Search Results (138)

To investigate the genetic diversity and structure of farmed Chinese three-keeled pond turtles (Mauremys reevesii), we performed whole-genome resequencing on 238 individuals from eight farms across six Chinese regions. Genetic diversity indices (nucleotide diversity π, inbreeding coefficient F_HOM, polymorphism information content PIC, observed heterozygosity Ho), principal component analysis (PCA), phylogenetic reconstruction, and population structure analysis were integrated. The results revealed that the Guangdong Maoming (MM) and Anhui Wuwei (WW) populations exhibited the highest genetic diversity (MM: PIC = 0.149, Ho = 0.299; WW: PIC = 0.144, Ho = 0.287), while the Guangdong Huizhou (HZ) and Hunan Changhan (CH) populations showed the lowest diversity due to elevated inbreeding coefficients (HZ: F_HOM = 0.043; CH: F_HOM = 0.041). Low genetic differentiation (F_st = 0.00043–0.04758) indicated limited population divergence. However, PCA and phylogenetic analysis demonstrated that MM and Guangxi Pingxiang (PX) populations formed distinct genetic clusters, suggesting that management differences might contribute to their genetic uniqueness. Admixture analysis identified K = 2 (based on the lowest cross-validation error) as the optimal ancestral cluster number, with MM and PX populations displaying admixed genetic backgrounds while others showed homogeneous compositions. Conservation priorities should focus on preserving MM and PX’s unique genetic resources, introducing genetic material to high-inbreeding populations, and establishing interregional breeding networks. This study provides genomic insights for germplasm conservation and sustainable utilisation of M. reevesii. Full article

A breeding program of Asian seabass (Lates calcarifer, also called barramundi) was established for sustainable aquaculture in Thailand. Estimated breeding values (EBVs) for growth of the base population (G0, 51 families, N = 1655) were evaluated. Fish exhibited either high (HEBV, averaged body weight = 1036.80 ± 250.80 g, N = 133) or low (LEBV, averaged body weight = 294.50 ± 167.20 g, N = 147) growth EBVs, and their parental fish (N = 26) were analyzed by Specific Locus Amplified Fragment Sequencing (SLAF-Seq). An average of 159,769 SLAF tags/sample was generated, covering 13.79-fold of the genome size, and 225,498 SNPs were applied for population genomics. Observed (H_o) and expected (H_e) heterozygosity values were 0.224 and 0.308, 0.178 and 0.246, and 0.184 and 0.305, respectively. Polymorphic information content (PIC) ranged from 0.205–0.251. A selective sweep was performed based on Fst, and nucleotide polymorphism (π) revealed significant differences between allelic contents of growth- and immune-related genes in HEBV and LEBV populations. Kinship analysis revealed that 84.38% of examined fish showed r values < 0.2, and population admixture analysis revealed three subpopulations in HEBV and four subpopulations in LEBV groups. Fish that possessed a single cluster were found in each subgroup of both populations, along with those exhibiting mixed ancestral clusters. This information is critically important for further applications in our ongoing seabass improvement breeding program. Full article

Background/Objectives: The Carpathian Basin is a genetically and culturally diverse region shaped by complex historical migrations and various ethnic groups. While studies based on Y-chromosomal and mitochondrial DNA have provided valuable insights into the genetic diversity of these populations, genome-wide autosomal SNP data remain underutilized in understanding the genetic structure of these groups. This study presents the first genome-wide autosomal SNP-based analysis of key Hungarian-speaking ethnic groups in the region, focusing on admixture patterns and the extent of preserved historical genetic components. Methods: We analyzed genome-wide autosomal SNP data from 597 individuals representing several ethnic groups in the Carpathian Basin. Standard population genetic methods were applied to assess genetic structure, admixture and differentiation, with comparisons to broader European reference populations. Results: Most ethnic groups displayed genetic affinities with Eastern European populations, consistent with historical and geographical proximity. The Swabian group, of German descent, exhibited a distinct Western European genetic component, likely due to historical isolation. Transylvanian populations appeared relatively homogeneous, indicating a shared ancestral background. In contrast, Csangos showed distinct sub-clusters, suggesting population isolation and distinct histories. Overall, genetic homogeneity characterizes the region, though certain isolated groups retain distinct ancestral signatures. Conclusions: Autosomal SNP analysis revealed mild overall genetic structuring among Carpathian Basin ethnic groups. However, historical isolation has preserved unique genetic components in specific groups, highlighting the value of genome-wide data in uncovering fine-scale population structure. These findings contribute to a deeper understanding of regional genetic diversity, which has implications for both population history and health-related genetic research. Full article

The yellowfin seabream Acanthopagrus latus (Houttuyn, 1782) belongs to the order Spariformes and family Sparidae and is tender, rich in fat, and nutritious, making it a high-value seafood variety along the China coast. The fry can be used for large-scale aquaculture in both seawater and freshwater. Due to environmental pollution and excessive fishing, natural A. latus populations have declined significantly in recent years, which severely depletes genetic diversity. Here, we analyzed the genetic structure of four wild A. latus populations in the South China Sea to provide insights into the genetic resources. In particular, we analyzed 40 samples from four sampling sites through whole-genome resequencing, yielding 515 Gb of raw data and 132,505,081 single nucleotide polymorphisms. Population structure, phylogenetic, and principal component analyses revealed that the four populations were homogeneous and did not show clustering based on geographical origin, indicating extensive admixture. This could be attributed to recent enhancement and release activities in the South China Sea. This information may help to protect and utilize A. latus germplasm resources. Full article

A key feature in sheep biology is reproduction seasonality which concerns the cyclical occurrence of natural breeding, which therefore does not take place throughout the year. Since sheep are short-day breeders, the amount of daylight has an impact on their reproductive activity. The melatonin receptor subtype 1A (MTNR1A) gene is the primary gene that has been linked with seasonality. Nonetheless, information regarding the potential genetic association between other loci and the seasonality of sheep reproduction is scarce. Genome-wide association study (GWAS) is considered a cutting-edge methodology for comprehending the genetic architecture of complex traits since it enables the discovery of many markers linked to different features. In the present study, three indigenous Greek sheep breeds were investigated using GWAS—two of which presented strict patterns of reproduction seasonality, i.e., the Florina and Karagkouniko breeds, while the third one, i.e., the Chios breed had the ability to exhibit estrus throughout the year—in an attempt to detect the genetic loci linked with reproduction seasonality. All three breeds of investigated animals were purebred with Chios and Florina breeds originating from the Greek national stationary stock, whereas Karagkouniko originated from a commercial farm. Interestingly, a significant genetic differentiation of the national stationary stock groups was suggested by principal component analysis, phylogenetic analysis, and admixture and spatial point patterns, with these two breeds being less heterogeneous. This finding highlights the value of stationary stocks towards the maintenance of genetic integrity in indigenous sheep, demonstrating the Greek station’s critical role in the conservation of native sheep breeds. On the other hand, according to the GWAS data analysis, no genetic loci were correlated with reproduction seasonality, emphasizing the MTNR1A gene as the main determinant of the seasonality in native non genetically improved breeds. Full article

The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding its phylogenetic history and genomic composition has hindered its long-term conservation and utilization. This study evaluated the genetic diversity, population phylogenetics, and genome-wide selective sweep analysis (GWSA) of 100 newly obtained Bazhou yaks through genome resequencing, as well as 340 public yak genomes from nine other populations on the Qinghai–Tibet Plateau. The results revealed moderate diversity, lower genomic inbreeding levels, and rapid linkage disequilibrium (LD) decay in Bazhou yaks. Principal component analysis (PCA) and phylogenetic analysis showed a clear separation of Bazhou yaks from other yak populations, indicating the Bazhou yak as an independent genetic population. Furthermore, less genetic differentiation was found between the Bazhou yak and the Huanhu yak, while ADMIXTURE analysis revealed a common ancestral lineage between Bazhou yaks and Huanhu yaks, indicating an important genetic contribution of the Qinghai yak population to Bazhou yaks. The GWSA identified a total of 833 selected genes in Bazhou yaks using the top 5% interaction windows of both parameters (F_ST, Pi ratio, and XP-EHH). A significant number of these genes are related to fat synthesis and deposition, such as MTOR, APOA1, and GPAT4. In summary, this study sheds light on the phylogenetic status and distinctive genomic features of Bazhou yaks, which facilitates our understanding of the genetic basis of the IMF phenotype in Bazhou yaks. Full article

The European rabbit exists in the wild and has several highly bred domesticated forms. There are well-separated wild European rabbit populations, and intensive breeding has resulted in various forms and utilizations. In this work, we aimed to carry out an extended WGS-based population genomics study on several wild European rabbit populations and selected breeds. Utilizing multiple methods, we showed that although domestic and wild populations were clearly separated, there was evidence of admixture between them in France and Hungary. The populations showed various levels of inbreeding, with one of the Hungarian subpopulations having excess runs of homozygosity. We identified numerous variants fixed in either domestic or wild animals, two of which were found to be fixed at different alleles in the two populations. Some putatively selected regions did not overlap with any known genes in the rabbit genome, suggesting some importance to these intergenic sites. The enrichment of selected regions in certain types of transcription factor binding sites suggests a possible role for these regulatory elements during domestication. In addition, the new high-coverage rabbit whole-genome sequences may provide helpful material for further population genetics analyses. Full article

Peach (Prunus persica (L.)) is one of the major commercial stone fruit crops. A genetic analysis of peach collections around the world is essential for effective breeding programmes, and the development of genomic and marker-assisted selection. This study focuses on research on peach collection at the Nikita Botanical Garden and aims to identify single-nucleotide polymorphisms (SNPs) at the genome level and analyse the genetic diversity, population structure, and the linkage disequilibrium (LD) pattern among 161 cultivars and hybrids. A total of 288,784 SNPs were identified using the genotyping-by-sequencing (GBS) approach and, after filtering, 7803 high-quality SNPs were used in the analyses. The 161 accessions were clustered into two groups using principal component analyses (PCoA) and seven populations by ADMIXTURE v.1.3 software, which was confirmed using phylogenetic analyses. The distribution of the genotypes within subpopulations reflected any fruit-related traits. A low level of genetic diversity and medium linkage disequilibrium was detected in peach cultivars. The observed heterozygosity was lower than expected and varied from 0.11 to 0.22 in genotypes with different origins. Our results based on 7803 SNPs were compared with those based on 12 microsatellite markers and differences in clustering, observed heterozygosity, and phylogeny were identified. This highlights the need to analyse collections using whole-genome approaches. Full article

This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. F_ST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, Altai, and Kalmyk cattle. Principal component analysis and ancestry inference confirmed these patterns, with KWH genomes comprising 45% Hereford, 30% Altai, and 25% Kalmyk ancestries. Haplotype analysis revealed 73 regions under putative selection in KWH, some shared with Hereford (e.g., with the gene DCUN1D4) and some KWH-specific (e.g., with the gene SCMH1). F_ST analysis identified 105 putative intervals under selection, with key genes (KITLG, SLC9C1, and SCMH1) involved in coat colour and physiological adaptations. Functional enrichment using The Database for Annotation, Visualization, and Integrated Discovery (DAVID) in selected regions highlighted clusters associated with developmental processes, ubiquitination, and fatty acid metabolism. Point F_ST identified 42 missense variants in genes enriched in functions related to economically important traits. Local ancestry inference revealed genomic intervals with predominantly non-Hereford ancestry, including high Altai (e.g., SCAPER) and Kalmyk (e.g., SRD5A2) contributions, while Hereford-dominated regions included genes ENO1 and RERE. This work elucidates the genomic contributions and adaptive signatures of selection shaping the KWH breed, providing candidate genetic variants for breeding program improvement and enhanced genome predictions. Full article

Structural variants (SVs) are one of the main sources of genetic variants and have a significant impact on phenotype evolution, disease susceptibility, and environmental adaptations. We used 73 whole genome sequencing (12x) to apply a mapping approach to identify SVs in five turkey populations. A notable degree of genetic isolation was observed between the Basilicata and Apulian populations, as indicated by principal component analysis and admixture results. A total of 11,733 SVs were detected, including 6712 deletions, 2671 duplications, 1430 inversions, and 920 translocations. The Variant Effect Predictor (VEP) analysis predicted various consequences of filtered SVs as follows: intron variants (35.8%), intergenic variants (9.6%), coding sequence variants (8.3%), downstream gene variants (7.5%), and transcript ablations (7.3%). Our functional annotation of genes overlapping with SVs was mainly enriched in recognized pathways governing positive regulation of nucleoplasm, protein binding, mitochondrion, negative regulation of cell population proliferation, identical protein binding, and calcium signaling. We produced a comprehensive SV catalog utilizing unique whole-genome turkey data. This SV catalog not only increases our understanding of genetic diversity in turkeys but also enhances our knowledge of the role of SVs in their phenotypic traits. Full article

Two species of wild sheep inhabit Iran: Asiatic mouflon (Ovis gmelini) and urial (O. vignei). Phylogenetic relationships between populations distributed in this country are complex and still remain unclear. This study aimed to clarify, by genetic assessment, the phylogenetic status of Kerman wild sheep, considered to be a hybrid of the two species. For this purpose, we created a dataset that included specimens of O. gmelini, O. vignei, and Kerman sheep. We applied genome-wide SNP genotyping technology to analyze population structure and genetic diversity of these groups. Using Neighbor-Net and PCA plots, it was demonstrated that Kerman sheep were differentiated from other groups and occupy an intermediate position between O. gmelini and O. vignei. Using Admixture analysis, two ancestral components were identified in this population; however, admixed ancestry was not confirmed by f3 statistics. Genetic diversity in Kerman wild sheep was significantly higher than in any group of O. vignei, but lower than in O. gmelini. Additionally, we examined complete mitochondrial genomes and it was demonstrated that the matrilineal ancestor of Kerman sheep belonged to O. vignei. Our results lead to the conclusion that Kerman wild sheep can be recognized as a separate subspecies of O. vignei. Full article

This study investigates genetic diversity among five morphotypes and five chemotypes of Ocimum basilicum L. (sweet basil) using amplified fragment length polymorphism (AFLP) markers. Conducted on 80 basil accessions from the Collection of Medicinal and Aromatic Plants of the National Plant Gene Bank of the Republic of Croatia, this research aims to enhance the conservation and utilization of sweet basil’s genetic resources. AFLP analysis using extracted genomic DNA revealed high levels of polymorphism, particularly within the True basil morphotype, which displayed 95.6% polymorphic markers. The results showed genetic differentiation between the morphotypes, particularly between the ’green’ and ’purple’ groups, and within certain chemotypes, such as the High-linalool chemotype (Chemotype A). Principal coordinate analysis (PCoA) and Bayesian clustering further highlighted the genetic structures, with some admixture observed, particularly in the Purple basil B morphotype. Analysis of molecular variance (AMOVA) indicated that most of the genetic diversity was between accessions, emphasizing the value of individual variability. These findings underscore the genetic potential within sweet basil accessions, offering valuable insights for future breeding programs aimed at selecting basil cultivars with tailored biochemical and morphological traits suited for pharmaceutical, culinary, and ornamental applications. The study provides an important basis for the conservation and improvement of basil genetic resources. Full article

Background: Eastern Finnic populations, including Karelians, Veps, Votes, Ingrians, and Ingrian Finns, are a significant component of the history of Finnic populations, which have developed over ~3 kya. Yet, these groups remain understudied from a genetic point of view. Methods: In this work, we explore the gene pools of Karelians (Northern, Tver, Ludic, and Livvi), Veps, Ingrians, Votes, and Ingrian Finns using Y-chromosome markers (N = 357) and genome-wide autosomes (N = 67) and in comparison with selected Russians populations of the area (N = 763). The data are analyzed using statistical, bioinformatic, and cartographic methods. Results: The autosomal gene pool of Eastern Finnic populations can be divided into two large categories based on the results of the PCA and ADMIXTURE modeling: (a) “Karelia”: Veps, Northern, Ludic, Livvi, and Tver Karelians; (b) “Ingria”: Ingrians, Votes, Ingrian Finns. The Y-chromosomal gene pool of Baltic Finns is more diverse and is composed of four genetic components. The “Northern” component prevails in Northern Karelians and Ingrian Finns, the “Karelian” in Livvi, Ludic, and Tver Karelians, the “Ingrian-Veps” in Ingrians and Veps (a heterogeneous cluster occupying an intermediate position between the “Northern” and the “Karelian” ones), and the “Southern” in Votes. Moreover, our phylogeographic analysis has found that the Y-haplogroup N3a4-Z1927 carriers are frequent among most Eastern Finnic populations, as well as among some Northern Russian and Central Russian populations. Conclusions: The autosomal clustering reflects the major areal groupings of the populations in question, while the Y-chromosomal gene pool correlates with the known history of these groups. The overlap of the four Y-chromosomal patterns may reflect the eastern part of the homeland of the Proto-Finnic gene pool. The carriers of the Y-haplogroup N3a4-Z1927, frequent in the sample, had a common ancestor at ~2.4 kya, but the active spread of N3a4-Z1927 happened only at ~1.7–2 kya, during the “golden” age of the Proto-Finnic culture (the archaeological period of the “typical” Tarand graves). A heterogeneous Y-chromosomal cluster containing Ingrians, Veps, and Northern Russian populations, should be further studied. Full article

Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot (P. armeniaca) varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the “Yinxiangbai” apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software. The average comparison ratio between the sequencing results and the reference genome was 97.66%. After strict screening, 88,332,238 high-quality SNP sites were finally obtained. Based on the statistical SNP variation type, it was found that LNLJX had the largest number of variations (3,951,322) and the lowest base transition/base transversion ratio (ts/tv = 1.77), indicating that its gene exchange events occurred less frequently. Based on the SNP point estimation of the relationship and genetic distance between samples, the relationship between species was 1.41–0.01, among which PLDJX and BK1 had the closest relationship of 1.41, and YZH and LGWSX had the farthest relationship of 0.01. The genetic distance between species was 0.00367–0.264344, the genetic distance between HMX and JM was the closest, and the genetic distance between WYX and YX was the farthest, which was the largest. Phylogenetic tree, PCA, and genetic structure analysis results all divided 53 common apricot varieties into four groups, and the classification results were consistent. The SNP markers mined using WGRS technology are useful not only to analyze the variation of common apricots, but also to effectively identify their kinship and genetic structure, which plays a critical role in the classification and utilization of common apricot germplasm resources. Full article

The radiation of cichlid species in the East African Great Lakes is remarkable and rapid. The population genetics of two deep-water Cyphotilapia species along the east coast of Lake Tanganyika from Burundi to southern Tanzania was determined using ddRAD-seq. A combination of ADMIXTURE, PCA, genome polarization, and 2D site frequency spectrum analyses confirmed the presence of two species, C. frontosa in the north and C. gibberosa in the south, as documented in other studies. We also found evidence of a potential hybrid zone connecting the two species at a sharp genetic cline centered in the middle of the lake and apparent introgression in both directions, but predominantly from ‘gibberosa’ into ‘frontosa’. The highest proportion of introgressed ‘gibberosa’ ancestry was present in the southernmost populations of C. frontosa collected near Karilani Island and Cape Kabogo. At the intra-specific level, there was support for between 1 and 3 populations of C. frontosa, whereas the results indicated only a single homogeneous population of C. gibberosa. The presence of different morphs in the lake despite the low levels of heterozygosity suggests that a small number of loci may be involved in the morphological variation and/or that there is a more complex interplay between genetics and the environment in different locations. Full article