Search Results (252)

Rumex crispus L. is a globally distributed invasive species that has naturalized in South Korea, where its use as a medicinal, edible, and ecological restoration resource continues to expand. However, its genetic background remains insufficiently understood, underscoring the need for species-specific molecular markers to enable accurate assessments of intraspecific genetic diversity and population structure. Using 19 newly developed microsatellite markers, we analyzed 120 plants from 6 populations in the riparian zone. A total of 166 alleles were detected, with a mean polymorphism information content of 0.637. Across the six populations, genetic diversity analysis showed mean observed (Ho = 0.304) and expected (He = 0.588) heterozygosity values indicative of heterozygote deficiency (inbreeding coefficient F_IS = 0.456–0.559). Genetic differentiation was low in AMOVA (10%) and F_ST (0.048–0.120) but higher in Jost’s D (0.096–0.342). STRUCTURE analysis identified two major genetic clusters (ΔK = 2), and spatial Bayesian clustering revealed six distinct genetic units (K = 6), suggesting that partial barriers to gene flow may have influenced population structure. These findings provide essential genetic insights that can support the effective control of R. crispus spread and its potential use as a valuable plant resource. Full article

The average pairwise dissimilarity (APD) between one plant sample and other assayed samples based on genetic markers was developed in 2006 to assess genetic distinctness and genetic redundancy in a plant germplasm collection. With the availability of abundant genomic variants across a genome, APD can be expanded to measure individual genomic distinctness. This study was conducted to assess the applicability of APD estimates in measuring the individual genomic distinctness of 1789 indica and 854 japonica rice samples based on published genome-wide single-nucleotide polymorphism (SNP) and structural variant (SV) data. It was found that the acquired APD estimates were weakly or not correlated between the SNP and SV data sets in the indica or japonica samples, respectively. For the indica samples, the APD estimates based on the SNP and SV data ranged from 0.1779 to 0.3277 and from 0.2297 to 0.4096, respectively. For the japonica samples, the SNP-based and SV-based APD estimates varied from 0.1774 to 0.3029 and from 0.1534 to 0.3459, respectively. These APD estimates were highly negatively correlated with the estimates of individual inbreeding coefficients and can identify the most genomically distinct rice germplasm that are compatible with those revealed through principal component analysis. Also, a reliable APD estimation was found to require 5000 to 10,000 random genomic SNPs or SVs. These findings together are significant, not only in demonstrating the informativeness of APD estimates in the identification of individuals with variable genomic distinctness, but also in providing guidance for APD applications to measure individual genomic distinctness. Full article

Fengjing pigs are a Chinese native breed known for their high reproductive ability. Runs of homozygosity (ROHs) have emerged as an effective tool for evaluating inbreeding levels and identifying relevant genes in selection. However, the declining population of Fengjing pigs in recent years has raised concerns about inbreeding. Therefore, this study aimed to investigate the ROH patterns, estimate genomic inbreeding levels, and identify candidate genes associated with economic traits using whole-genome resequencing data from 105 Fengjing pigs. A total of 2448 ROHs were identified, with an average of 23.31 ROHs per individual and an average length of 9.50 Mb. The inbreeding coefficient, based on ROHs, was 0.098. Additionally, three genomic regions with a high frequency of ROHs were identified. These regions contained 64 unique genes, including 14 genes associated with important economic traits. Moreover, six overlapping quantitative trait loci (QTLs) and four candidate genes (HSPG2, CDC42, EPHB2, and GRHL3) were identified on Sus scrofa chromosome (SSC) 6. These QTLs are associated with birth traits (health and reproductive efficiency) and meat development traits (meat quality and growth). This study identified many candidate genes and QTLs that overlapped with ROHs and are associated with economically significant traits. These findings can be used in future breeding, conservation, and utilization of specific Chinese native pig breeds. Full article

We studied Lycaena helle (Lepidoptera: Lycaenidae) population genetics in lowlands and mountains of East-Central Europe using the microsatellite markers previously applied in population studies mainly in mountains of Western Europe. As in the West, the East-Central populations are genetically diverse (mean expected/observed heterozygosity 0.67/0.49), affected by drift processes (mean inbreeding coefficient 0.277) and widely differentiated (mean F_ST 0.209). The Polish lowland populations, all of them bivoltine in contrast to mountain populations, are less differentiated than Romanian populations, which are bivoltine in low and univoltine in high altitudes. The lowland Romanian population Vad is extremely genetically impoverished. A transferred CZ population from Western Europe is impoverished relative to its donor population, but the genetic parameters remain within a range of other studied so far. Dendrogram of allelic frequencies suggests that the populations form two branches, one rooted in southeastern Poland and branching towards Carpathians in Romania, one encompassing populations in central and northern Poland. We conclude that the lowland Romanian populations, plus populations in unglaciated southeastern Poland, represent sites where the species survived the glacial cycles in situ, comprising rear edge of subsequent upslope expansion, while northern Poland was colonised from more easterly regions. Full article

Genetic variability in terrestrial mammals is essential for understanding population and evolutionary dynamics, as well as for establishing effective strategies in conservation biology. This comprehensive review aimed to critically analyze invasive and non-invasive techniques used to assess genetic variability in wild terrestrial mammals. Using the PICO (Population, Intervention, Comparison, Outcome) format and following PRISMA guidelines, a comprehensive literature search was conducted in Web of Science, Scopus and Science Direct databases, including articles published in English from January 2015 to April 2025. Thirty-one experimental studies were selected that met specific criteria related to genetic evaluation using invasive (direct blood or tissue collection) and non-invasive (stool, hair and saliva collection) techniques. The results indicate that invasive techniques provide samples of high genetic quality, albeit with important ethical and animal welfare considerations. In contrast, non-invasive techniques offer less disruptive methods, although they present significant challenges in terms of quantity and purity of DNA obtained, potentially affecting the accuracy and confidence of genetic analysis. Detailed analysis of selected studies showed diverse patterns of heterozygosity and inbreeding coefficients between different taxonomic orders (Carnivora, Artiodactyla, Proboscidea, Primates and Rodentia). In addition, the main anthropogenic threats and current conservation strategies implemented in different species were identified. An overall genetic variability ranging from high to moderate was observed, with large species being more vulnerable to genetic reduction due to changes in habitat and human activities. Rather than a static comparison, our synthesis traces a clear methodological arc from small short tandem repeats (STR, or microsatellites) panels towards SNP-based approaches enabled by next-generation sequencing, including reduced representation (ddRAD), amplicon panels (GT-seq), and hybridisation capture tailored to degraded DNA from hair, faeces, and environmental substrates. Over 2015–2025, study designs shifted from presence/absence and coarse diversity estimates to robust inference of relatedness, assignment, effective population size, and gene flow using hundreds–thousands of SNPs and genotype-likelihood frameworks tolerant of allelic dropout and low coverage. Laboratory practice converged on multi-tube replication, synthetic blocking oligos, and capture-based enrichment; bioinformatics adopted probabilistic genotype calling, error-aware filtering, and replication-based consensus. This review provides a solid basis for optimizing genetic sampling methods, allowing for more ethical and efficient studies. Furthermore, it contributes to strengthening conservation strategies by underlining the importance of adapting the sampling method to the biological and ecological particularities of each species studied. Ultimately, these findings can significantly improve genetic conservation decision-making, benefiting the sustainability and resilience of wild land mammal populations. Full article

Background: Longfin batfish (Platax teira) is an important economic species in southern China. In recent years, its wild population has significantly declined due to overfishing. Around 2015, breakthroughs in the artificial large-scale seedling technology for P. teira have promoted the growth of its aquaculture scale in regions such as Hainan and Guangdong. Methods: To study the genetic diversity, inbreeding status, and population structure of the current P. teira farming populations in China, we performed whole-genome resequencing technology and high-density SNP markers to analyze the genetics of four main farming populations. A total of 109 individuals from four populations (NA, ZP, XL, and XC) were sequenced, identifying 5,384,029 high-quality SNPs. Results: The results showed that the nucleotide diversity (π) of each population ranged from 0.00155 to 0.00165 and observed heterozygosity (Ho) ranged from 0.253 to 0.282, which indicated low levels of genetic diversity. The results of the ROH analysis show significant inbreeding in the NA population. Genetic differentiation analysis revealed that the genetic differentiation among NA, XC, and ZP populations was relatively low (F_ST = 0.021–0.029). Conclusions: NA, XC, and ZP populations likely share a common origin of their fry stocks. Based on a phylogenetic tree, principal component analysis (PCA), and population structure analysis, the four populations were divided into four genetic groups. This study is the first analysis of the genetic diversity and population structure of P. teira farming populations in China, laying the foundation for the establishment of a base breeding population and the implementation of genetic improvement programs. Full article

Background: Inbreeding is a major genetic problem that reduces fertility and causes genetic disorders. Some breeders of dromedary camels use the same bull for many years due to its excellent characteristics, leading to mating with offspring and subsequent generations, resulting in increased homozygosity and genetic disorders. We hypothesize that inbreeding is associated with infertility in dromedary camels with normal and uninfected reproductive tracts. Methods: We genotyped 96 samples from seven camel breeds using the Illumina 55K SNP BeadChip, including five confirmed infertile individuals. Inbreeding coefficients (F) were calculated using PLINK based on heterozygosity and runs of homozygosity. Genome-wide association analysis using logistic regression was performed to identify potential genomic regions associated with infertility. Results: All five infertile camels showed significantly higher F values (>0.15) compared to 91 fertile individuals (<0.10, p < 0.001). The genome-wide association analysis failed to identify specific genomic regions linked to infertility, likely due to limited statistical power (n = 5 cases) and the polygenic nature of fertility traits. Population structure analysis revealed genetic differentiation related to coat color, with two significant SNPs on chromosome 3 near SLC30A5 (p < ${10}^{-7}$). Conclusions: Our results demonstrate that elevated inbreeding is strongly associated with infertility in dromedary camels. Future studies should employ larger sample sizes (≥50 infertile individuals) or whole-genome sequencing (35× coverage) to identify specific genomic regions. Implementation of breeding strategies avoiding related matings (F < 0.10) is recommended to maintain reproductive performance in camel herds. Full article

Angulyagra polyzonata is a significant freshwater snail species in southern China. However, its wild resources have sharply declined due to overfishing. To assess the current status of germplasm resources in the Guangxi region, during this study, we first successfully developed nine pairs of primers that enable the amplification of highly polymorphic microsatellite markers (SSRs) with trinucleotide and tetranucleotide repeat sequences (PIC values ranging from 0.662 to 0.861) using transcriptomic data. Then, these designed primers were tested and applied for the genetic investigation of selected wild populations of the species. Finally, a genetic diversity analysis was conducted based on 12 wild populations (360 individuals) in Guangxi. After 798,244 SSR loci were screened out via high-throughput sequencing, the results showed that dinucleotide repeats accounted for the highest proportion (47.64%), mainly consisting of (AC/GT)n repeat units. Among the SSR loci in A. polyzonata, microsatellite loci with 5 to 20+ repeats are the most abundant. All nine selected and tested SSR loci significantly deviated from Hardy–Weinberg equilibrium (p < 0.001) and had heterozygote deficiency (average inbreeding coefficient of F = 0.390), indicating widespread inbreeding. The fixation index among populations was high (average Fst = 0.175), with 73% of the genetic variation occurring within populations and 27% between populations. Gene flow (Nm) was generally restricted (most population pairs had Nm < 1), with the (Tiandeng) TD and (Long’an) LA populations showing the smallest differentiation (Fst = 0.017), and the (Qinnan) QN and (Yinhai) YH populations showing the greatest differentiation (Fst = 0.409). UPGMA clustering and structure analysis (K = 2) divided the 12 populations into two subgroups. Overall, our research suggests that the genetic diversity of the wild population of A. polyzonata in the Guangxi region has declined. Thus, prioritizing the protection of highly genetically diverse populations, such as the LA population, is urgently needed. This study provides a scientific basis for the protection and sustainable utilization of A. polyzonata resources in Guangxi. Full article

Simulation-based studies can support breeders’ decisions inexpensively, since there is no need to perform a new procedure. The objective was to assess the efficiency of recurrent genomic selection in panmictic population under additive–dominance and additive–dominance with epistasis models. We assumed two broiler chicken populations with contrasting linkage disequilibrium (LD) levels, 38,500 SNPs, and 1000 genes controlling feed conversion ratio. We applied recurrent genomic selection over seven cycles. The genomic selection efficacy, expressed as realized total genetic gain, was proportional to the LD level and genotypic variance. Genomic selection required model updating to achieve a higher efficacy. The training set size required by genomic selection can be as low as 10%/generation. Under this low-cost scenario, the genomic selection efficacy was slightly lower than the maximum efficacy. There is no difference between genetic evaluation methods regarding the decrease in the genotypic variance due to selection. In general, additive value prediction accuracies and realized genetic gains were highly correlated. The accumulated inbreeding level was not high due to avoidance of sib cross. The genomic inbreeding coefficient over generations was close to zero. Except for dominant epistasis, the efficacy of genomic selection was 4.1 to 46.2% lower than the efficacy under no epistasis. Full article

The wild yak (Bos mutus) is a flagship species on the Qinghai–Tibet Plateau, possessing significant ecological functions and conservation value. Using single-nucleotide polymorphism markers from whole-genome resequencing, we systematically analyzed golden wild yak (n = 37), common wild yak (n = 106), and domestic yak (Bos grunniens) (n = 20) to characterize the population genetic structure and adaptive selection signals in the golden wild yak. Genetic diversity analyses revealed that the golden wild yak had the lowest nucleotide diversity (π = 0.00148) and the highest inbreeding coefficient (F_Hom = 0.043). Population structure analyses integrating principal component analysis, phylogenetic tree, and ancestral component clustering indicated that the golden wild yak formed a relatively independent evolutionary lineage. However, its genetic differentiation from sympatric common wild yak population was limited (fixation index = 0.031). Selective sweep analysis identified a set of candidate positively selected genes in the golden wild yak genome associated with key traits and physiological functions, including coat color (TYRP1), hypoxia adaptation (MYH11, POLQ), reproductive function (SLC9C1, SPAG16, CFAP97D1), and immune response (CASP8, PGGT1B, BIRC6). Overall, our study reveals a distinct genetic background and selection signatures in the golden wild yak and provides genomic insights to inform the conservation and management of the wild yak. Full article

Bahaba taipingensis (Chinese bahaba) is a critically endangered fish endemic to China’s coastal waters, valued for both ecological and economic reasons and known as the “panda of the sea”. Captive breeding and stock enhancement are key conservation strategies, yet the genetic composition of released individuals directly affects program outcomes. This study combined mitochondrial and whole-genome resequencing to compare F₁-generation fish with wild populations. At the mitochondrial level, 60 SNPs were detected in F₁ individuals and 72 in wild populations, with haplotype analyses revealing retention of most common maternal lineages but reduced diversity. Nuclear genome analysis showed comparable genetic diversity between groups. Nucleotide diversity (π) was 0.000423 in F₁ fish and 0.000401 in the wild population. However, the F₁ cohort exhibited a higher inbreeding coefficient (F_IS = −0.030) than the wild group (F_IS = −0.118), suggesting early allele frequency shifts, thereby suggesting early genotype frequency shifts. Runs of homozygosity (ROH) analysis showed that the total number and length of ROH regions in the F₁ cohort (686, 283,089.25 kb) were significantly greater than those in the wild population (171, 52,607.30 kb). Genome-wide F_ST between groups was 0.035, and PCA indicated genetic homogenization in F₁ fish. N_e analysis showed that the wild population declined rapidly over generations and stabilized at a low level, indicating genetic diversity loss under environmental stress and highlighting the role of artificial breeding. These findings highlight the need for improved broodstock management and long-term genetic monitoring. Full article

Prosopis cineraria (L.) Druce is a keystone tree species in the arid and semi-arid regions of West and South Asia, with critical ecological, cultural, and conservation significance. In the United Arab Emirates (UAE) and other regions of the Arabian Peninsula, this beneficial tree is called Ghaf. Despite its importance, genomic resources and population-level diversity data for the tree remain limited. Here, we present the first comprehensive population genomics study of Ghaf based on whole-genome resequencing of 204 individual trees collected across the UAE. Following Single-Nucleotide Polymorphism (SNP) discovery and stringent filtering, we analyzed 57,183 high-quality LD-pruned SNPs to assess population structure, diversity, and gene flow. Principal component analysis (PCA), sparse non-negative matrix factorization (sNMF), and discriminant analysis of principal components (DAPC) revealed four well-defined genetic clusters, broadly corresponding to geographic origins. The genetic diversity varied significantly among the groups, with observed heterozygosity (Ho), inbreeding coefficients (F), and nucleotide diversity ($\pi$) showing strong population-specific trends. Genome-wide fixation index F_ST scans identified multiple highly differentiated genomic regions, enriched for genes involved in stress response, transport, and signaling. Functional enrichment using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam annotations indicated overrepresentation of protein kinase activity, ATP binding, and hormone signaling pathways. TreeMix analysis revealed gene flow into one of the genetic clusters from both others, suggesting historical admixture and geographic connectivity. This work provides foundational insights into the population genomic profile of P. cineraria, supporting conservation planning, restoration strategies, and long-term genetic monitoring in arid ecosystems. Full article

In small, closed populations such as the Lipizzan horse, maintaining genetic diversity while limiting inbreeding is a key challenge in conservation breeding. The Lipizzan is an indigenous Slovenian breed with a small population and restricted gene flow from other subpopulations. Inbreeding is traditionally monitored with pedigree-based coefficients, but these often underestimate realised autozygosity, particularly when pedigree depth is limited. This study compared pedigree-based inbreeding (F_PED) with four genomic estimators (F_HOM, F_ROH, F_HBD, F_GRM) in 329 Slovenian Lipizzan horses genotyped with a 70K SNP array. Data were processed in PLINK and R. Segment-based estimators (F_ROH, F_HBD) revealed higher inbreeding than F_PED and partitioned autozygosity into recent and distant components. F_ROH identified long homozygous segments reflecting recent inbreeding, whereas HBD classification showed that most autozygosity came from distant ancestors. Correlations between pedigree- and genomic-based coefficients were moderate (ρ = −0.18–0.56), while genomic estimators showed strong agreement. These results demonstrate that genomic measures complement pedigree-based metrics by providing a fuller picture of inbreeding and its temporal origin. Incorporating genomic estimators into routine monitoring can improve mate selection, reduce inbreeding depression, and support sustainable management of genetic diversity in the Lipizzan horse, while offering a case study for other small populations with conservation goals. Full article

Sheep breeding is an important sector of livestock production in the Republic of Kazakhstan. The Kazakh fat-tailed coarse-wool sheep holds a prominent position among local breeds due to its high meat productivity, resilience to extreme climatic conditions, and efficient use of pasture resources. This study focuses on the analysis of runs of homozygosity (ROH) to evaluate the genetic diversity level, inbreeding and to detect selection signatures in the Kazakh fat-tailed coarse-wool sheep breed. A total of 500 animals were genotyped using the OvineSNP50 BeadChip (Illumina, San Diego, CA, USA). As a result, a total of 41,728 ROH segments were identified, with an average length of 1.59 Mb, distributed across the entire genome. The most prominent homozygous regions were detected on chromosomes OAR10, OAR13, and OAR22, which might be associated with selection signatures. Genomic inbreeding coefficients (F_ROH and F_GRM) showed a strong positive correlation (r = 0.58, p < 0.001), supporting the effectiveness of ROH-based analysis. Several candidate genes were detected, including MYF5, PRDM16, TGM3, SLC26A4 and SMAD5 which are notably involved in muscle formation, wool traits, and fat metabolism. The findings have substantial practical value for breeding programs and for managing genetic diversity in sheep farming enterprises in the Republic of Kazakhstan. Full article

Background: Ash dieback, driven by the invasive fungal pathogen Hymenoscyphus fraxineus, has precipitated severe declines in Fraxinus excelsior L. populations across Europe, threatening genetic diversity and ecosystem stability. Methods: This study investigates the interplay between phenotypic vitality and genetic variation in five Polish ash stands using nuclear simple sequence repeat (nSSR) and chloroplast DNA (cpDNA) markers. Vitality assessments of 186 trees across three reserves (from Białowieża Primeval Forest and Wolica Reserve) were conducted. Results: Vitality assessments revealed a slight predominance of dying individuals (36%, 3rd degree of Roloff classification). Nuclear analyses indicated moderate to high diversity (mean H_E = 0.826), significant inbreeding (F_IS = 0.178, p < 0.001), and low inter-population differentiation (F_ST = 0.044) among all five stands. Chloroplast markers showed elevated differentiation ($\mathsf{\Phi }$_ST = 0.228, p < 0.0001), reflecting phylogeographic structure. Vitality degrees assessed in three chosen populations (Browsk FD, Hajnówka FD, and Chojnów FD) exhibited negligible genetic differentiation (nSSR F_ST = 0.009; cpDNA $\mathsf{\Phi }$_ST = 0.003), suggesting gene flow mitigates pathogen-induced selection. Bayesian clustering (STRUCTURE, K = 3) revealed admixture with distinct genotypes in dying trees, potentially linked to susceptibility. Conclusions: These findings underscore the resilience of ash genetic pools and advocate for selective breeding in nurseries to prevent the spread of dieback, prioritizing resistant genotypes for conservation. Full article