Search Results (675)

The objectives of this paper were to assess the genetic diversity, population structure, genetic differentiation, and phylogenetic relationships among seven duck populations using 14 microsatellite (MS) markers. This paper included 176 individuals representing seven duck populations of Bangladesh: indigenous duck (BLD), Nageswari (NAG), Rupali (RUP), Jinding (JIN), Pekin (PEK), BAU Black and White (BWC), and BAU White (WHC). A total of 133 alleles were observed with a mean of 9.50 alleles per locus. Genetic diversity was evaluated using measures such as allele frequency, observed and expected heterozygosity, and Shannon’s information index with average values of 5.44 ± 0.31, 0.59 ± 0.02, 0.64 ± 0.02, and 1.28 ± 0.05, respectively. Population differentiation and inbreeding analysis (F-statistics) indicated moderate genetic diversity and a slight degree of inbreeding across populations. Analysis of molecular variance indicated that 75% of the total genetic diversity was attributable to the within-population variation, whereas 9% and 16% were attributed to the variation among individuals and population differentiation, respectively. Indigenous duck populations (BLD, NAG, and RUP) had a close genetic relationship with JIN ducks and an intermediate relationship with two crossbreds (BWC and WHC), and the highest genetic distance was observed with PEK ducks. Neighbor-joining phylogenetic analysis revealed that the Bangladeshi indigenous duck populations formed a single cluster, while the two crossbreds (BWC and WHC) and PEK exhibited their distinct genetic identities in separate clusters. Furthermore, structure analysis at K = 2 to 5 confirmed the distinct genetic architecture (ΔK = 4.00) of the studied duck populations. This paper provides important insights into genetic diversity measures and population differentiation that will be helpful in future genetic improvement, conservation initiatives, and the design of appropriate breeding programs. Full article

Populations of several billfish species are declining due to overfishing and bycatch, and fundamental aspects of their biology and population dynamics remain poorly understood. We provide the first assessment of the population genetic structure of longbill spearfish (Tetrapturus pfluegeri) in the western Atlantic Ocean. We screened variation at 12 nuclear microsatellite loci (n = 144) and mitochondrial DNA control region sequences (mtCR, n = 177). Both marker types revealed three genetically differentiated clusters, with mean values for microsatellites showing differentiation of F_ST = 0.136 and D_EST = 0.201, and for mtCR F_ST = 0.645. Microsatellite markers demonstrated moderate-to-high genetic diversity, with a mean allelic richness of 6.73 alleles per locus, moderate heterozygosities (Ho = 0.446, He = 0.604), and a positive inbreeding coefficient (F_IS = 0.22) across the three sample collection sites. The overall estimated effective population size was 789.2 (95% CI: 246.7–∞). The mtCR exhibited 96 haplotypes, with high haplotype (0.989 ± 0.003) and nucleotide (0.025 ± 1.3%) diversities. We found higher mean relatedness within clusters than among them, supporting the interpretation of population subdivision and the Wahlund effect. Tajima’s D and Fu’s Fs were negative across all localities, with significant values observed along the Brazilian coast but not in the Caribbean Sea. These neutrality test results, together with low Harpending’s raggedness indices from DNA sequence mismatch distributions, are consistent with historical demographic expansion. Our findings establish a genetic baseline for fishery monitoring and management, contributing to the conservation of T. pfluegeri populations in the western Atlantic Ocean. Full article

Genetic diversity is fundamental for the conservation and sustainable utilization of plant species. Triadica cochinchinensis, a tree species native to southern China, is an important ornamental and nectar-producing plant with considerable economic value. However, the levels of genetic diversity and the patterns of population differentiation across its natural populations remain unexplored. Here, we developed 24 highly polymorphic SSR markers and used them to assess the genetic diversity and differentiation among 280 individuals collected from 10 natural populations of T. cochinchinensis. The results showed that the average expected heterozygosity (He) revealed by the SSR markers was 0.774, and the average Shannon diversity index (I) was 1.660, indicating a high level of genetic diversity at the species level of T. cochinchinensis. Analysis using SSR markers revealed a low average observed heterozygosity (Ho = 0.323) and a relatively high average inbreeding coefficient within populations (F = 0.466). These findings suggest that inbreeding is likely occurring, which may contribute to a loss of heterozygosity within the studied populations. Notably, not all populations had high genetic diversity. For example, the He of SC2 population (0.490), QY population (0.568), and SC1 population (0.585) were all below the mean He (0.607), suggesting that attention should be given to protecting populations with low genetic diversity. The results further showed that the average genetic differentiation coefficient (F_ST) between populations was 0.094, and the average gene flow (Nm) was 2.278, indicating that the natural populations of T. cochinchinensis had low genetic differentiation and relatively high gene flow. AMOVA indicated that 74% of the total variation was distributed within populations. Notably, populations SC1 and SC2 exhibited higher genetic differentiation from all others (F_ST > 0.1), which is likely attributed to mountain barriers restricting gene flow. Therefore, it is recommended to enhance in situ conservation efforts while also facilitating assisted gene flow, such as through artificial introduction. For the first time, this study reveals the genetic information of natural populations of T. cochinchinensis at the molecular level, thereby offering a valuable reference for the conservation and utilization of its germplasm resources. Full article

Background: Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), is a devastating forest disease. It has been reported in five provincial-level regions in Southwest China (Chongqing, Guizhou, Sichuan, Yunnan, and Tibet), threatening local pine forest ecosystems. Methods: To unravel the population genetic variation and population differentiation of PWN isolates in this region, we purified eighty-one isolates for whole-genome resequencing and bioinformatics analysis, identifying candidate genes associated with runs of homozygosity (ROH). Results: Population structure analysis clustered the 81 isolates into three distinct genetic groups (Groups 1, 2, and 3). Notably, Group 1 exhibited fewer and shorter ROH segments compared to Groups 2 and 3, indicating higher genetic diversity and a different inbreeding history. Functional annotation of genes overlapping ROH regions revealed that Group 1 contained a subset of the genes identified in Groups 2 and 3, primarily enriched in specific molecular function categories. Conclusions: The PWN populations in Southwest China exhibit genetic differentiation, forming three distinct groups. Group 1 shows a reduced ROH burden and lower inbreeding levels, whereas Groups 2 and 3 display more extensive ROH patterns that may reflect historical demographic processes or potential adaptive selection. The differential distribution of ROH-associated genes across groups suggests possible variation in historical demographic processes and could suggest possible directional selection. These findings contribute to understanding the population history and genomic characteristics of PWN in Southwest China, providing insights that could support disease management strategies. Full article

The aim of this study was to characterise the pedigree and genetic structure of Polish Sport Horses competing in Grand Prix show jumping events and to assess the implications for international sport horse breeding. Pedigrees of 513 horses were analysed, encompassing a total of 18,836 individuals over a maximum of 16 generations. The completeness and depth of the pedigrees allowed for a reliable estimation of inbreeding coefficients and genetic diversity. The mean inbreeding coefficient was low (0.645%), yet 82% of the horses exhibited some degree of inbreeding. The greatest loss of genetic variability was observed in non-founder generations, most likely due to the intensive use of a limited number of high-value stallions with domestic mares—a bottleneck effect. The most significant founders contributing to the population were the Thoroughbred stallions Ladykiller and Rantzau, as well as the Anglo-Arab stallion Ramzes, highlighting the international influence on the contemporary population. These findings emphasise the need for systematic monitoring of genetic diversity and the strategic use of pedigree data to minimise inbreeding and preserve the genetic potential of Polish Sport Horses for international breeding programmes. Full article

The conservation of genetic diversity in historically structured horse breeds requires fi-ne-scale population genetic evaluation beyond conventional pedigree-based approaches. The present study assessed genetic diversity, population structure, and mare family differentiation in a Lipizzan horse population using 16 ISAG/FAO-recommended microsatellite markers. A total of 172 mares representing 29 mare families were genotyped. All loci were polymorphic, with a mean number of alleles per locus of 6.69 and a mean effective number of alleles of 3.56. The average polymorphism information content (PIC = 0.66) indicated high marker informativeness. Mean observed heterozygosity was slightly lower than expected heterozygosity, although the overall negative inbreeding coefficient suggested general heterozygote excess and low population-level inbreeding, whilst the genetic differentiation among mare families was moderate. The principal components and the STRUCTURE analysis indicated admixture among mare families. Seven private alleles were detected across six loci, highlighting the presence of rare lineage-specific variants. These findings emphasize the importance of mare family-based analyses for identifying hidden genetic structures that may not be captured by population-level averages. The integration of microsatellite-based diversity evaluation provides a robust framework for de-signing sustainable breeding and conservation strategies aimed at preserving both overall variability and rare lineage-specific genetic components. Full article

Inbreeding is a quantitative measure of autozygosity that underlies the assessment of genetic risks and the management of genetic progress in livestock populations. The development of methods for its estimation reflects a transition from probabilistic pedigree-based models to the direct analysis of genome structure. This review systematizes the evolution of approaches to inbreeding assessment—from the classical inbreeding coefficient F based on identity by descent (IBD) to marker-based, segment-based runs of homozygosity (ROH) and probabilistic homozygous-by-descent (HBD) models. It is shown that the coefficients F_ped, F_GRM, F_ROH, and F_HBD capture related but distinct aspects of autozygosity and are therefore not fully interchangeable. Particular attention is paid to the transition from integral indicators to spatially and temporally stratified analyses of autozygosity, enabling the differentiation between ancient and recent inbreeding. Methodological assumptions, limitations, and the sensitivity of various approaches to marker density, detection parameters, and population demographic structure are discussed. A comparative analysis of methods for calculating F_ROH and segment-based autozygosity is presented. The necessity of a comprehensive assessment of inbreeding and the standardization of analytical protocols for its application in modern breeding programs is substantiated. Full article

The guinea fowl (Numida meleagris), a thermo-tolerant and disease-resilient poultry species, holds great potential for sustainable poultry production in climate-vulnerable regions. The genomic aspects of this species remain largely understudied. The present study aims to delineate the patterns of domestication and understand the evolutionary dynamics of guinea fowl populations (wild and domestic) across three continents, utilizing whole-genome sequencing data from 122 genomes. The population structure analyses (ADMIXTURE, PCA, phylogeny, F_ST, LD, and MAF) revealed that Indian guinea fowl (CARI) shared close ancestry with Iranian (IRAD) and Chinese (CHID) domesticated populations while remaining distinct from wild lineages. The runs of homozygosity (ROH) identified 49,088 segments, with short fragments (ROHs) preponderant in Indian and domestic populations, reflecting historical inbreeding and effects of domestication cum selection. Copy number variation (CNV) analysis revealed 105,178 CNVs concatenated into 40,067 CNV regions (CNVRs) across 11 populations, establishing the first CNV atlas for guinea fowl at the global level. Gene annotation of overlapping ROH and CNVRs revealed 1080 common candidates across Asian guinea fowl populations, i.e., the Indian guinea fowl (CARI), IRAD, and CHID, including FOS, EPAS1, CD74, and CSF1R. These genes have earlier been associated with immune regulation, stress response, and thermal adaptation. Selection signature scans, integrating intra-population (iHS) and inter-population (XP-EHH) approaches, uncovered genes under positive selection linked to immune response (like BCL11B, IL18, and GPC3), thermo-tolerance (like TRPV4 and BAG3), lipid metabolism (like AACS and ELOVL4), and pigmentation (BCO2). These signatures highlight the molecular basis of resilience in guinea fowl and their potential to withstand climate-induced stresses. This study presents the first global CNV atlas for guinea fowl and provides the first comprehensive genomic characterization of the Indian domestic population, integrating ROH, CNV, and selection signature analyses. It offers a comprehensive assessment of guinea fowl genomes (wild and domesticated) across three continents, offering insights into domestication, evolutionary dynamics, and the genetic basis of their adaptation and resilience. Full article

Argali (Ovis ammon), the largest wild sheep in Asia, are of high conservation concern and remain taxonomically and genetically debated across parts of their range. We investigated population structure, relatedness, and inbreeding within Argali sampled in Kyrgyzstan using the Illumina Ovine High-Density SNP array, with an emphasis on dense within-population sampling rather than range-wide comparisons. After quality control, 72 individuals and 135,242 markers were retained for analysis. Principal component analysis revealed subtle genetic variation within the sampled population, but no clustering consistent with discrete subspecies. In particular, we found no genomic support for separating O. a. polii and O. a. karelini within Kyrgyzstan, suggesting that they represent a single genetic unit in this region. Estimates of identity by descent indicated a high average relatedness (0.35), consistent with harem-based breeding systems typical of wild sheep, while individual inbreeding coefficients averaged near zero, with some evidence of moderate inbreeding in a subset of animals. Together, these results characterize fine-scale genetic structure and kinship within Tian Shan Argali and provide a regional genomic baseline for conservation planning in Kyrgyzstan. Our findings highlight the importance of maintaining connectivity within and among managed populations while acknowledging that broader inference will require sampling across the core Pamir range and other parts of the species’ distribution. Full article

Accurate genealogical records are essential in livestock breeding for maintaining genetic diversity, preventing inbreeding, and mapping of economically important traits in beef production. This study aimed to assess parent–offspring relationships within South African Bonsmara and Nguni cattle populations using both traditional pedigree records and genomic data. Hair samples from 119 Nguni and 311 Bonsmara cattle were genotyped using the BovineSNP50 array, and these were imputed to Illumina BovineHD BeadChip using updated SNP coordinates from the assembly genome (ARC—UCSD 1.2). Quality control and data filtering were performed using PLINK v1.9, while relationship inference was conducted using KING v2.2.8 and PLINK v1.9 software for principal component analysis, IBD metrics and Mendelian error-based exclusion. Categories of relatedness through network relationship analysis revealed a predominance of half-sibling relationships in both breeds, with 2317 such relationships identified in Nguni and 1221 in Bonsmara. Inference of parent–offspring pairs showed discrepancies with the recorded pedigrees, with 49 inferred pairs compared to 47 recorded pairs in Nguni, and 62 inferred pairs compared to 75 pairs recorded in Bonsmara. Relationships based on IBD using PLINK with a ‘PI-HAT’ threshold greater than 0.45 revealed unique parent–offspring inferences that differed from those obtained using KING v2.2.8. Phylogenetic network analysis assigned each individual’s genomic origin independent of the pedigree records, supporting the efficiency of SNP data for genetic assignment. These results demonstrated that SNP-based pedigree verification can accurately identify parent–offspring and half-sibling relationships, providing a reliable foundation for recombination analysis and supporting precise trait mapping and informed selection in breeding programs. Full article

As an elite indigenous poultry breed under national protection in China, the Xupu goose is renowned for its large body size, superior fatty liver production, premium meat quality, and high tolerance to roughage. To elucidate its genomic architecture, genetic diversity, and evolutionary selection signatures, we conducted whole-genome resequencing on 15 purposively selected, unrelated male Xupu geese. An average of 6.79 Gb of high-quality sequence data was generated per individual, yielding approximately 4.27 million single-nucleotide polymorphisms (SNPs) with a transition/transversion (Ti/Tv) ratio of 2.49. Population genomic analyses revealed that while the population retains a moderate genetic reservoir (H_E = 0.298), it exhibits a distinct heterozygote deficit (H_O = 0.217) and a moderate genomic inbreeding coefficient F_ROH = 0.204). This structural pattern underscores the genetic impact of historical ex situ closed-flock conservation and the consequent formation of cryptic family lineages. Furthermore, genome-wide integrated haplotype score (iHS) scans detected distinct regions under recent positive selection. Functional annotation of these regions highlighted candidate genes tightly associated with the breed’s hallmark traits, specifically lipid metabolism and hepatic fat deposition (ACSS2, ACSS3, PECR), alongside muscle development (CMYA5, MTPN, LEPR). Conclusively, this study delineates a comprehensive genomic landscape of the Xupu goose, providing a robust foundational resource for future germplasm conservation, molecular marker development, and precision breeding programs. Full article

Honeybee (Apis mellifera L.) populations are a vital resource for pollination and honey production, yet their genetic diversity in Central Asia remains poorly understood. This study provides a comprehensive genetic assessment of 16 honeybee populations from Kazakhstan, with comparative samples from Russia, Georgia and Kyrgyzstan, utilizing mitochondrial COI–COII intergenic region and 12 highly polymorphic nuclear STR markers. Mitochondrial DNA analysis revealed the predominance of the Eastern European C lineage (A. m. carnica), while a few populations from East Kazakhstan and Russia attributed the M lineage (A. m. mellifera), indicating local introgression and the persistence of relict lineages. STR analyses showed high levels of polymorphism and genetic diversity, with variation in heterozygosity and inbreeding across populations. Analyses of population genetic structure delineated four principal genetic clusters shaped by regional differentiation, historical gene flow, and sporadic admixture. Concordance between mitochondrial and nuclear markers confirms the robustness of these findings. Overall, this study highlights the rich genetic diversity of honeybees from Kazakhstan and emphasizes the importance of conserving local populations and implementing selective breeding programs to sustain adaptive potential and long-term apiculture. Full article

Phascolosoma esculenta is an economic species endemic in China and a highly prized delicacy along the country’s southeastern coast. This study focused on five P. esculenta populations and investigated their genetic diversity, population structure, and historical population dynamics. These populations were sampled from five locations, namely Beihai (BH) and Fangchenggang (FCG), in Guangxi; Putian, in Fujian (FJ); Danzhou, in Hainan (HN); and Zhanjiang (ZJ), in Guangdong. Genomic data were obtained through restriction site-associated DNA sequencing (RAD-seq) of 100 individuals. After quality filtering, a panel of 158,264 high-quality single nucleotide polymorphism (SNP) markers was established for subsequent analysis. The results revealed that the observed heterozygosity (Ho = 0.1872–0.2065) was lower than the expected heterozygosity (He = 0.2304–0.2382), with inbreeding coefficients (Fis) ranging from 0.1114 to 0.1592, indicating heterozygote deficiency and moderate inbreeding. Genetic diversity was moderate across all populations, as reflected in the values I (0.5220–0.5530), π (0.2415–0.2478), and PIC (0.1914–0.1982). Low genetic differentiation was observed among populations (Fst: 0.0339–0.0509) accompanied by high gene flow (Nm = 4.6658–7.1192), suggesting ongoing genetic exchange between populations. Analysis of Molecular Variance (AMOVA) indicated that most genetic variation occurred within populations. Genetic distance and genetic similarity ranged from 0.0345 to 0.0522 and 0.9491 to 0.9661, respectively, with no significant isolation by distance (Mantel test, R = 0.0793, p = 0.4307). Analysis of the species’ historical population dynamics suggests that P. esculenta may have experienced a substantial population contraction beginning approximately 300 years ago. Overall, the five populations exhibit moderate genetic diversity, though signs of inbreeding and recent population decline may indicate early stages of germplasm degradation. These findings provide important insights for the conservation and sustainable aquaculture of this species. Full article

Background: The Xinjiang Black pig is an excellent breed developed by the Xinjiang Production and Construction Corps in the 1990s; however, it has been endangered by the impact of commercial breeds. Methods: Whole genomes of 224 individuals from the Xinjiang Black pig conservation population were resequenced. Results: Genetic structure and diversity analyses revealed that Xinjiang Black pigs underwent severe inbreeding and were genetically closely linked to Landrace pigs. The genetic diversity of the F₂ generation was well preserved in the existing breeding scheme. A total of 686 significant selection regions and 406 candidate genes were identified using F_ST and θπ complementary methods, with Xinjiang Black pigs, Min pigs, and Laiwu pigs as ancestral populations, and F₂. Based on Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and quantitative trait loci annotations, potential germplasm candidate genes were identified. Among these, SOX5, HMG20A, and NEDD4 are associated with fat deposition; SPRY1, MNS1, DMXL2, and ALB are closely associated with male reproductive ability; ARPP19 and TLN2 are strongly associated with oestrous cycle regulation and oocyte maturation; and SLC4A4 and SLC12A1 are extremely important for osmotic regulation and foetal survival. Conclusions: These findings deepen our understanding of the genetic mechanisms of artificial selection in Xinjiang Black pigs and provide a theoretical basis for subsequent breeding and genetic research on this breed. Full article

The emergence of Sundaland during the Pleistocene glaciation has played a crucial role, as the Indo-Pacific Barrier (IPB), in shaping the genetic structure of marine taxa and coastal flora, specifically mangroves. This study investigated the genetic diversity, population structure, demographic history and phylogeography of Avicennia marina and two other Indo-West Pacific (IWP) Avicennia species, Avicennia alba and Avicennia officinalis, across the Andaman Sea (Indian Ocean) and the Gulf of Thailand (Pacific Ocean). Using Restriction-site-Associated DNA sequencing (RADseq), we generated thousands of genome-wide SNPs for 362 Avicennia individuals and revealed a pronounced East–West genetic divergence, separating the Andaman and Gulf of Thailand populations. Phylogeographic and demographic analyses suggest that colonization events by distinct ancestral lineages (Indian and West Pacific Ocean lineages), the Indo-Pacific Barrier (Sundaland), and Pleistocene sea-level fluctuations shaped the population structure and contributed to low genetic diversity (H_o = 0.073–0.083) and high inbreeding coefficients (F_IS = 0.169–0.501). This study highlights the importance of Thailand, as part of the Indo-Pacific interface, in harboring genetic resources from both Indian and West Pacific Ocean lineages, as exemplified in A. marina. Consequently, Andaman and Thai Gulf populations should be managed as distinct evolutionarily significant units (ESUs). Full article