Analysis Of Genetic Structure Research Articles

Material Selection for Restoration of Genetic Diversity of Abies koreana on Mt. Jirisan in South Korea

A strategy is required for selecting appropriate materials for the restoration of Abies koreana on Mt. Jirisan, where the habitat of A. koreana is continuously shrinking. The current study aimed to analyze the genetic characteristics of A. koreana in three subpopulations (Banyabong, Byeoksoryeng, and Cheonwangbong) on Mt. Jirisan using 10 nuclear simple sequence repeat (nSSR) markers and calculate the sampling distance for each subpopulation for avoiding genetically similar samples. Based on the calculated sampling distance, we proposed the size of a sample containing more than 95% of the alleles at a frequency greater than 0.05. AMOVA showed that the difference in genetic variation across subpopulations of A. koreana on Mt. Jirisan was small, approximately 3% of the total. Spatial genetic structure analysis results suggested that it would be appropriate to collect samples of the Banyabong subpopulation at intervals of 10 m or more, when sampling A. koreana, whereas for the Byeoksoryeong and Cheonwangbong subpopulations, samples should be collected at intervals of 20 m or more. Results of random sampling of 5 to 30 individuals indicated that, by applying a 10 m distance within the Banyabong subpopulation, more than 95% of the total alleles with a frequency ≥ 0.05 were secured when more than 25 individuals were extracted. Therefore, as a restoration strategy for A. koreana on Mt. Jirisan, we proposed the collection of more than 25 samples, keeping 10 m distance within the Banyabong subpopulation, which has a relatively high genetic diversity.

Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae).

The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.

Analysis of genetic diversity and population structure in some Egyptian Berseem (Trifolium alexandrinum) accessions based on ISSR, SCoT and SRAP markers

Analysis of genetic diversity and population structure in some Egyptian Berseem (Trifolium alexandrinum) accessions based on ISSR, SCoT and SRAP markers

Evidence for the Use of Karst Tiankengs as Shelters: The Effect of Karst Tiankengs on Genetic Diversity and Population Differentiation in Manglietia aromatica

Karst tiankengs in China are globally significant locations for studying ecological environments and plant diversity. However, there are few reports on how the unique geographical environment of tiankengs affects plant genetic diversity and genetic structure. This study used Hyper-seq gene sequencing technology to develop large-scale genomic SNPs of Manglietia aromatica, both within and outside the tiankengs. Its aim was to investigate the impact of tiankengs on the genetic diversity and genetic structure of the M. aromatica population. The analysis results indicate that the genetic diversity of the populations within the tiankeng (π = 0.2044) is higher than that of the populations outside of it (π = 0.1671), indicating that the tiankengs have a positive impact on species diversity. The genetic differentiation coefficient (FST) between the populations inside and outside the tiankeng was 0.0534 and the FST values of populations within the tiankeng were 0.077, 0.082, and 0.141, meaning that the genetic variation in the tiankengs is very high. The genetic similarity outside the tiankengs is also very high, indicating that the tiankengs are effectively preserving the genetic diversity of M. aromatica. Furthermore, the gene introgression analysis results gave no proof of gene flow between the three tiankeng populations. This suggests that the tiankengs not only protect species diversity, but also hinder gene flow between populations to some extent. However, this hindrance may gradually subside with the evolution of the tiankengs. The genetic structure analysis revealed that the M. aromatica population in Guangxi, China, can be classified into three subpopulations. The first is the tiankeng subpopulation, including all the populations in tiankengs. The second subpopulation consists of populations surrounding the tiankengs. These two subpopulations are distributed in Leye County in northwestern Guangxi, China, and are very close to each other. The third is the Huanjiang subpopulation, which is located far away from the tiankengs. Considering the direction of gene flow and genetic structure, it is speculated that the populations in the tiankengs evolved from the populations near the pit mouth. This study confirms that the tiankengs are shelters and provide a suitable habitat for the endangered plant M. aromatica, because its genetic diversity is well conserved and the species is well adapted to the habitat within the tiankengs.

Surveys on Baylisascaris procyonis in two of the three French wild raccoon populations

Human infection by Baylisascaris procyonis can result in larva migrans syndromes, which can cause severe neurological sequelae and fatal cases. The raccoon serves as the definitive host of the nematode, harboring adult worms in its intestine and excreting millions of eggs into the environment via its feces. Transmission to paratenic hosts (such as rodents, birds and rabbits) or to humans occurs by accidental ingestion of eggs. The occurrence of B. procyonis in wild raccoons has been reported in several Western European countries. In France, raccoons have currently established three separate and expanding populations as a result of at least three independent introductions. Until now the presence of B. procyonis in these French raccoon populations has not been investigated. Between 2011 and 2021, 300 raccoons were collected from both the south-western and north-eastern populations. The core parts of the south-western and north-eastern French raccoon populations were free of B. procyonis. However, three worms (molecularly confirmed) were detected in a young raccoon found at the edge of the north-eastern French raccoon population, close to the Belgian and Luxemburg borders. Population genetic structure analysis, genetic exclusion tests and factorial correspondence analysis all confirmed that the infected raccoon originated from the local genetic population, while the same three approaches showed that the worms were genetically distinct from the two nearest known populations in Germany and the Netherlands. The detection of an infected raccoon sampled east of the northeastern population raises strong questions about the routes of introduction of the roundworms. Further studies are required to test wild raccoons for the presence of B. procyonis in the area of the index case and further east towards the border with Germany.

Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae)

BackgroundThe sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization.ResultsIn this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation.ConclusionOur findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.

Determining the genetic basis of ginsenosides variation during ginseng domestication by evolutionary transcriptomics

Ginsenosides, the primary medicinally active substances in ginseng, are consistently used to treat a variety of diseases. Cultivated ginseng was domesticated from wild ginseng, for which the mode of domestication and the changes in the content of ginsenosides and their regulatory mechanisms during the domestication process were unclear. Here, transcriptome sequencing and metabolomic analysis were used to compare wild and cultivated ginsengs to gain insight into the genetic and ginsenosides content changes associated with domestication. Genetic structure analysis revealed that ginseng might have undergone independent domestication in China and Korea, respectively. A slightly reduced genetic diversity occurred in wild and cultivated ginsengs and ginseng was domesticated about 2000 years ago in China. 330 genes were identified as signatures of selective sweeps that occurred during ginseng domestication, including bZIP051, GARP222, HMGCS058, and UGTs225. The content of ginsenosides in leaves of cultivated ginseng was higher than leaves of wild ginseng, while substantial monomers content in wild ginseng was significantly higher than that in cultivated ginseng. The content of ginsenosides was higher in leaves than in roots and stems of both wild and cultivated ginsengs. Module-trait association analysis suggested abundant TFs, including MYB, AP2/ERF, NAC, and bZIP, were highly associated with expression level of ginsenosides synthetic genes and monomer content. The occurrence of alternative splicing events in genes was significantly reduced during ginseng domestication, with ginsenosides synthesis genes being particularly susceptible to alternative splicing. The variation of ginsenosides content was independently regulated by alternative splicing and transcription factors between cultivated and wild ginsengs. This study provided valuable genetic sources of ginsenosides that could contribute to ginseng breeding.

Molecular characterization and genetic analysis of Orthotospovirus tomatomaculae (tomato spotted wilt virus) and cucumber mosaic virus infecting tomato and pepper in Türkiye

Many viral diseases threaten the sustainable production of tomato (Solanum lycopersicum) and pepper (Capsicum annuum), which are among the most produced vegetables in the world and Türkiye. Eskişehir province of Türkiye produces a significant amount of vegetables both in the greenhouse and in the open-field. However, there have been no previous comprehensive study on the presence of viruses in tomato and pepper fields. In this study, 123 of 170 samples (72.4%) collected from tomato and pepper fields in Eskişehir in 2019 were infected with different viruses listed. While Orthotospovirus tomatomaculae (tomato spotted wilt virus, TSWV), cucumber mosaic virus (CMV), potato virus Y (PVY), tomato mosaic virus (ToMV), tobacco mosaic virus (TMV) viruses were detected by DAS-ELISA, pepino mosaic virus (PepMV), tomato chlorosis virus (ToCV) and tobacco necrosis virus (TNV) viruses could not be detected in both host plants. To molecularly characterize the selected isolates, the complete nucleocapsid (N) gene region specific to TSWV and a partial capsid protein (CP) gene region specific to CMV were amplified via RT-PCR, followed by sequencing. Phylogenetic trees were constructed with NCBI GenBank isolates and newly sequenced isolates. Genetic structure-related analyses such as genetic diversity, genetic differentiation, gene flow, neutrality tests, selection pressure, and recombination were performed on populations. In the phylogenetic tree of the TSWV N gene, the isolates are divided into three clades of geographical origin. Genetic structure analyses revealed that TSWV populations exhibited genetic diversity. In the phylogenetic tree of the CMV CP gene, the isolates are divided into known subgroups. The analyses indicate the presence of high genetic diversity and suggest that Subgroup IB, one of the clades, may contain subgroups within itself. In addition, there are indications for the existence of different CMV subgroups in Türkiye. Although different approaches were used for both the TSWV N gene and CMV CP gene, no recombination event could be detected. This study, marking the initial identification of viruses in tomatoes and peppers within the Eskişehir region, is believed to hold substantial potential for advancing future research endeavors and enhancing disease management not only within Türkiye but also globally.

Testing hypotheses of invasion pathways of the ladybird Harmonia axyridis into and across South Africa

Harmonia axyridis is an invasive beetle (Coleoptera: Coccinellidae), native to Asia, that has established on four continents beyond its native range and was first observed in South Africa in 2001. Using microsatellite data and a comprehensive geographic coverage of international (17 locations) and South African (14 locations) beetle samples, we inferred the source of colonists invading South Africa and the beetle’s movement within the country. Genetic structure analyses suggest that this species’ populations in South Africa are derived from admixture between beetles originating from eastern North America (which acted as a bridgehead population) and another population not directly sampled in our study. Genetic admixture prior its invasion into South Africa, along with the possibility of multiple introductions from the bridgehead population, may explain the high genetic diversity estimates for South African H. axyridis (HE = 0.582–0.625) compared to beetles from the native range (HE = 0.440–0.636). Harmonia axyridis appear to be frequently exchanging genetic material across South Africa, with no clear genetic structure between sampled locations. However, evidence of weak isolation-by-distance within South Africa suggests that beetles are dispersing less frequently between locations that are furthest apart. This study supports previous findings on global invasion pathways in this species but provides new insights in the context of the invasion in South Africa. We highlight how mixing of distinct lineages from divergent origins prior to the invasion into South Africa has augmented genetic diversity in the region. The high dispersal rates and large effective population sizes inferred from genetic markers suggest that slowing the spread or reducing population abundances of the species in South Africa will be challenging without an integrated, multi-faceted management approach.

Hatchery-Imposed Selection Does Not Impact the Genetic Diversity of Australian Farmed Blue Mussels (Mytilus spp.)

Australian blue mussels (Mytilus spp.) are an increasingly important sustainable product of the Australian aquaculture industry. Although important for commercial fisheries, aquaculture may have adverse environmental and ecological impacts. This study assessed the impact of standard hatchery-imposed selection practices on the genetic diversity of farmed blue mussels. Using microsatellite markers, relatedness and genetic structure analyses showed that hatchery-reared larvae have high levels of genetic diversity without a significant decline as they move through the hatchery rearing process. Selection and/or genetic drift does appear to be operating during the hatchery rearing process, however, evidenced by an increase in relatedness among larvae over time. Significant shifts in allele frequency as well as genetic clusters provides further evidence that selection is acting on larvae due to the selection practice applied at the hatchery. Comparison of the level of genetic diversity and genetic differentiation of adults from wild and farmed populations provided no evidence that farmed mussels have lower diversity, or that they are genetically swamping local natural populations. The data suggest that careful design and implementation of mussel breeding programs can maintain high genetic diversity among larvae that does not lead to genetic swamping of natural mussel populations in the surrounding area.

Genomic insights into the population history and adaptive traits of Latin American Criollo cattle.

Criollo cattle, the descendants of animals brought by Iberian colonists to the Americas, have been the subject of natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds have evolved distinct characteristics such as resistance to diseases and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian indicine (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.

Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers

The nutritional and medicinal significance of jujube (Ziziphus jujuba) has led to persistent efforts in genomics to accelerate the utilization of its germplasm resources. However, the absence of accurate genetic identity of existing germplasm limits these studies. In the United States, different names were frequently given to the same jujube cultivars because the pedigrees of the imported germplasm are unclear. The present study selected a panel of 147 single nucleotide polymorphism (SNP) markers distributed across the jujube genome to examine genetic identity, genetic diversity, and population structure in 177 jujube cultivars sampled from different locations in the United States. SNP profile multilocus matching reported a total of 23 synonymous groups including 116 samples that were identical to at least one other sample. This led to the detection of 74 unique genotypes for subsequent diversity analysis. Model-based genetic structure analysis divided the distinctive genotypes into three major groups, with some admixtures among the groups. The genetic differentiation among these groups was further validated by analysis of molecular variance (Fst = 0.199, P value < 0.001), principal coordinate analysis, and clustering analysis. Morphological traits were studied in some of the genetically identical commercial cultivar groups, (i.e., Li, Lang, and Jinsi). Results demonstrated significant morphological differences within genetically identical cultivars in the Jinsi group, indicating phenotypic variation resulting from mutations in these clones.

The impact of climate change and the conservation of the keystone Asian honeybee using niche models and systematic prioritization.

Global warming has seriously disturbed the Earth's ecosystems, and in this context, Asian honeybee (Apis cerana) has experienced a dramatic decline in recent decades. Here, we examined both direct and indirect effects of climate change on A. cerana through ecological niche modeling of A. cerana, and its disease pathogens (i.e., Chinese sacbrood virus and Melissococcus plutonius) and enemies (i.e., Galleria mellonella and Vespa mandarinia). Ecological niche modeling predicts that climate change will increase the potential suitability of A. cerana, but it will also cause some of the original habitat areas to become unsuitable. Outbreak risks of Chinese sacbrood disease and European Foulbrood will increase dramatically, while those of G. mellonella and V. mandarinia will decrease only slightly. Thus, climate change will produce an unfavorable situation for even maintaining some A. cerana populations in China in the future. Genetic structure analyses showed that the A. cerana population from Hainan Island had significant genetic differentiation from that of the mainland, and there was almost no gene flow between the 2, suggesting that urgent measures are needed to protect the unique genetic resources there. Through taking an integrated planning technique with the Marxan approach, we optimized conservation planning, and identified potential nature reserves (mainly in western Sichuan and southern Tibet) for conservation of A. cerana populations. Our results can provide insights into the potential impact of climate change on A. cerana, and will help to promote the conservation of the keystone honeybee in China and the long-term sustainability of its ecosystem services.

Nuclear SSR-based genetic diversity and STRUCTURE analysis of Greek tomato landraces and the Greek Tomato Database (GTD)

AbstractTomato has been cultivated in Greece for more than 200 years, even though is not native to the country. Greece with a favourable environment all-round the year, has become a major competitor in tomato production around Europe. However, there is an increasing demand to improve tomato crop, to withstand harsh environmental conditions (extreme temperatures, salinity, etc.), and to develop high-quality final products. People have devoted a significant effort to crop improvement through phenotypic screening resulting in a large number of tomato landraces. An increasing demand to clarify the relationships among local tomato landraces and hybrids utilizing the most preferred molecular markers the simple sequence repeats (SSR-markers) is the main objective of this study. Twenty-seven tomato landraces and two tomato hybrids cultivated in Crete, Greece, were genotyped utilizing eleven simple sequence repeats (SSR) along with the Structure analysis of the germplasm. A neighbour-joining dendrogram of the 27 landraces and the two hybrids was produced. The Structure analysis indicated that nine ancestral populations are hidden inside the group of all the genotypes tested, using Evanno's method. The final objective was to make these data publicly available through the first Greek relational database (Greek Tomato Database-GTD). GTD was developed allowing the users to update and enrich the database, with new and supplemental information. This work is the first molecular fingerprint of the 27 landraces of Greece which is documented along with the phenotypic information in the GTD.

Ecological and Biogeographical Imprints in a Beech Glacial Refugium

The distribution of vascular plant species and assemblages existing in beech (Fagus sylvatica L.) forests was compared with the distribution of beech chloroplast DNA (cpDNA) haplotypes, aiming to identify possible interpretable trends of co-occurrence, on a small geographical scale, and to infer the relevant historical factors. Vegetation and genetic (cpSSR) data were collected from 60 plots on Mt. Menikio (northeastern Greece). Classification and ordination analyses were applied on the vegetation data, while on the cpSSR data, diversity measures and genetic structure analyses were employed. A probabilistic co-occurrence analysis was performed on haplotypes and taxa. The results show that a plant biogeographical border exists on Mt. Menikio which, in addition, has acted both as a refugium and as a meeting point of lineages for more than one glacial cycle. Significant associations of co-occurrence between haplotypes and vascular taxa were found but no common distribution patterns between the former and species assemblages were identified. The combined consideration of the distribution profiles of species assemblages, plant species and cpDNA haplotypes (corresponding to the three levels of biodiversity) provides concrete information on historical events, leading to a comprehensive understanding of the evolutionary and biogeographical processes that have shaped specific spatial patterns of biodiversity.

Analyses of genetic diversity and population structure of endemic and endangered species Sideritis gulendamii (Lamiaceae) and implications for its conservation

Sideritis gulendamii is a perennial, endangered plant endemic to Türkiye with narrow and fragmented populations encountered in gypsum and marl soil. This species is known as mountain tea and also has a significant potential for use for medicinal and aromatic purposes. Assessing the genetic diversity of this species holds significant importance in its conservation efforts due to its specific habitat requirements, small and isolated populations, and recent threats imposed on these populations. This study determined genetic diversity at the species and population levels using the inter simple sequence repeat (ISSR) fingerprinting method on 157 individuals from seven natural populations. We observed that the species-level genetic diversity is relatively high (H = 0.189, I = 0.298), but the population-level is low (H = 0.150, I = 0.231). The greater total genetic variation within populations was determined as 76% using the analysis of molecular variance (AMOVA). The obtained value of genetic differentiation (Gst = 0.208, Φpt = 0.24) among populations is considered to be at a moderate level, whereas gene flow appears to be high (Nm = 1.899). Supportive results were reached using the STRUCTURE cluster analysis, Unweighted Pair Group Method with Arithmetic Averages (UPGMA) dendrogram, and Principal Coordinate Analysis (PCoA). The positive correlation between the matrices of genetic distance and geographic distance is determined to be statistically significant, with values of r = 0.566 and p < 0.001 in the Mantel test. Some strategies were developed using the genetic variability pattern of this endangered species for its conservation.

Analysis of Genetic Diversity and Structure of Eight Populations of Nerita yoldii along the Coast of China Based on Mitochondrial COI Gene.

Nerita yoldii is a euryhaline species commonly found in the intertidal zone. To investigate the genetic diversity of 233 N. yoldii individuals from eight locations along the coast of China, we utilized the mitochondrial COI gene as a molecular marker. A total of 34 haplotypes were detected, exhibiting a mean haplotype diversity (Hd) of 0.5915 and a mean nucleotide diversity (Pi) of 0.0025, indicating high levels of genetic diversity among all populations. An analysis of molecular variance (AMOVA) indicated that the primary source of genetic variation occurs within populations. In addition, neutral tests and mismatch analyses suggested that N. yoldii populations may have experienced bottleneck events. Moderate genetic differentiation was observed between Xiapu and other populations, excluding the Taizhou population, and may be attributed to the ocean currents. Intensively studying the genetic variation and population structure of N. yoldii populations contributes to understanding the current population genetics of N. yoldii in the coastal regions of China. This not only provides a reference for the study of other organisms in the same region but also lays the foundation for the systematic evolution of the Neritidae family.

Population genetics reveals new introgression in the nucleus herd of min pigs.

Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs. We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs. The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content = 0.713, expected heterozygosity = 0.662, observed heterozygosity = 0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes. Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.

Paternal genetic structure analysis of the modern Han populations based on Y-SNP and Y-STR.

The Han populations represent the largest ethnic group in China. Previous studies have primarily focused on investigating their genetic origins, migration and integration, as well as paternal genetic relationships within specific regional Han populations. However, a comprehensive analysis of the global paternal genetic structure of Han populations is lacking. In this study, we performed Y-chromosome sequencing on 362 unrelated male samples from Chinese Han individuals collected from Qinghai, Sichuan and Liaoning provinces. We then integrated relevant data from reported studies. Our final dataset comprised 1830 samples from 16 Han populations across 15 provinces in China, encompassing information on 89 Y-SNPs and 16 Y-STRs. Statistical analyses were conducted to assess Y-STR haplotype diversity (HD) and Y-SNP haplogroup frequencies. Additionally, we employed principal component analysis (PCA), phylogenetic tree and haplotype network to explore genetic differentiation within Han populations and the genetic relationships between Han populations and ethnic minorities surrounding them. Our results demonstrated that the O-M175 haplogroup represents the predominant paternal lineage in Han populations, with frequencies ranging from 60.53% (Qinghai Han) to 92.7% (Guangdong Han). Moreover, the subclades downstream of O-M175 showed distinct regional variations in their distribution patterns. The O2-M122 haplogroup was prevalent in all Han populations and demonstrated a gradual decline in frequency from north to south. Conversely, the distribution frequency of the O1b-M268 haplogroup decreased from south to north, particularly showed significant presence among Han populations in the Lingnan region. Haplogroup O1a-M119 distributed more frequently in the central Han populations. Our findings revealed that Chinese Han populations can be categorized into three subgroups: northern, central, and southern. Notably, there were significant differences among Han in Qinghai and other regions. Regarding the genetic relationships between Han populations and surrounding ethnic minorities, we observed a closer genetic affinity between different Han populations, but northern Han demonstrated a stronger relationship with the Hui ethnic group, while southern Han exhibited a closer connection with the Gelao and Li ethnic groups. In summary, this study presented a systematic analysis of haplogroup distribution, genetic substructure of Han populations and genetic relationships between Han populations and surrounding ethnic minorities based on 89 Y-SNPs and 16 Y-STRs systematically. Our research supplemented valuable insights into population genetics and forensic genetics, and provided data support for the forensic application of Y chromosome. The integration of Y-SNP haplogroups with Y-STR haplotypes offers enhanced understanding of the genetic substructure within Han populations, which holds significance for both population genetics research and forensic science applications.

Retraction: Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y-STRs.

Adnan A., Kasimu K., Rakha A., He G., Yang T., Wang C-C., Lu J., Xuan J-f. (2020). Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y-STRs. Molecular Genetics & Genomic Medicine, 8(3), e1149. https://doi.org/10.1002/mgg3.1149 The above article, published online on 27 January 2020 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor in Chief, Suzanne Hart, and Wiley Periodicals LLC. Following publication of this article, concerns were raised by a third party regarding consent and ethical approval for the research undertaken and reported in the article. The publisher and representatives of the journal's editorial board undertook a review of the consent documentation provided, against the research performed and reported in the article. The review uncovered inconsistencies between the consent documentation and the research reported; the documentation was not sufficiently detailed to resolve the concerns raised. As a result, the parties have made the decision to retract the article. In addition, consent documentation did not give approval for data associated with this article to be shared publicly. The associated data for this article has been withdrawn from the publication record following a concern that the data could be used to identify those who have participated in the research. Atif Adnan responded on behalf of all the authors, who disagree with the retraction.