Polymorphic Loci Research Articles

Assessment of conservation status of Ferula huber‐morathii: association with population genetic structure and regional climate

Ferula huber‐morathii is an endemic and medicinally important plant. This species is distributed in eight Turkish localities, including three newly identified ones. Its extent of occurrence and area of occupancy is determined to be 3963 km2 and 32 km2 respectively. All localities are characterized by East Mediterranean and sub‐Mediterranean precipitation regimes; however, temperatures increase excessively and precipitation decreases during the flowering period of the species. The population sizes are quite small, and the number of reproducing individuals in some populations is below ten. Analyses of ISSR markers showed the percentage of polymorphic loci to be 94% at the species level and 56% at the population level. The level of genetic differentiation (measured by GST) was 0.37 and the estimated level of gene flow among populations (NM) was 0.84. The percentage of variance occurring within and among populations, determined by AMOVA, was 75% and 25%, respectively. STRUCTURE analysis revealed two genetic clusters of individuals with a geographic structure, similar to that found in UPGMA and an ordination analysis. Some populations turned out to have both low numbers of individuals and low genetic diversity. Since many of the populations are subject to anthropogenic disturbance, the species should remain in the EN category. At the same time, it is suggested that a new in‐situ conservation area should be created around nearby dams, situated in the same climate area as the currently known populations.

Genetic Diversity and Forensic Utility of X-STR Loci in Punjabi and Kashmiri Populations: Insights into Population Structure and Ancestry

Background: X-chromosomal short tandem repeats (X-STRs) are crucial in forensic applications, particularly in complex kinship cases, and play an important role in population genetics. However, there is limited data on X-STR variation in Pakistani populations, especially among ethnic groups like Kashmiri and Punjabi. Methodology: This study investigates the forensic and genetic properties of 12 X-STRs from the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 125 families (75 Kashmiri, 50 Punjabi) from Azad Jammu and Kashmir and Punjab, Pakistan. Results: In both populations, a total of 222 alleles were identified across the 12 X-STR loci (Punjabi 171 alleles, Kashmiri 161 alleles), with allele frequencies ranging from 0.0056 to 0.3033. DXS10148 was the most polymorphic locus with 28 alleles, while DXS7132 was the least polymorphic with 9 alleles. Most loci were in linkage equilibrium, except for the DXS10135/DXS10148 pair in males, with no loci exhibiting significant linkage disequilibrium in females. The combined power of discrimination was 0.999 999 9977 for Kashmiri males, 0.999 999 999 999 9746 for Kashmiri females, and 0.999 999 999 999 9781 for Punjabi females. In Kashmiri males, 34, 31, 28, and 32 haplotypes were observed across the four linkage groups (LG1, LG2, LG3, and LG4), though these groups did not form stable haplotypes, as indicated by Linkage Equilibrium within and significant Linkage Disequilibrium between groups. Conclusions: Genetic structure analysis using Principal Component Analysis and STRUCTURE revealed distinct clustering patterns for the Kashmiri and Punjabi populations, indicating unique genetic backgrounds and ancestry influences, particularly distinguishing them from East Asian populations. This study provides a comprehensive analysis of X-STR variation in Punjabi and Kashmiri populations, offering valuable insights for forensic and population genetic studies.

Population genetics of the freshwater red alga Batrachospermum gelatinosum (Rhodophyta) I: Frequent intragametophytic selfing in a monoicous, haploid-diploid species.

Life cycles with a prolonged haploid phase are thought to be correlated with greater rates of selfing and asexual reproduction. In red algae, recent population genetic studies have aimed to test this prediction but have mostly focused on marine species with separate sexes. We characterized the reproductive system of the obligately monoicous (i.e., hermaphroditic) freshwater red alga Batrachospermum gelatinosum and predicted that we would find genetic signatures of uniparental reproduction because of its haploid-diploid life cycle. We sampled 18 sites and genotyped 311 gametophytes with 10 polymorphic microsatellite loci to describe the reproductive system. Genotypic richness was low (<0.5) and pareto β values (describing clonal membership) were <0.7 for most sites. In taxa with separate sexes, these patterns are typically indicative of asexual reproduction. However, the genetic consequences of selfing in monoicous gametophytes are indistinguishable from those caused by asexual processes. Since we sampled gametophytes and have not yet genotyped the chantransia (i.e., the diploid phase), we interpretedlow diversity as a signature of intragametophytic selfing. Additionally, to understand the factors that drive selfing, we tested latitude and several other environmental variables, but none was significantly correlated with the genetic variation we observed. Nevertheless, future studies should genotype the chantransia to measure observed heterozygosity among other summary statistics to disentangle the effects of selfing versus asexual reproduction. Together, these data, coupled with further characterization of abiotic factors that influence population genetic patterns, will allow us to test potential drivers of reproductive system evolution.

Development and Application of Microsatellite Markers for Genetic Diversity Assessment and Construction of a Core Collection of Myrciaria dubia (Kunth) McVaugh Germplasm from the Peruvian Amazon

The Amazonian shrub Myrciaria dubia (camu-camu) produces vitamin C-rich fruits of growing commercial interest. However, sustainable utilization requires assessment and protection of the genetic diversity of the available germplasm. This study aimed to develop and apply microsatellite markers to assess genetic diversity and construct a core collection of M. dubia germplasm from the Peruvian Amazon. Sixteen polymorphic microsatellite loci were developed using an enrichment approach. The evaluation of 336 genotypes from 43 accessions of the germplasm bank, originating from eight river basins, was conducted using these newly developed markers. Genetic diversity parameters, including observed and expected heterozygosity, were calculated. Analysis of molecular variance (AMOVA) was performed to assess the distribution of genetic variation within and among accessions and river basins. Bayesian clustering analysis was employed to infer population structure. A core collection was constructed to maximize allelic richness. High genetic diversity was observed, with heterozygosity values ranging from 0.468 to 0.644 (observed) and 0.684 to 0.817 (expected) at the river basin level. AMOVA indicated significant genetic variation within (73–86%) compared to among (14–27%) accessions and river basins. Bayesian clustering detected ten genetic clusters, with several degrees of admixture among river basins, except for the genetically homogeneous Putumayo River basin. A core collection comprising 84 plant genotypes (25% of the full collection) was established, representing 90.82% of the overall allelic diversity. These results have important implications for M. dubia conservation strategies and breeding programs, in demonstrating a need for genetic connectivity between populations but preserving unique genetic resources in isolated basins. These results validate the expected levels of diversity and population subdivision in a crop and stress the need to secure genetically diverse germplasms, underscoring the importance of thorough genetic characterization for ex situ germplasm management.

Black flies (Diptera: Simuliidae) in the Galapagos Islands: Native or adventive?

Invasive species are a threat to ecosystems worldwide, but determining if a species is adventive or native is not always straightforward. The black flies that inhabit the Galapagos Islands, long known as Simulium ochraceum, are blood-feeding pests of humans and livestock. They first came to the attention of residents in 1989, suggesting a recent arrival. Earlier colonization, however, has been suggested, based largely on polymorphic genetic loci. To address questions of origin, provenance, and length of residency, we conducted a macrogenomic analysis of the polytene chromosomes of the S. ochraceum complex from seven sites in the Galapagos Islands and 30 sites in mainland Ecuador, Central America, and the Caribbean. Among 500 analyzed larvae, we discovered 88 chromosomal rearrangements representing 13 cytoforms, at least seven of which are probably full species. All evidence points to a single, cohesive cytoform with full species status in the Galapagos, conspecific with mainland populations, and widely distributed in the Neotropical Region. It has an identical, nearly monomorphic banding sequence with 10 novel fixed inversions and a subtle but unique Y-linked chromosomal rearrangement across all populations sampled in the Galapagos, the mainland, and the Caribbean. We recalled the name Simulium antillarum from synonymy with S. ochraceum and applied it to the Galapagos black flies, and we established that wolcotti is a junior synonym of antillarum. The time(s) and mode(s) of arrival of S. antillarum in the Galapagos remain uncertain, although the wide geographic distribution, including islands in the Caribbean, suggests that the species is an adept colonizer. Regardless of how long it has been in the archipelago, S. antillarum might have assumed a functional role in the streams of San Cristobal, but otherwise has had a detrimental effect on humans and livestock and potentially on the unique birds and mammals of the Galapagos Islands.

Genomic Analysis of the Giant Red Shrimp (Aristaeomorpha foliacea) Using Next-Generation Sequencing: Set of Tools for Population Studies

Background/Objectives: The giant red shrimp, Aristaeomorpha foliacea, is a valuable marine fishing resource. The conservation of species, especially exploited ones, depends on a good knowledge of their biology, as well as the development of appropriate management plans based on the identification of genetically differentiated units or genetic stocks. Microsatellites are widely used molecular markers to detect genetic stocks in penaeoid shrimps and prawns. This study aimed to develop and characterize new microsatellites for A. foliacea. Methods: Next-generation sequencing based on 454 pyrosequencing revealed 58 candidate microsatellite loci for A. foliacea. These were tested on a panel of 8 individuals representative of its worldwide geographical distribution, and 19 polymorphic loci were identified and subsequently validated and characterized in 30 individuals from a single population in the Mediterranean Sea. Results: As a result, 10 polymorphic loci were identified, which did not present linkage disequilibrium and showed a range of alleles per locus and an observed and expected heterozygosity of 2–10, 0.0667–0.5567, and 0.0661–0.8511, respectively. Nine out of these loci were under Hardy–Weinberg equilibrium and showed a combined exclusion probability of 0.9202 and 0.9968 in parentage and identity analysis, respectively. Conclusions: This large set of loci will provide a strong set of tools to (i) perform parentage studies and (ii) examine connectivity patterns (horizontal and vertical), including examining the population structure of this species at a variety of geographical scales and, particularly, between exploited populations in shallow waters and deeper unexploited populations.

Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism of Pinus sylvestris L. Populations in the Urals

Background: Scots Pine is one of the main forest-forming species in boreal forests; it has great economic and ecological significance. This study aimed to develop and test primers for detecting nucleotide polymorphisms in genes that are promising for detecting adaptive genetic variability in populations of Pinus sylvestris in the Urals and adjacent territories. Objectives: The objects of the study were 13 populations of Scots Pine located in the Perm Territory, Chelyabinsk Region, and the Republic of Bashkortostan. Results: Sixteen pairs of primers to loci of potentially adaptively significant genes were developed, from which three pairs of primers were selected to detect the nucleotide diversity of the studied populations. The indicator of total haplotype diversity determined in the three studied loci varied from 0.620 (Pinus-12 locus) to 0.737 (Pinus-11 locus) and, on average, amounted to 0.662. The nucleotide diversity indicators in P. sylvestris in the study region were, on average, low (π = 0.004, θW = 0.013). Their highest values were found at the Pinus-12 locus (π = 0.005; θW = 0.032), and the lowest were found at the Pinus-15 locus (π = 0.003; θW = 0.002). This indicates that Pinus-15 is the most conserved of the three studied loci. In the three studied P. sylvestris loci associated with adaptation to environmental factors, 97 polymorphic positions were identified. The 13 populations of P. sylvestris are characterized by an average level of genetic diversity (Hd = 0.662; π = 0.004; θ = 0.013). Conclusions: The polymorphic loci of adaptively significant genes of P. sylvestris can help identify the adaptive potential of pine forests in conditions of increasing ambient temperatures.

Genetic and functional diversity of allorecognition receptors in the urochordate, Botryllus schlosseri.

Allorecognition in Botryllus schlosseri is controlled by a highly polymorphic locus (the fuhc ), and functionally similar to missing-self recognition utilized by Natural Killer cells-compatibility is determined by sharing a self-allele, and integration of activating and inhibitory signals determines outcome. We had found these signals were generated by two fuhc -encoded receptors, called fester and uncle fester . Here we show that fester genes are members of an extended family consisting of >37 loci, and co-expressed with an even more diverse gene family-the fester co-receptors ( FcoR ). The FcoRs are membrane proteins related to fester , but include conserved tyrosine motifs, including ITIMs and hemITAMs. Both genes are encoded in highly polymorphic haplotypes on multiple chromosomes, revealing an unparalleled level of diversity of innate receptors. Our results also suggest that ITAM/ITIM signal integration is a deeply conserved mechanism that has allowed convergent evolution of innate and adaptive cell-based recognition systems.

FAM13A polymorphism is associated with a usual interstitial pneumonia pattern in patients with systemic sclerosis-associated interstitial lung disease.

The MUC5B promoter single nucleotide polymorphism (SNP) rs35705950 has been associated with idiopathic pulmonary fibrosis (IPF) and rheumatoid arthritis (RA)-related interstitial lung disease (ILD), but not with systemic sclerosis (SSc)-ILD. We hypothesized that the MUC5B promoter polymorphism or other IPF susceptibility loci are associated with an increased risk for the uncommon SSc-usual interstitial pneumonia (UIP) endophenotype, rather than SSc-ILD in general. We performed a cross-sectional study of SSc-ILD patients from 4 US Scleroderma Programs to investigate the frequency of MUC5B rs35705950 and 12 additional IPF susceptibility loci. SSc-ILD patients were stratified by high resolution chest CT (HRCT) imaging findings into UIP and non-UIP groups. Analysis of HRCTs performed by a thoracic radiologist blinded to participants' characteristics classified each scan as definite UIP, probable UIP, indeterminate, or alternative diagnosis, according to American Thoracic Society criteria. Four-hundred eighty-nine SSc-ILD patients were included; 80% were female and 75% were White. Twenty-three (4.7%) patients had a definite UIP pattern. The MUC5B SNP rs35705950 was not associated with a definite UIP pattern in SSc-ILD. In contrast, patients carrying 2 copies of the IPF risk gene FAM13A minor allele rs2609255 had significantly higher odds of a definite UIP pattern compared with the other patterns (OR 3.40, 95% CI 1.19-9.70), and compared with an alternative diagnosis (OR 3.65, 95% CI 1.25-10.65). We demonstrated a novel association between FAM13A and SSc-UIP. Contrary to IPF and RA-ILD, the MUC5B promoter polymorphism was not associated with a definite UIP pattern in SSc-ILD.

TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline.

The recognition that transposable elements (TEs) play important roles in many biological processes has elicited growing interest in analyzing sequencing data derived from this 'dark genome'. This is however complicated by the highly repetitive nature of these sequences in genomes, requiring the deployment of several problem-specific tools as well as the curation of appropriate genome annotations. This pipeline aims to make the analysis of TE sequences and their expression more generally accessible. The TE-Seq pipeline conducts an end-to-end analysis of RNA sequencing data, examining both genes and TEs. It implements the most current computational methods tailor- made for TEs, and produces a comprehensive analysis of TE expression at both the level of the individual element and at the TE clade level. Furthermore, if supplied with long-read DNA sequencing data, it is able to assess TE expression from non-reference (polymorphic) loci. As a demonstration, we analyzed proliferating, early senescent, and late senescent lung fibroblast RNA-Seq data, and created a custom reference genome and annotations for this cell strain using Nanopore sequencing data. We found that several retrotransposable element (RTE) clades were upregulated in senescence, which included non-reference, intact, and potentially active elements. TE-Seq is made available as a Snakemake pipeline which can be obtained at https://github.com/maxfieldk/TE-Seq . All software dependencies besides Snakemake and Docker/Singularity are packaged into a container which is automatically built and deployed by the pipeline at runtime.

Variation in SSRs at different genomic regions and implications for the evolution and identification of Armillaria gallica.

Armillaria spp. are devastating forest pathogens. Due to its low pathogenicity and abundant genetic variation, Armillaria gallica exhibited a unique and beneficial symbiosis with Gastrodia elata, which was used as a traditional Chinese medicine. However, the variation and population structure of A. gallica populations have rarely been investigated. Hence, we analyzed the evolution and variation in simple sequence repeats (SSRs) in three Armillaria genomes: A. gallica, A. cepistipes, and A. ostoyae to assess the genetic diversity and population structure of 14 A. gallica strains. Genome analysis revealed that SSRs were more abundant in the intergenic region than the intron and exon region, as was the SSR density. Compared with other two genomes, SSR density was the lowest in exon region and largest in the intron region of A. gallica, with significant variation in genic region. There were 17 polymorphic markers in A. gallica genome was identified, with 26.7% in genic region, which is higher than that of 18.8% in the intergenic region. Moreover, a total of 50 alleles and 42 polymorphic loci were detected among these A. gallica strains. The averaged polymorphism information content (PIC) was 0.4487, ranged from 0.2577 to 0.6786. Both principal coordinate analysis (PCoA) and population structure analyses based on the genotype data of SSRs divided the strains into two clusters. The cluster I included all the strains from high-altitude G. elata producing areas and some low-altitude areas, while the strains in Cluster II originated from low-altitude G. elata producing areas. These results indicated that substantial genome-specific variation in SSRs within the genic region of A. gallica and provide new insights for further studies on the evolution and breeding of A. gallica.

Making sense of recent models of the "sheltering" hypothesis for recombination arrest between sex chromosomes.

In their most extreme form, sex chromosomes exhibit a complete lack of genetic recombination along much of their length in the heterogametic sex. Some recent models explain the evolution of such suppressed recombination by the "sheltering" of deleterious mutations by chromosomal inversions that prevent recombination around a polymorphic locus controlling sex. This sheltering hypothesis is based on the following reasoning. An inversion that is associated with the male-determining allele (with male heterogamety) is present only in the heterozygous state. If such an inversion carries a lower-than-average number of deleterious mutations, it will accrue a selective advantage, and will be sheltered from homozygosity for any mutations that it carries due to the enforced heterozygosity for the inversion itself. It can therefore become fixed among all carriers of the male-determining allele. Recent population genetics models of this process are discussed. It is shown that, except under the unlikely scenario of a high degree of recessivity of most deleterious mutations, inversions of this type that lack any other fitness effects will have at best a modest selective advantage; they will usually accumulate on proto-Y chromosomes at a rate close to, or less than, the neutral expectation. While the existence of deleterious mutations does not necessarily prevent the spread of Y-linked inversions, it is unlikely to provide a significant selective advantage to them.

Genetic structure of cattle of the siberian branch by microsatellite loci

Molecular-genetic methods are essential tools for the utilization and conservation of animal genetic resources. These methods facilitate more efficient management and control of breeding programs within livestock production systems. For studying the genetic diversity of a population, the use of STR markers is relevant due to the high variability of repeats. This study presents a genetic characterization of a Holstein and Black Pied cattle population (n = 10233) in Western Siberia using 12 microsatellite loci (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53). A total of 145 alleles were identified across all loci, with frequencies ranging from 0.00005 to 0.68961. The highest level of genetic diversity was observed at the TGLA122 locus (25 alleles) with an average number of effective alleles (Ne) of 4.5. The least polymorphic locus was BM1824 (7 alleles) with an average Ne of 3.27. The average observed (Ho) and expected (He) heterozygosity across all loci was 0.6. The highest variability was observed at the TGLA53 locus, with a Wright’s fixation index (Fis) of 0.161, indicating a heterozygote deficiency. A similar deficiency was observed at the BM1818 locus. All other loci exhibited a positive Fis, with the highest value observed at the ETH3 locus (-0.074), indicating an excess of heterozygotes. The average Fis across all loci was -0.02, suggesting a sufficient level of heterozygosity within the studied population. These findings provide valuable information for population studies and practical breeding programs aiming to manage genetic diversity and improve selection efficiency in this cattle population.

Differentiation of wild accessions within the Panax bipinnatifidus complex using newly developed polymorphic microsatellite markers

Abstract Panax L., renowned as ginseng genus, is a famous medicinal group of family Araliaceae. Within this genus, the taxa of Panax bipinnatifidus complex are mainly distributed in Himalayas and Hengduan Mountain areas. Due to the complex evolutionary history and short-term rapid radiation, the relationships among species within the complex have not been clearly resolved, and the taxa identification is difficult due to the intermediate morphological traits. This study aimed to use the available restriction-site associated DNA sequence data from 29 individuals of P. bipinnatifidus complex to mine high-polymorphic simple sequence repeat (SSR) markers, with the goal of evaluating their utility in taxa identification. Eleven polymorphic SSR loci were ultimately selected and validated through polymerase chain reactions amplifying across 63 individuals of P. bipinnatifidus complex and 13 individuals of three outgroup species. The subsequent genetic diversity analysis uncovered 76 alleles in total, ranging from 5 to 15 per locus. Observed heterozygosity spanned 0.241–0.512, while expected heterozygosity ranged between 0.345 and 0.644. The genetic kinship analysis revealed a sister relationship between Panax zingiberensis and Panax vietnamensis. The analysis result also supported the classification of samples from Hunan and Hubei provinces into a single genetic unit within the P. bipinnatifidus complex. These newly developed SSR markers will facilitate the identification of wild ginseng plants.

The serotonin 1A receptor promoter polymorphism, rs6295, is associated with morphofunctional features

Introduction. The tendency to weight gain is influenced by many genetic and environmental factors (nutrition, level of physical activity, social well-being, etc.), as well as complex interactions of these factors. Studying the genetic factors of obesity can help in developing individual strategies for the prevention and treatment of this common disease. One of the most important hereditary factors is the neurotransmitter systems gene polymorphism, (including the serotonin system gene polymorphism). The aim of the investigation is to study the associations of single nucleotide polymorphism of the rs6295 locus of the serotonin receptor gene 1A HTR1A with morphofunctional features and body weight gain. Material and methods. The study used the materials of a comprehensive anthropogenetic examination of 386 men and 418 women aged 17 to 30 years. More than 20 morphofunctional indicators were measured using the traditional anthropometric method. The material for genetic analysis was genomic DNA isolated from buccal epithelium. The reliability of intergroup differences was assessed using the Mann-Whitney criterion, while canonical discriminant analysis was used to study intergroup variability. Results. For the first time, a significant correlation was shown between the polymorphism of the serotonin receptor type 1 gene HTR1A and morphofunctional features: individuals with the G/G genotype with greater body weight have lower (compared to carriers of the C/C and C/G genotypes) values of the indicators of the level of metabolic processes and specific metabolism. Conclusion. The statistically significant obtained results may be used in the development of individual strategies for the prevention and treatment of obesity, and also allow us to supplement the information on the association of serotonin system gene polymorphism with morphofunctional features and contribute to expanding our understanding of the human physique features formation and their relationships with hereditary predisposition.

Association between programmed death protein 1-related single-nucleotide polymorphisms and immune-related adverse events induced by programmed death protein 1 inhibitors—a pilot study

Programmed death protein 1 (PD-1) inhibitors have potent anti-tumor activities. However, they often result in immune-related adverse events (irAEs) of varying severity. Therefore, the factors affecting the incidence of irAEs warrant urgent investigation. This study aimed to identify specific and sensitive predictors of irAEs in a Chinese population. We conducted a genome-wide association study (GWAS) comprising 80 patients with malignant tumors to evaluate single-nucleotide polymorphism (SNP) loci associated with the incidence of irAEs. The SNP rs2157775 on the LOC339166 gene had the lowest P value but did not reach the significance threshold after Bonferroni correction. Therefore, potentially associated SNPs were further investigated through the mechanism-related PD-1 pathway using the ImmPort and PathCards Human Gene Databases. A binary logistic regression model revealed that CD3E (rs3782040) A/A was associated with a lower incidence of irAEs in patients with malignant tumors who received PD-1 inhibitors. In contrast, PTPN11 (rs143894582) C/CA was associated with a higher incidence of irAEs. These findings provide a basis for the verification and identification of new loci to provide insight into the etiology of irAEs.

MicroRNA binding site variants-new potential markers of primary osteoporosis in men and women.

The identification of significant DNA markers of primary osteoporosis may gain new insights by studying genome regions involved in mechanisms of epigenetic regulation through interactions with microRNAs. The authors searched for associations of polymorphic variants of microRNA binding sites of mRNA target genes and polymorphic loci of microRNA genes with primary osteoporosis in a cohort of women and men from the Volga-Ural region of Russia (N = 1.177). Using case-control association analysis, the authors found that rs1061947 (COL1A1), rs10793442 (ZNF239), rs6854081 (FGF2), and rs11614913 (miR-196a) were associated with osteoporotic fractures; rs5854 (MMP1) and rs2910164 (miR-146a) were associated with low bone mineral density; and rs10098470 (TPD52), rs11540149 (VDR), rs1042673 (SOX9), rs1054204 (SPARC), and rs1712 (FBXO5) were markers of both fractures and low bone mineral density. Among the identified associations, ethno specific trends were found, as well as sex-specific associations. Prognostic models were developed, among which the model for predicting osteoporosis in general in women (Area Under Curve = 0.909) achieved the highest level of predictive value. Thus, the potential role of polymorphic variants of microRNA binding sites in the development of primary osteoporosis in men and women from the Volga-Ural region of Russia was demonstrated.

HLA Diversity in Transylvanian Ethnic Groups: Consequences for Hematopoietic Cell Transplantation

The HLA profile is essential in cell and tissue transplantation, particularly in patients with autoimmune conditions and infections. Due to the extreme polymorphism in certain HLA loci, it also serves as a key tool for population genetic analysis. This study aimed to identify the allele and haplotype distributions of HLA class I (A, B, and C) and class II (DRB1) genotypes in unrelated hematopoietic stem cell donors. A retrospective analysis was conducted between 2016 and 2020 on 9832 Transylvanian volunteers, divided into Romanian and Hungarian groups based on self-reported ethnicity. Using PCR-SSO for HLA typing, significant differences were found in allele frequencies between ethnic groups. A total of 19 HLA-A, 31 HLA-B, 14 HLA-C, and 13 HLA-DRB1 distinct allele groups were identified between ethnic groups. Notably, B*18, B*51, and C*12 were more frequent in Romanians, while B*44, B*40, and C*07 were more common in Hungarians. Differences in haplotype distributions were also observed, with HLA-A*02~B*18~C*07~DRB1*11 being significantly more frequent in Romanians. Understanding these population-specific HLA profiles can improve donor matching for hematologic diseases, enhancing patient outcomes and access to life-saving hematopoietic stem cell transplantation.

Morphological characterization and genetic diversity of mini core collection of Rosa damascena from Morocco

Damask rose (Rosa damascena Mill.) is a popular Rosa species cultivated for the industrial production of rose oil worldwide. In the current study, the morphological characteristics and genetic diversity among 12 populations of these species collected from Kelaat M’gouna in Morocco were examined to identify more variable traits and compare their genetic structure. Observations were recorded for a total of 24 morphological traits. The phenotypic variation coefficient (CV) of the studied traits varied from 4.79 % to 42.52 %, confirming the high phenotypic variation between accessions. Cluster analysis grouped accessions into two major clusters based on their morphological resemblance. For molecular investigations, nuclear DNA was amplified using 13 ISSR markers. Analysis of molecular variance (AMOVA) indicated that the highest proportion was within populations (87 %) rather than between them (13 %). Boutaghrar region recorded high values of genetic diversity (He = 0.237), percentage polymorphic loci (PPL = 67 %) and Shannon information index (I = 0.358) Clustering based on Jaccard similarity divided studied the accessions into three distinct clusters. STRUCTURE analysis and principal coordinate analysis (PCoA) were consistent with the genetic relationships derived from cluster analysis. Our study suggests that the wide genetic variation and haplotype observed in Moroccan Damascene roses are valuable for future improvement and conservation of rose programs, particularly for enhancing commercial traits, flower yield, and breeding stability.

Needle and Branch Trait Variation Analysis and Associated SNP Loci Mining in Larix olgensis.

Needles play key roles in photosynthesis and branch growth in Larix olgensis. However, genetic variation and SNP marker mining associated with needle and branch-related traits have not been reported yet. In this study, we examined 131 samples of unrelated genotypes from L. olgensis provenance trails. We investigated phenotypic data for seven needle and one branch-related traits before whole genome resequencing (WGRS) was employed to perform a genome-wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci that were significantly correlated with the studied traits. We identified a total of 243,090,868 SNP loci, and among them, we discovered a total of 161 SNP loci that were significantly associated with these traits using a general linear model (GLM). Based on the GWAS results, Kompetitive Allele-Specific PCR (KASP), designed based on the DNA of population samples, were used to validate the loci associated with L. olgensis phenotypes. In total, 20 KASP markers were selected from the 161 SNPs loci, and BSBM01000635.1_4693780, BSBM01000114.1_5114757, and BSBM01000114.1_5128586 were successfully amplified, were polymorphic, and were associated with the phenotypic variation. These developed KASP markers could be used for the genetic improvement of needle and branch-related traits in L. olgensis.