genetic variability of Indian garlic through morphological, biochemical, and molecular markers. Twenty-nine genotypes along with three Allium species as outgroup were included in the present study. Observations were recorded on 14 quantitative traits, 17 qualitative traits, and 9 biochemical traits in fresh garlic. Significant variability was observed among genotypes for different characters. All the morphological and biochemical traits showed higher phenotypic coefficient of variation (PCV) than genotypic coefficient of variation (GCV) revealing the role of environment in trait expression. High to moderate heritability and genetic advance as percent mean were recorded for different traits except dry matter and Total Soluble Solids (TSS). Correlation analysis revealed the highest positive correlation between total yield, marketable yield, Ferric Reducing Antioxidant Potential (FRAP) and 2,2-diphenyl-1-picrylhyrazyl (DPPH). Cluster analysis differentiated all the genotypes into three major clusters based on morphological and biochemical traits. 214 Simple Sequence Repeats (SSRs) were screened and nine markers exhibited polymorphism. Cluster analysis using molecular markers revealed 4 distinct clusters. The observations from this study will help in the identification of diverse garlic germplasm for its efficient management and duplicate identification of germplasm resources.

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Y chromosome analysis is used in a number of practical applications, including investigations of criminal cases, establishment of paternity, searching for missing persons, studies on human migration, evolutionary research, and historical and genealogical investigations. Questions about the origin of individual ethnic groups are addressed not only through archaeological, linguistic, and ethnographic methods but also through molecular genetics methods. The study of genetic diversity in Romania is particularly interesting from several perspectives because Romania, located in Southeast Europe, is distinguished by the fact that the Carpathians and the Danube served as natural barriers against the migrations of peoples for centuries, thus influencing the genetic mixture of the population. This is relevant for understanding the history and formation of ethnic groups in the region. In addition, many ethnic minorities live in Romania, which adds an additional dimension of genetic and cultural diversity. This article aims to provide an updated picture of the genetic diversity in Romania and to highlight the significant studies carried out among the Romanian population. By analyzing the articles published in the Web of Science, Scopus, or PubMed databases, which explore genetic diversity using the Y chromosome, the aim is to better understand the current genetic panorama in Romania.

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Alternaria pathogens are a global agronomic challenge affecting the health of Solanaceae crops. Crop debris, seeds, and perennial weeds are potential inoculum reservoirs, but knowledge on their relative importance remains limited. Plants of Convolvulus arvensis showing early blight and brown leaf spot symptoms were collected from in and around potato and tomato fields in Serbia, grown both in open conditions and in tunnels, in the late season of 2021 - 2022. Morphological and phylogenetic analysis was conducted on collected samples, using three genes (GPD, CAL, RPB2) for large-spored species and six genes (Alt a1, ATP, HIS3, endoPG, TEF-1, OPA10-2) for small-spored species of Alternaria. A total of 58 strains were identified - four large-spored species (A. grandis, A. solani, A. protenta, and A. linariae) and two small-spored species (A. alternata and A. arborescens). Phylogenetic analyses of concatenated loci and haplotype network for every investigated locus revealed that large-spored isolates from C. arvensis exhibit a low genetic variability, suggesting common haplotypes in a broad solanaceous host range. Meanwhile, small-spored Alternaria isolates displayed high genetic diversity in all examined gene regions indicating potential geographical haplotype distribution per HIS3 locus. Pathogenicity tests confirmed the virulence of all isolates on original hosts, with crop plants of potato and tomato also showing high susceptibility. Notably, this research documents six Alternaria species on C. arvensis in Serbia for the first time, significantly broadening our understanding of the pathogen's diversity and suggesting new sources of inoculum in solanaceous crops.

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Humans have selectively bred domestic pigeons (Columba livia domestica) to create breeds with a diversity of shapes, colors and other attributes. Since Darwin, the domestic pigeon has always been a popular model species for scientific research because of its richness of form, colouration and behaviour. It is believed that the world's squab pigeon industry uses breeds and hybrids from the Mediterranean region. An exception is the indigenous giant pigeon breeds of the Carpathian Basin, whose origin is not known. Therefore, our aims were 1) to understand the phylogenetic relationships of giant pigeons, which sheds light on the origin of Hungarian breeds and their relationship to the Mediterranean giant pigeon breed group; 2) to contribute molecular genetic data to the genealogy of 2 Iraqi pigeon breeds close to the pigeon domestication center, including the culturally important Iraqi Red Pigeon, and 3) to compare the genetic diversity of European and Middle Eastern domestic pigeon populations and to draw conclusions on the phylogenetic relationships between pigeon breeds and molecular clues to their different breeding practices of both regions. A 655-bp-long sequence of the cytochrome oxidase 1 (COI) region of the mitochondrial DNA was studied in a total of 276 pigeons (19 breeds). A total of 27 haplotypes were found, of which 22 were unique. The highest genetic diversity was found in the Carpathian Basin, and the lowest in the Iraqi region. STRUCTURE analysis revealed low structurality, K=3 was the most likely. The majority of the samples belong to the most ancient haplotype H_2=219, however the Jacobin pigeon is on a very separate evolutionary branch with a large number of mutations. None of the 19 breeds investigated in this study have been previously studied in phylogenetics, and most of these breeds have potential as squab pigeons, and have good meat forms for utilization, therefore the results of this study may also be of help to the squab pigeon industry.

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The Entada landrace of enset (Ensete ventricosum (Welw.) Chessman) is probably the most unique indigenous crop in Ethiopia, being maintained and utilized by the Ari people in the South of Ethiopia. Here we describe genetic diversity, selection signatures and relationship of Entada with cultivated and wild enset using 117 Entada genotypes collected from three Entada growing regions in Ethiopia (Sidama, South and North Ari). A total number of 1,617 high-quality SNP markers, obtained from ddRAD-sequences, were used for the diversity studies. Phylogenetic analysis detected a clear distinction between cultivated enset, Entada and wild enset with Entada forming a completely separated clade. However, extremely short branch lengths among the Entada genotypes indicate very little molecular evolution in the Entada lineages. Observed and expected heterozygosities were high, 0.73 and 0.50, respectively. Overall, our results strongly indicate that the Entada genotypes we have studied originated from one or a few clonal lineages that have been propagated and spread among farmers as clones. Prolonged clonal propagation of heterozygous genotypes from a single or few founding lineages has led to populations with very little or no diversity between genotypes, and high heterozygosity within genotypes. Signatures of directional selection were identified at eight loci based on an FST outlier analysis. Four candidate genes detected are involved in axillary shoot growth and might be involved in controlling natural sucker formation in Entada.

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The high-yielding Houdan chicken (GGF) is characterized by high egg production and disease resistance. This study conducted whole genome resequencing of the GGF population and compared it to data from other breeds. Genetic diversity analysis revealed higher observed heterozygosity (Ho), Polymorphism information content (PIC), number of runs of homozygosity (ROH), and inbreeding coefficient (FROH) in GGF. Linkage disequilibrium (LD) decay was slowest in GGF, indicating intensive inbreeding and strong selection. These findings suggest a need for appropriate strategies to enhance genetic diversity conservation in this breed. Population structure analysis demonstrated that GGF was genetically distinct from both the red jungle fowl (RJF) and Chinese indigenous chicken (CIC) populations, highlighting GGF as a unique genetic resource warranting intensive protection and utilization. Selective sweep analysis identified genes under selection in GGF, primarily enriched in signaling pathways related to oocyte meiosis and progesterone-mediated oocyte maturation. Key candidate genes included: CCNE1, SKP1, CDC20, CDK2, ADCY8, RPS6KA6, PPP3CB, PDE3B, HSP90AB1, and AKT3. These findings provide a theoretical foundation for their potential application in poultry breeding. Additionally, this study combined bioinformatics analysis with PCR amplification and Sanger sequencing to identify 4 SNPs that can serve as a molecular identity card (ID) for GGF: SNP1 (Chr2: 136130976), SNP3 (Chr4:11705164), SNP4 (Chr4: 63255588), and SNP5 (Chr24: 3271008). This study provides a scientific basis for effective management and conservation of GGF genetic resources, and establishes a simple, economical, and accurate set of molecular IDs to combat the proliferation of inferior breeds and protect genetic resources.

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Macrophyte habitats exhibit remarkable heterogeneity, encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors. Environmental factors are thought to be important drivers shaping the genetic and epigenetic variation of aquatic plants. However, the links among genetic diversity, epigenetic variation, and environmental variables remain largely unclear, especially for clonal aquatic plants. Here, we performed population genetic and epigenetic analyses in conjunction with habitat discrimination to elucidate the environmental factors driving intraspecies genetic and epigenetic variation in hornwort (Ceratophyllum demersum) in a subtropical lake. Environmental factors were highly correlated with the genetic and epigenetic variation of C. demersum, with temperature being a key driver of the genetic variation. Lower temperature was detected to be correlated with greater genetic and epigenetic variation. Genetic and epigenetic variation were positively driven by water temperature, but were negatively affected by ambient air temperature. These findings indicate that the genetic and epigenetic variation of this clonal aquatic herb is not related to the geographic feature but is instead driven by environmental conditions, and demonstrate the effects of temperature on local genetic and epigenetic variation in aquatic systems.

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BACKGROUND: Kelps are not only ecologically important, being primary producers and habitat forming species, they also hold substantial economic potential. Expansion of the kelp cultivation industry raises the interest for genetic improvement of kelp for cultivation, as well as concerns about genetic introgression from cultivated to wild populations. Thus, increased understanding of population genetics in natural kelp populations is crucial. Genotyping-by-sequencing (GBS) is a powerful tool for studying population genetics. Here, using Saccharina latissima (sugar kelp) as our study species, we characterize the population genetics at a fine geographic scale, while also investigating the influence of marker type (biallelic SNPs versus multi-allelic short read-backed haplotypes) and minor allele count (MAC) thresholds on estimated population genetic metrics. RESULTS: We examined 150 sporophytes from 10 locations within a small area in Mid-Norway. Employing GBS, we detected 20,710 bi-allelic SNPs and 42,264 haplotype alleles at 20,297 high quality GBS loci. We used both marker types as well as two MAC filtering thresholds (3 and 15) in the analyses. Overall, higher genetic diversity, more outbreeding and stronger substructure was estimated using haplotypes compared to SNPs, and with MAC 15 compared to MAC 3. The population displayed high genetic diversity (HE ranging from 0.18-0.37) and significant outbreeding (FIS ≤ - 0.076). Construction of a genomic relationship matrix, however, revealed a few close relatives within sampling locations. The connectivity between sampling locations was high (FST ≤ 0.09), but subtle, yet significant, genetic substructure was detected, even between sampling locations separated by less than 2 km. Isolation-by-distance was significant and explained 15% of the genetic variation, while incorporation of predicted currents in an "isolation-by-oceanography" model explained a larger proportion (~ 27%). CONCLUSION: The studied population is diverse, significantly outbred and exhibits high connectivity, partly due to local currents. The use of genome-wide markers combined with permutation testing provides high statistical power to detect subtle population substructure and inbreeding or outbreeding. Short haplotypes extracted from GBS data and removal of rare alleles enhances the resolution. Careful consideration of marker type and filtering thresholds is crucial when comparing independent studies, as they profoundly influence numerical estimates of population genetic metrics.

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BACKGROUND: The Tibetan sheep is one of the three major primitive sheep breeds in China, representing a unique and high-quality genetic resource in the Qinghai-Tibet Plateau and neighboring high-altitude regions, exhibiting exceptional adaptability to high-altitude climatic environments. However, research on the genetic relationships among different populations of Tibetan sheep at the whole-genome level remains insufficient. This study aims to explore the population structure and historical dynamics among 11 Tibetan sheep populations, accurately assess the genetic diversity within the populations, and providing a theoretical basis for the development of targeted genetic breeding strategies for Tibetan sheep. RESULTS: In this study, a total of 10,884,454 high-quality SNPs were obtained. All Tibetan sheep populations exhibited varying degrees of linkage disequilibrium, with similar decay rates; among them, the WT population showed the fastest decay, while the TS population exhibited the slowest decay rate. Analyses using Tajima's D and π indicated that the genetic diversity levels of the Tibetan sheep populations are generally low. Fst results revealed that most populations exhibited moderate to low levels of genetic differentiation. The effective population size among Tibetan sheep populations showed an increasing trend over time. The evolutionary relationships among Tibetan sheep populations reflect the correlation between their geographical locations and genomic genetic distances, while also indirectly confirming the impact of historical activities such as early human migration, admixture, fusion, and expansion on the population sizes and distributions of Tibetan sheep. CONCLUSIONS: The results indicate that the genetic diversity levels and genetic differentiation among Tibetan sheep populations are relatively low. In this study, we identified the genetic characteristics of Tibetan sheep populations, which exhibit low levels of diversity, genetic differentiation, and a strong population structure. A deeper genomic exploration of the population structure and diversity status of Tibetan sheep populations will provide theoretical support for subsequent genetic breeding and diversity conservation efforts.

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BACKGROUND: The shea tree is a well-known carbon sink in Africa that requires a sustainable conservation of its gene pool. However, the genetic structure of its population is not well studied, especially in Côte d'Ivoire. In this study, 333 superior shea tree genotypes conserved in situ in Côte d'Ivoire were collected and genotyped with the aim of investigating its genetic diversity and population structure to facilitate suitable conservation and support future breeding efforts to adapt to climate change effects. RESULTS: A total of 7,559 filtered high-quality single nucleotide polymorphisms (SNPs) were identified using the genotyping by sequencing technology. The gene diversity (HE) ranged between 0.1 to 0.5 with an average of 0.26, while the polymorphism information content (PIC) value ranged between 0.1 to 0.5 with an average of 0.24, indicating a moderate genetic diversity among the studied genotypes. The population structure model classified the 333 genotypes into three genetic groups (GP1, GP2, and GP3). GP1 contained shea trees that mainly originated from the Poro, Tchologo, and Hambol districts, while GP2 and GP3 contained shea trees collected from the Bagoué district. Analysis of molecular variance (AMOVA) identified 55% variance within populations and 45% variance within individuals, indicating a very low genetic differentiation (or very high gene exchange) between these three groups (FST = 0.004, gene flow Nm = 59.02). Morphologically, GP1 displayed spreading tree growth habit, oval nut shape, higher mean nut weight (10.62 g), wide leaf (limb width = 4.63 cm), and small trunk size (trunk circumference = 133.4 cm). Meanwhile, GP2 and GP3 showed similar morphological characteristics: erect and spreading tree growth habit, ovoid nut shape, lower mean nut weight (GP2: 8.89 g; GP3: 8.36 g), thin leaf (limb width = 4.45 cm), and large trunk size ( GP2: 160.5 cm, GP3: 149.1 cm). A core set of 100 superior shea trees, representing 30% of the original population size and including individuals from all four study districts, was proposed using the "maximum length sub-tree function" in DARwin v. 6.0.21. CONCLUSION: These findings provide new knowledge of the genetic diversity and population structure of Ivorian shea tree genetic resources for the design of effective collection and conservation strategies for the efficient use of inbreeding.

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