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        <title>Frontiers in Genetics | Evolutionary, Population, and Conservation Genetics section | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/genetics/sections/evolutionary-population-and-conservation-genetics</link>
        <description>RSS Feed for Evolutionary, Population, and Conservation Genetics section in the Frontiers in Genetics journal | New and Recent Articles</description>
        <language>en-us</language>
        <generator>Frontiers Feed Generator,version:1</generator>
        <pubDate>2026-05-14T19:12:56.17+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1819401</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1819401</link>
        <title><![CDATA[Adaptive radiation and structural tailoring of the Vietnamese Blec2 immunogenetic reservoir]]></title>
        <pubdate>2026-05-07T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Anh Huynh Luu</author><author>Trifan Budi</author><author>Worapong Singchat</author><author>Chien Tran Phuoc Nguyen</author><author>Thitipong Panthum</author><author>Nivit Tanglertpaibul</author><author>Kanithaporn Vangnai</author><author>Aingorn Chaiyes</author><author>Chotika Yokthongwattana</author><author>Chomdao Sinthuvanich</author><author>Orathai Sawatdichaikul</author><author>Kyudong Han</author><author>Narongrit Muangmai</author><author>Darren K. Griffin</author><author>Prateep Duengkae</author><author>Ngu Trong Nguyen</author><author>Kornsorn Srikulnath</author>
        <description><![CDATA[BackgroundThe global poultry industry faces a critical sustainability crisis driven by climate change and escalating disease threats, necessitating the identification of novel genetic reservoirs for resilience. The Major Histocompatibility Complex (MHC)-linked Blec2 gene, a member of the Killer Cell Lectin-like Receptor (KLR) family, serves as a molecular sentinel regulating Natural Killer (NK) cell-mediated immunity; however, its diversity remains poorly characterized in Southeast Asian avian populations.MethodsThis study utilized Illumina short-read sequencing and AlphaFold 3 modeling to investigate Blec2 polymorphism across 15 Vietnamese populations that comprised 13 indigenous breeds and two ancestral Red Junglefowl (Gallus gallus) lineages.ResultsWe identified 11 unique alleles, including the novel variant VN11, that establish the Vietnamese gene pool as a distinct reservoir of immune diversity. Notably, eight alleles were restricted to indigenous breeds, which exhibited a higher nucleotide diversity (π = 0.012) than their wild progenitors (π = 0.009), suggesting that localized diversification has been driven by breed-specific selective pressures. Evolutionary analysis revealed a dual mechanism: (1) intense global purifying selection (ω ≤ 0.035) preserving the receptor’s structural scaffold and (2) localized positive selection at codons 11 and 18 that is predicted in silico to influence the receptor’s binding affinity for the MHC Class I (BF2) ligand. The hypothesized functional relevance of this diversity is highlighted by the identification of alleles homologous to haplotypes previously associated with high resistance, such as Blec2*VN2 (linked to H5N1 and Marek’s disease resistance in prior studies) and Blec2*VN9 (associated with respiratory virus resilience).ConclusionBy integrating population genomics with in silico structural biology, this study provides the foundational data proposing Blec2 as a candidate locus for future Marker-Assisted Selection (MAS) research. While experimental functional validation remains necessary, our findings establish a hypothesis-driven framework for investigating how genetic reservoirs might be leveraged to enhance avian immunocompetence and secure sustainable poultry production against emerging viral threats.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1810782</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1810782</link>
        <title><![CDATA[Mating portfolio and neutral mechanisms are primary causes of genet-ramet frequencies and spatial distributions in smooth cordgrass (Spartina alterniflora) along salt marsh tidal gradients]]></title>
        <pubdate>2026-05-01T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Jewel Tomasula</author><author>Seamus Caslin</author><author>Gina M. Wimp</author><author>Matthew B. Hamilton</author>
        <description><![CDATA[Partially clonal plants are common and often act as ecological foundation species. Patterns of clonal genotypes (genets) and their vegetative modules (ramets) in natural populations remain poorly documented. Knowledge gaps in ecological genetics include if environmental variation promotes or limits ramet production, and if random mechanisms or natural selection mainly shape variation in the frequency distributions and spatial organization of ramets and genets. We used genetic markers to measure genet and ramet patterns of Spartina alterniflora, a foundation plant species in North American Atlantic coastal salt marshes, along its natural gradient of tidal inundation and interspecific competition. In ten patches in a natural salt marsh, we sampled 935 S. alterniflora stems on 1 m grid transects spanning natural environmental gradients. Samples were genotyped with ten microsatellite loci that provided high exclusion probabilities. Genotypes showed 223 multilocus lineage genets (MLLs) genets that were unique to patches (except a single MLL) and excess homozygosity consistent with biparental mating among relatives or as much as 50% selfing. Patches showed low to no genetic differentiation and there was no isolation by distance within nor between patches. Distributions of ramets per genet were consistent with random sampling with replacement that was heterogeneous among patches, except three MLLs from two patches with high ramet counts. Spatial patterns of ramets within MLLs exhibited intermediate aggregation and interspersion consistent with vegetative expansion by rhizomes. Genotype frequencies, ramet and genet spatial patterns, and distributions of ramets per genet were overall consistent with life history (mating portfolio, vegetative growth by rhizomes) and neutral sampling mechanisms. The three MLLs with high ramet counts could be explained by a range of neutral mechanisms such as patch disturbance history or priority effects, while adaptation to environmental gradients of a few meters is unlikely since these MLLs spanned large areas. As ecosystems dominated by partially clonal species experience a myriad of anthropogenic impacts, our results support wider recognition of combined sexual and vegetative mating portfolios in foundation plant species and improved quantification of clonal patterns on landscapes to better understand and predict ecological genetic variation.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1808090</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1808090</link>
        <title><![CDATA[Genomic basis of adaptation to cardiac glycosides in three insect orders]]></title>
        <pubdate>2026-04-22T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Kangli Zhu</author><author>Chengqi Zhu</author><author>Ying Zhen</author>
        <description><![CDATA[Insects across different orders have convergently evolved adaptations to toxic cardiac glycosides (CGs), which are derived either from their diet or via endogenous synthesis. Previous studies on CG-resistance focused on changes in ATPα that is the direct inhibition target of CGs. Adaptation of whole organisms to toxic CGs could involve orchestrated changes at multiple genes and at multiple biological levels. Here, we explore this possibility by using whole genome sequences to identify several signatures of molecular convergence across multiple CG-adapted species. We identify gene families that changed convergently in CG-adapted species, including one member of stable fatty acyl-CoA reductase, CG5065, carboxylesterases and gustatory receptors that expanded in two of the three species. We find a number of candidate genes under positive selection in all CG-adapted species. We also identify convergent amino acid substitutions that have independently evolved in CG-adapted insects, including a conserved gene involved in the septate junction, Gliotactin (Gli). We used CRISPR–Cas9 to generate viable, homozygous Gli knock-in Drosophila lines with the convergent substitution. Through egg-larva and larva-adult survival experiments, we found that mutant flies consistently exhibit a lower survival rate compared to wild-type lines. Transmission electron microscopy (TEM) analysis of stage 17 embryos showed that in Gli mutants, the dihedral angles of bicellular membranes near the tricellular junction (TCJ) were unequal, and electron-dense materials were absent in the TCJ center. We propose that this convergently evolved Gli variant may contribute to CG adaptation by modulating epithelial permeability, potentially facilitating the sequestration of toxic CGs.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1753780</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1753780</link>
        <title><![CDATA[Moonshine.jl: a Julia package for genome-scale model-based ancestral recombination graph inference]]></title>
        <pubdate>2026-04-13T00:00:00Z</pubdate>
        <category>Technology and Code</category>
        <author>Patrick Fournier</author><author>Fabrice Larribe</author>
        <description><![CDATA[The ancestral recombination graph (ARG) is the model of choice in statistical genetics to model population ancestries. Software capable of inferring ARGs on a genome scale within a reasonable amount of time are now widely available for most practical use cases. While the inverse problem of inferring ancestries from a sample of haplotypes has seen major progress in the last decade, it does not enjoy the same level of advancement as its counterpart. Up until recently, even moderately sized samples could only be handled using heuristics. In recent years, the possibility of model-based inference for datasets closer to ”real world” scenarios has become a reality, largely due to the development of threading-based algorithms. This article introduces Moonshine.jl, a Julia package that has the ability, among other things, to infer ARGs for samples of thousands of human haplotypes of sizes on the order of hundreds of megabases within a reasonable amount of time. On recent hardware, our package is able to infer an ARG for samples of densely haplotyped (over one marker/kilobase) human chromosomes of sizes up to 10,000 in well under a day on data simulated by msprime. Scaling up simulation on a compute cluster is straightforward since each ARG is inferred independently using a single thread. While model-based, it does not resort to threading but rather places restrictions on probability distributions typically used in simulation software in order to enforce sample consistency. In addition to being efficient, a strong emphasis is placed on ease of use and integration into the biostatistical software ecosystem.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1784283</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1784283</link>
        <title><![CDATA[Genetic distribution of selected obesity-related SNVs in the FTO, DRD2, MC4R, FABP2, ADRB2, and SH2B1 genes in a Mexico city population]]></title>
        <pubdate>2026-04-10T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Carlos Perezcano</author><author>Andrea Sánchez</author><author>Gerardo Cendejas</author><author>Francisco Borrayo</author><author>Mariana Pérez-Coria</author><author>Gerardo Pérez-Hernández</author>
        <description><![CDATA[IntroductionObesity represents a significant health challenge worldwide, with an increasing trend and high prevalence in Mexico. This metabolic disease, characterized by an increase in body mass index (BMI), leads to abnormal fat accumulation that contributes to several pathologies, and is determined by a complex interaction between diet, lifestyle and genetic factors, such as single nucleotide variants (SNVs) that may influence appetite regulation, adipose tissue function, energy metabolism, reward mechanisms, motivation, food intake behavior control, energy expenditure, fatty acid transport, lipid accumulation, lipolysis, insulin sensitivity, glucose metabolism, among other biochemical processes. However, the frequency of obesity-associated genetic variants remains poorly characterized in Mexican populations–which are highly admixed–as demonstrated by population genetic studies which have established the influence of this admixture in the prevalence and distribution of obesity-related SNVs.MethodsThis descriptive population genetic study aimed to characterize the genotype and allele frequency distributions of six SNVs previously associated with obesity and metabolic traits: FTO rs9939609, ANKK1/DRD2 rs1800497, MC4R rs17782313, FABP2 rs1799883, ADRB2 rs1042714, and SH2B1 rs4788102 through a cross-sectional design conducted in a cohort from Mexico City (N = 129).Results and DiscussionThe genotyping results revealed substantial variability in allelic frequencies across the analyzed variants, with SH2B1 rs4788102 showing the highest minor allele frequency (MAF) (0.41), followed by ANKK1/DRD2 rs1800497 (0.32) and FTO rs9939609 (0.31), whereas MC4R rs17782313 presented the lowest MAF (0.12). All SNVs were in HWE (p > 0.05). Understanding the prevalence of these obesity-related genetic markers in Mexican populations provides a reference for future genomic and nutrigenomic studies, and may support the development of personalized prevention strategies contributing to deeper insight into the molecular basis of metabolic diseases in Mexico, given the serious public health challenge they represent.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1795443</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1795443</link>
        <title><![CDATA[Raloxifene ameliorates cartilage and subchondral bone microstructural degeneration in the ovariectomy-induced spontaneous postmenopausal osteoarthritis]]></title>
        <pubdate>2026-03-30T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Ya-Ping Xiao</author><author>Mu-Wei Dai</author><author>Fa-Ming Tian</author><author>Li-Tao Shao</author><author>Ming-Jian Bei</author><author>Liu Zhang</author><author>Zhang-Hua Li</author>
        <description><![CDATA[The prevalence and incidence of osteoarthritis (OA) increase significantly in women after menopause, indicating an important role of estrogen in the pathogenesis of OA. This type of OA is termed postmenopausal OA. This study aimed to investigate the feasibility of using bilateral ovariectomy (OVX) in adult SD rats to simulate the human postmenopausal OA model and evaluate the effect of early raloxifene (RAL) intervention on this model. Twenty-four SD rats were randomly divided into 4 groups: Baseline group, Sham + V group, OVX + V group, and OVX + RAL group. Rats in the Baseline group were euthanized for sample collection at the start of the experiment. Rats in the OVX + V and OVX + RAL groups underwent bilateral OVX, while those in the Sham + V group received a sham operation without actual ovarian resection. After surgery, the OVX + RAL group was given RAL (6.2 mg/kg·day) by gavage, and the OVX + V and Sham + V groups received an equal volume of normal saline. Samples were collected 3 months after drug administration. Micro-CT was used to determine the bone histomorphometry of the right proximal tibia. Following Micro-CT analysis, the right knee joints of all animals were decalcified for 8–12 weeks, embedded in paraffin, and sectioned. The sections were subjected to toluidine blue staining and immunohistochemical staining for collagen-II, Caspase-3, and matrix metalloproteinase-13 (MMP-13). The toluidine blue-stained sections were scored using the OARSI histological scoring system, and the positive protein expression in immunohistochemical staining was evaluated using the IOD. The OARSI score revealed that the degree of cartilage degeneration in the OVX + V group was more severe than that in the Sham + V group and the OVX + RAL group. The expression of collagen-II in the OVX + V group was significantly lower than that in the Sham + V group and the OVX + RAL group, while the expressions of MMP-13 and Caspase-3 increased. Micro-CT revealed that the microstructure of subchondral bone in the OVX + V group deteriorated compared with the Sham + V group, while that in the OVX + RAL group improved compared with the OVX + V group. Compared with the Baseline group, the microstructure of subchondral bone and cartilage in the Sham + V group was somewhat degraded. We reached a conclusion that OVX-induced degeneration of subchondral bone and articular cartilage is relatively mild, suggesting that 6-month-old OVX rats are a mild model of postmenopausal OA. RAL can delay OVX-induced postmenopausal subchondral bone and cartilage degeneration. Notably, this study further clarifies the protective effect of RAL on the medial joint capsule and refines the regulatory mechanism of RAL on subchondral bone microstructure in mild postmenopausal OA, which supplements the existing research on RAL in OA intervention.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1766303</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1766303</link>
        <title><![CDATA[QTL mapping for young leaf color trait in eggplant (Solanum melongena L.) using BSA-seq]]></title>
        <pubdate>2026-02-20T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Fang Hu</author><author>Shaobin Zhang</author><author>Chengming Li</author><author>Fanchong Yuan</author><author>Zhao Song</author><author>Kailin Hu</author><author>Jiaowen Cheng</author>
        <description><![CDATA[Young leaf color is a crucial agronomic trait in eggplant (Solanum melongena L.) significantly influencing photosynthetic efficiency, stress resistance, fruit quality, and ornamental value. However, research focusing on this trait remains relatively scarce. In this study, an F2 (EP02×EP01) segregating population (n = 646) was developed from a cross between the purple young-leaved line EP02 and green young-leaved line EP01. Phenotypic characterization of the F2 population revealed that the segregation ratio of green, purple-green, and purple phenotypes conformed to the expected 1:2:1 Mendelian ratio (χ2 = 3.40, P > 0.05), indicating that the young leaf color trait in eggplant is controlled by a single incompletely dominant gene. To identify candidate loci associated with young leaf color, 30 individuals with extreme purple phenotypes and 30 individuals with extreme green phenotypes were selected from the F2 population to establish two DNA bulks, namely, the purple trait bulk (ZS-pool) and the green trait bulk (LS-pool), respectively. Bulked Segregant Analysis (BSA) combined with whole-genome resequencing was performed on the two parental lines (EP02 and EP01) and the two bulks (ZS-pool and LS-pool). A total of 1,416,609 high-quality single nucleotide polymorphisms (SNPs) were generated and used for quantitative trait locus (QTL) mapping. Using the SNP-index method and Euclidean Distance (ED) analysis, a single QTL associated with young leaf color was identified on chromosome 10, covering a physical interval of 17.49 Mb (59,315,357-76,806,837 bp). Integrated analysis of SNP indices, ED values, and gene functional annotations suggested that Smechr1002213, Smechr1001752, and Smechr1001815 might be the candidate gene regulating young leaf color formation in eggplant. The findings of this study will lay a foundation for gene isolation and the elucidation of the genetic mechanisms underlying young leaf coloration in eggplant.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1753621</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1753621</link>
        <title><![CDATA[Chromosome-level reference genome of Tylorrhynchus heterochaetus (Annelida, Nereididae)]]></title>
        <pubdate>2026-01-28T00:00:00Z</pubdate>
        <category>Data Report</category>
        <author>Wei Yang</author><author>Xuemin Zhang</author><author>Bin Fan</author><author>Yuanyuan Si</author><author>Ruiwen Xu</author><author>Shengkang Li</author><author>Zining Meng</author><author>Xinghan Chen</author>
        <description><![CDATA[The Tylorrhynchus heterochaetus, a polychaete benthic invertebrate belonging to the Nereididae family, has emerged as a promising aquaculture species. It is highly regarded for its nutritional profile, with protein accounting for up to 60% of its dry weight, as well as its balanced amino acid composition. This has earned it the nickname “aquatic cordyceps”. However, wild populations of this species have declined significantly due to environmental shifts and human activities, with local extinctions reported in certain regions. A critical barrier to advancing its population genetics and conservation biology has been the absence of a chromosomal-level reference genome for T. heterochaetus. To address this gap, we present the first chromosome-level genome assembly of T. heterochaetus, generated using PacBio HiFi sequencing data and Hi-C technology. The final assembly spans 782.25 Mb with a scaffold N50 of 75.39 Mb, successfully anchored to 11 pseudo-chromosomes. Repetitive sequences account for 428.09 Mb (54.73%) of the genome, and 20,145 protein-coding genes were annotated. This study provides foundational insights into the genetics, genomics, and evolutionary history of T. heterochaetus, laying a critical groundwork for future research and enabling the development of targeted genetic conservation strategies.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1721789</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1721789</link>
        <title><![CDATA[Snail 3G: genomics, genetics, and gene-editing of Biomphalaria glabrata]]></title>
        <pubdate>2026-01-21T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Si-Ming Zhang</author>
        <description><![CDATA[This review highlights recent advances and ongoing challenges in the genomics, genetics, and gene-editing (3G) of the freshwater snail Biomphalaria glabrata, based on insights gained from a novel model system we initiated two decades ago. B. glabrata is an intermediate host of the human blood fluke Schistosoma mansoni and serves as the principal model organism for schistosomiasis research. We developed two homozygous lines of B. glabrata, the iM line and iBS90, through 81 and 41 generations of selfing the commonly used M line and BS90, respectively. These lines display contrasting infection phenotypes: susceptibility or resistance to S. mansoni. High-quality scaffold-based genome assemblies were generated for both lines, followed by a chromosome-level assembly of the iM line genome. An F2 segregating population derived from these lines enabled the identification of three loci, two linked to resistance or susceptibility and one associated with pigmentation, using a double digest restriction-site associated DNA sequencing (ddRADseq) approach. Recombinant inbred lines (RILs) were developed through two crosses and ten generations of selfing. Genetic mapping with RILs refined the resistance locus on chromosome 5 from 8 to 3 Mb through individual-based whole-genome sequencing. Ongoing work includes comparative transcriptome analyses of the two homozygous lines and RILs in response to schistosome infection, along with fine-scale mapping of advanced intercross lines to elucidate the molecular basis of the snail’s anti-schistosome defenses. Over the past 10 years, we have made extensive efforts to achieve germline delivery and generate genetically modified snails. Although pantropic lentiviral and yolk protein–mediated germline delivery methods were unsuccessful, these pioneering experiments provide valuable insights for future research. Finally, we successfully generated germline-edited B. glabrata, the first genetically modified schistosomiasis vector snail, by microinjecting CRISPR/Cas9 and guide RNA (gRNA) targeting the fibrinogen-related protein 3.1 (FREP3.1) gene into decapsulated embryos, followed by ex ovo culture. This breakthrough establishes a foundation for innovative genetic strategies to control this neglected tropical disease.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1695593</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1695593</link>
        <title><![CDATA[Identification of major QTLs for seed vigor and growth-related traits using a biparental population in soybean]]></title>
        <pubdate>2026-01-14T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Neeraj Kumar</author><author>James R. Smith</author><author>Jeffery D. Ray</author><author>Jason D. Gillman</author><author>Nacer Bellaloui</author>
        <description><![CDATA[Soybean [Glycine max (L.) Merr.] is one of the most widely cultivated crops globally and serves as a primary source of plant-based protein and oil for human consumption. Seed vigor is a critical trait for germination and rapid seedling establishment, especially under sub-optimal environmental conditions. Genetic control of seed vigor measured as accelerated aging (AA%) was investigated using a quantitative trait locus (QTL) mapping approach. Associations of AA with six other traits: pubescence color (PC), beginning bloom (R1), reproductive period (RP), maturity (R8), plant height (PH), and stem termination (ST) were examined. A recombinant inbred line (RIL) population (247 F6-derived RILs) from a cross between DS25-1 and DT97-4290 was developed and genotyped using genotyping-by-sequencing (GBS), which yielded a set of 8,445 curated single-nucleotide polymorphism (SNP) markers from ∼90,000 SNPs. A subset of 201 RILs was phenotyped in Stoneville, Mississippi, over 3 years (2017–2019). A molecular linkage map was constructed using the SNP marker dataset, and composite interval mapping was performed using the R/qtl package. In total, 33 QTLs associated with seven phenotypic traits were identified across 12 chromosomes, using means of individual environments and best linear unbiased prediction (BLUP). Phenotypic variation of individual QTLs ranged from 0.56% to 89.77%, and the additive effects varied from −10.52% to 15.12%. Twelve QTLs detected across multiple environments on Gm03, Gm06, Gm07, and Gm19 were classified as stable. Notably, four genomic regions demonstrated QTL co-localization: Gm06 (all traits except ST), Gm07 (AA, R1, RP, and R8), Gm03 (AA and R1), and Gm19 (PH, R8, and ST). Major QTLs were in proximity to previously known genes: the T locus for pubescence color (Gm06), E1 (Gm06) and E11 (Gm07) loci for flowering and maturity, and Dt1 (Gm19) for stem termination. The closest SNPs associated with stable QTLs can be used to develop KASP markers for marker-assisted selection programs.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1727583</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1727583</link>
        <title><![CDATA[Integrative linkage and recombination analysis of 25 X-STRs across 7 linkage groups using pedigree-based and SNP-based strategies]]></title>
        <pubdate>2025-12-18T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Jinglei Qian</author><author>Xiaoqin Qian</author><author>Qiqi Ji</author><author>Zhimin Li</author><author>Chengchen Shao</author><author>Hongmei Xu</author><author>Fan Yang</author><author>Jianhui Xie</author>
        <description><![CDATA[IntroductionX-chromosomal short tandem repeats (X-STRs) are valuable genetic markers in forensic science for resolving complex kinship scenarios. However, the linkage relationship and recombination of X-STRs remain poorly characterized.MethodsBased on high-density SNP data with relatively low mutation rates, we developed a pedigree-based method to analyze the recombination relationships between these X-STR linkage groups (LGs). We used X-STRs data from 66 two-generation families and X-SNPs data from 602 X-chromosomal SNP trios from the 1000 Genomes Project. We investigated the linkage relationships among 25 X-STR loci, grouped into seven LGs, including three identified regions (Xp21.1, Xq21.31, Xq23) and four Argus X-12 (Xp22.2, Xq12, Xq26, Xq28), provided broader coverage linkage groups of X-STR.ResultsWe found strong intra-group linkage (Maximum logarithm of odds (MLOD) > 5) and near independence between groups (MLOD <1). Estimated recombination rates of X-STR data ranged from 0.0000 to 0.0487 within LGs, and from 0.1561 to 0.4133 between LGs, while the recombination fraction between the 7 linkage groups occurred in approximately 50% of informative meioses. LD decay analysis showed that R2 dropped to 0.1 at a distance of approximately 3.7 kb, supporting the feasibility of using SNP-derived LD signals to infer STR recombination patterns at fine scale.DiscussionThe family-based methods with X-SNP provide a more robust framework for evaluating X-STR linkage with the advantage of a relatively low mutation rate, high density and phased, particularly for newly developed loci lacking extensive haplotype databases.ConclusionThese findings contribute to a more precise understanding of X-STR inheritance and enhance their reliability in forensic kinship analysis.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1605675</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1605675</link>
        <title><![CDATA[Structural heterogeneity and functional convergence of transposable elements]]></title>
        <pubdate>2025-12-16T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Gleb Yu. Kosovsky</author><author>Galina V. Glazko</author><author>Tatiana T. Glazko</author>
        <description><![CDATA[Almost half the mammalian genomes consist of transposable elements (TEs) and their derivatives. The distribution density of TEs can be associated with genomic regions of chromosomal rearrangements in different mammalian species and with the genomic localization of protein-coding genes that differ in length and function. To evaluate these characteristics at the local genomic level, an analysis of the distribution of various TEs (retrotransposons and DNA transposons) was performed in three mammalian species (human, cattle, and domestic rabbit) in genes with different functions and chromosomal localizations and their flanking regions. In humans and rabbits, melanophilin (MLPH) and myostatin (MSTN) are syntenic, but not in cattle. In the latter, MLPH and the leptin receptor (LEPR) are syntenic, but not in humans and rabbits. The alpha-thalassemia gene is always located on chromosome X. The results indicate that the frequencies of different TEs are species-specific and do not depend on the length of genes, their function, or chromosomal localization. There were also species-specific differences in the ratio of “ancient” and “young” short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs). There was a statistically significant positive correlation between ancient SINE + LINE and LTR-ERV (p < 0.01) and a significant negative correlation between young SINE + LINE and DNA transposons (p < 0.05). Competitive relationships between TEs are probably defined by the presence of identical regulatory motifs in different TEs, associated with the reliance of TE amplification on the host’s own regulatory systems.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1730668</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1730668</link>
        <title><![CDATA[Genomic analysis reveals genetic diversity and selection signatures of the Yantai Black pig during domestication and breeding]]></title>
        <pubdate>2025-11-25T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Ming Qin</author><author>Cai Ma</author><author>Mingzhi Liang</author><author>Yuxin Zhang</author><author>Zengguang Wang</author><author>Jingyu Wang</author><author>Guodong Li</author><author>Yufen Sha</author><author>Peng Jin</author><author>Lingling Ju</author><author>Xueping Liu</author><author>Yongqing Zeng</author><author>Ruili Li</author>
        <description><![CDATA[ObjectiveYantai Black pig (YT), as a native population of the eastern China’s Jiaodong Peninsula of Shandong province, characterized by coarse feeding tolerance, strong disease resistance, early sexual maturity, high litter size, and superior meat quality. However, the genetic characteristics and variations underlying its crucial economic traits remain poorly understood.MethodsIn this study, we resequenced the whole genome of 17 YT individuals from distinctly different lineages breeding in three conservation farms to detect single nucleotide polymorphism (SNP) density, pairwise fixation index (FST), nucleotide diversity (π), runs of homozygosity (ROHs).ResultsOur findings revealed that YT has higher genomic diversity compared to Chinese partial indigenous pig populations and Western commercial pig populations, but lower diversity than Asian wild boars (AWB). Based on FST and values (top 1%), we identified 321 selected regions, encompassing 156 genes, between YT and AWB. Functional annotation analysis suggested that these genes are potentially responsible for growth, reproduction, and immune responses. The RBFOX3 and WDR27 genes were confirmed to be strong positively selected in YT’s breeding. Combining the results of selection sweeps and ROH islands of YT, three overlapping regions were detected. Furthermore, we found that the quantitative trait loci (QTLs) with the most overlapping regions were related to teat number, body weight, and mean corpuscular hemoglobin concentration.ConclusionWe characterized the genomic features and population structure and identified selection signals in genomic regions linked to important germplasm characteristics of YT. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of YT and its valuable genetic resources.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1699402</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1699402</link>
        <title><![CDATA[Ecuador genetic mosaic: biological and adaptive variations across Mestizos, Native Amerindians, and Afro-Ecuadorians. Implications for public health and precision medicine]]></title>
        <pubdate>2025-11-24T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Fabricio González-Andrade</author>
        <description><![CDATA[IntroductionUnderstanding human biological diversity is fundamental to improving health and addressing inequities, yet most genomic and biomedical studies remain focused on European and Asian populations. Latin American groups—particularly mestizos, Native Amerindians, and Afro-descendants—are underrepresented, limiting the applicability of global findings. Ecuador, with its tri-hybrid ancestry shaped by Amerindian, European, and African lineages, provides a valuable model to explore how genetic, environmental, and sociocultural factors jointly influence adaptation and disease.ObjectiveTo synthesize and critically evaluate evidence on biological and adaptive variation among Ecuadorian populations, emphasizing methodological transparency, representational equity, and implications for public health and precision medicine.MethodsA narrative review of studies published between 2007 and 2024 was conducted using PubMed, Scopus, and Google Scholar. Eligible works reported empirical data on genetics, immunogenetics, pharmacogenomics, adaptive physiology, or epidemiology among Mestizos, Native Amerindians, and Afro-Ecuadorians.ResultsEvidence supports a tri-hybrid ancestry structure: mestizos show predominantly Amerindian autosomal ancestry with European paternal input; Afro-Ecuadorians retain African heritage with notable Amerindian admixture; and Native Amerindians preserve distinctive lineages and HLA profiles. Well-documented adaptations include altitude tolerance in Andean groups, persistence of the sickle cell trait in Afro-Ecuadorians, and variation in vitamin D status and lactase persistence. Pharmacogenomic differences in CYP2D6, DPYD, and TPMT demonstrate clinical relevance but remain based on small, localized samples.ConclusionEcuadorian populations illustrate how genetic diversity intersects with environment and inequity. Strengthening representativeness, ethical engagement, and translation of genomic evidence into policy are essential to advance equitable precision medicine in Latin America.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1712106</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1712106</link>
        <title><![CDATA[Genetic evolution of parental populations and construction of core germplasm populations in qinghai spruce seed orchard based on SLAF-seq technology]]></title>
        <pubdate>2025-11-17T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Hu Zhao</author><author>Erwen Xu</author><author>Dong Lv</author><author>Wei Li</author><author>Xingpeng Zhao</author><author>Xin Jia</author><author>Hao Yuan</author><author>Rong Zhou</author>
        <description><![CDATA[In order to explore the genetic background and genetic basis of the parental population of Qinghai spruce (Picea crassifolia Kom.) seed orchard, to reduce the cycle of genetic improvement of Qinghai spruce and the scale of germplasm resources, and to enhance the level of genetic improvement of Qinghai spruce. This study utilized the SLAF-seq technology to conduct genetic and evolutionary analysis on 165 germplasms from 11 provenances of Qinghai spruce seed orchards, and developed a total of 1964178 high-consistency single nucleotide polymorphism markers. Phylogenetic analysis classified them into three major groups, while population structure analysis revealed two subgroups. Through the Core Hunter II software, 33 (20%) core germplasms were selected, retaining all genetic diversity. This research provides a scientific basis for the genetic improvement of Qinghai spruce.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1661527</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1661527</link>
        <title><![CDATA[Clarifying species boundaries between bocachico (Prochilodus magdalenae) and bocachico de Maracaibo (Prochilodus reticulatus) (characiformes: Prochilodontidae) using complete mitochondrial genomes]]></title>
        <pubdate>2025-11-06T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Jonny Yepes-Blandón</author><author>Diego Almansa-Villa</author><author>María José Benítez-Galeano</author><author>Daiana Mir</author><author>Jim Hernández-Rangel</author><author>Víctor Atencio-García</author><author>Ana Estrada-Posada</author><author>Nélida Rodríguez-Osorio</author>
        <description><![CDATA[The accurate phylogenetic distinction between Prochilodus magdalenae and Prochilodus reticulatus (Characiformes: Prochilodontidae) has been hindered by overlapping morphology and limited sequence data. Previous studies, relying on partial mitochondrial markers, have even suggested that Prochilodus magdalenae and Prochilodus reticulatus might be a single species. This study presents three annotated complete mitochondrial genomes for P. reticulatus and phylogenetic analyses that contribute to resolving uncertainty around these species’ boundaries. Our phylogenetic reconstructions, using both mitochondrial markers and complete mitogenomes, consistently support the segregation of P. magdalenae and P. reticulatus into distinct clades. Bayesian time-calibrated analysis estimates their divergence at approximately 6.9 mya (10.2–4.2 mya), coinciding with the Andean Eastern Cordillera’s final uplift. This study provides essential data for future taxonomic and conservation efforts. Our findings clarify the phylogenetic relationship between these species, emphasizing the utility of complete mitogenomes and demonstrating that sequence mislabeling, probably caused by the difficulty of accurately identifying these species based on morphological characteristics, has contributed to inconsistencies in previous phylogenetic studies within the genus Prochilodus.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1610942</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1610942</link>
        <title><![CDATA[Slavs in the closet: computational genomic analysis reveals cryptic slavic signatures in the Avar Khaganate and their contribution to medieval Croatian population formation]]></title>
        <pubdate>2025-09-22T00:00:00Z</pubdate>
        <category>Hypothesis and Theory</category>
        <author>Todor Chobanov</author><author>Svetoslav Stamov</author><author>for Bulgarian Academy of Science and Institute for Balkan Studies </author>
        <description><![CDATA[Our study applies a systematic computational genomic approach to investigate the complex population dynamics of Southern Slavs in the Hungarian Plain and Avar Khaganate, and their subsequent role in forming the medieval Croatian population. Using a quality-controlled dataset of 1,800 ancient DNA samples, we implemented a comprehensive analytical framework centered on systematic screening of marginal Principal Components to detect cryptic Slavic genetic signatures. This strategic methodological approach addresses the well-documented analytical challenge that Germanic and Slavic populations remain indistinguishable using conventional PC1-2 analysis due to shared Baltic Bronze Age ancestry. Through systematic evaluation of all principal components (PC1-20), we identified PC9 as a reliable indicator of Slavic ancestry within European ancient DNA samples when combined with PC4 and PC3. This approach revealed substantial Baltic genetic components in early Slavic populations (57% in Slovakia/Slovenia) decreasing to 39%–51% in medieval Croatian samples. Statistical modeling demonstrates that contemporary Croatian populations formed through three distinct migration waves, with 50%–60% total Slavic ancestry and 20%–25% pre-Slavic Balkan continuity. Significantly, we identified individuals with Slavic genetic profiles in prestigious Avar burial contexts, questioning established understanding of social hierarchies within the Khaganate. The genomic evidence indicates that key aspects of South Slavic genetic structure emerged through interactions within the Carpathian Basin rather than after Balkan arrival. Our findings demonstrate that Croatian ethnogenesis involved gradual integration rather than population replacement, with the Avar Khaganate serving as a crucial demographic interface where South Slavic genetic structure emerged. Our approach addresses longstanding historical questions regarding Croatian ethnogenesis by identifying specific genetic signatures and quantifying their population-level contributions, demonstrating how application of computational genomics provides unprecedented resolution in studying complex population transformations when traditional historical and archaeological approaches reach interpretive limits.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1631529</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1631529</link>
        <title><![CDATA[Rapid forensic ancestry inference in selected Northeast Asian populations: a Y-STR based attention-based ensemble framework for initial investigation guidance]]></title>
        <pubdate>2025-09-17T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Kyo-Chan Koo</author>
        <description><![CDATA[IntroductionRapid inference of ancestral origin fromDNA evidence is critical in time-sensitive forensic investigations, particularly during the initial hours when crucial investigative decisions must be made. Although comprehensive analyses using multiple genetic markers provide thorough results, they often require significant processing time and resources. Y-chromosome short tandem repeats (Y-STRs) exhibit population-specific allelic distributions that facilitate rapid analysis, making them particularly valuable for initial screening in forensic contexts.MethodsThis study aims to enhance population classification accuracy using Y-STR profile analysis, with a particular focus on Northeast Asian populations that are often merged into a single group by commercial ancestry panels. We developed a machine learning architecture centered on an attention-based ensemble mechanism that incorporates three complementary algorithms: a One-vs-Rest Random Forest, XGBoost, and Logistic Regression, each configured to effectively manage imbalanced datasets.ResultsUtilizing only Y-STR data, the model achieved an overall accuracy of 80%-81% and demonstrated high stability. Notably, the model effectively processes imbalanced datasets, generating reliable outcomes for rapid ancestry assessment in time-critical investigations.DiscussionBy addressing a key limitation in commercial ancestry panels--their failure to differentiate among Northeast Asian subpopulations--this framework provides valuable preliminary guidance in forensic cases involving Asian individuals. Consequently, our approach enhances rapid screening capabilities, which can inform early-stage investigations while complementing subsequent, more comprehensive genetic analyses.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1610364</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1610364</link>
        <title><![CDATA[Dopamine D2 receptor gene Taq 1A polymorphism: genetic architecture in Indian population and comparison to global populations]]></title>
        <pubdate>2025-07-14T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Amrita Chaudhary</author><author>Pradeep Kumar</author><author>Bechan Sharma</author><author>Vandana Rai</author>
        <description><![CDATA[ObjectiveThe Dopamine receptor D2 (DRD2) gene has been investigated as a candidate gene in several psychiatric and neurological disorders involving dopaminergic systems. Multiple polymorphisms have been reported in the DRD2 gene, where the DRD2 Taq1A is most widely studied and is reported to contribute to the development of several diseases/disorders. The objective was to study the DRD2 Taq1A polymorphism in the Indian population and compare it with the reported global frequency.MethodsThe DRD2 Taq1A polymorphism was genotyped using PCR-RFLP from 400 unrelated human blood samples. In addition, a literature search on the DRD2 Taq1A polymorphism has also been conducted from 1990 to 2025. All the data obtained was grouped according to the continent as a unit to get the distribution information of the DRD2 Taq1A genotypes and alleles in healthy populations of all six continents. This was accomplished for the comparison of frequency obtained in this study with the overall geographical distribution of the DRD2 Taq1A allele reported from other parts of the world.ResultsIn the total 400 samples analyzed, the TT genotype and T allele frequencies were 15% and 43%, respectively. Data from 136 studies from different continents were extracted and compared with the present study. The highest T allele frequency was observed in the Asia (0.35), followed by South America (0.33) and the lowest frequencies occur in Europe and Australia (0.19). Pattern of frequencies represented by the Indians is consistent to Asia and close to South America. The result show a high frequency of CT genotype and T allele in the study population, closely resembling the patterns observed in Mexicans. This study highlights the genetic diversity within Indian subpopulations and underscores the need for cautious interpretation of population genetic data.ConclusionThe present study observed a T allele frequency of 43%, comparable with the Asian population. In the comparison study, the T allele frequency in Global, Asian, Indian, and present studies was calculated as 26%, 35%, 33%, and 43%, respectively. This geographical gradient is clinically important in determination of the risk assessment which might be included in prevention strategies for psychiatric disorders.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1614541</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1614541</link>
        <title><![CDATA[Genome-wide identification of LHT gene family in Lonicera macranthoides Hand.-Mazz and their responses to abiotic stresses]]></title>
        <pubdate>2025-07-01T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Zhaowu Li</author><author>Yue Hu</author><author>Chunzhi Liang</author><author>Lu Chen</author><author>Yao Hu</author><author>Xiaoqiu Wu</author><author>Xia Chen</author>
        <description><![CDATA[Amino acid transporters (AATs) allow the transport of amino acids and play important roles in the various physiological processes and environmental responses of plants. The lysine and histidine transporter (LHT) subfamily is an important type of AAT. However, a genome-wide overview of the LHT gene family has not been conducted in L. macranthoides Hand.-mazz. In this study, 11 LHT genes were identified in the Lonicera macranthoides genome. To further understand the functions of LmLHT genes, the gene and protein characteristics, transmembrane helices, evolutionary relationships, chromosomal distribution, cis-acting elements of promoters, and expression patterns were systematically analyzed. According to the results, LmLHT genes were divided into two groups based on the phylogenetic analysis. Transmembrane helices of LmLHT proteins ranged from seven to 16. Gene structure and conserved motif analysis revealed that exon-intron structures and motifs were relatively conserved in the LmLHT family. LmLHT genes were distributed on six of the nine chromosomes and had the most collinear gene pairs with NtLHT genes. Additionally, phytohormones, low-temperature, drought-inducibility, defense and stress related cis-acting elements were enriched in the promoters of LmLHT genes. LmLHT genes showed distinct or preferential expression patterns in various tissues, signifying their potential roles in plant growth and development. We also found that some LmLHT genes were responsive to cold and drought stresses, indicating their roles in abiotic stress adaptation. Overall, our results provided comprehensive insight into the LmLHT gene family and will be useful for future functional analyses.]]></description>
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