Informative Markers Research Articles

Developmental Validation of a DIP-InDel/DIP-STR System for the Detection of Unbalanced DNA Mixtures.

Extracting "masked" minor donor information from an unbalanced DNA mixture stain is important for the identification of the person of interest. In recent years, a series of compound markers genotyped based on allele-specific amplifications have been proposed to detect minor contributors of mixed stains. In this study, we selected out 18 DIP-InDel markers from previous literatures and established a multiplex system encompassing 18 DIP-InDel markers and 6 DIP-STR markers in two separate reactions. The allele frequencies were estimated based on 200 samples, and 23 of the 24 DIP-linked length polymorphic markers had a relatively high probability of informative markers (I value >0.267), which indicated their potential usefulness in the Chinese Han population. Moreover, the multiplex was highly sensitive (requiring >0.025ng) and specific to human DNA. This system is capable of detecting the minor contributor comprising 1% in unbalanced mixtures of two individuals. The capacity of profiling cell-free DNA was also analyzed in few cases. At least one paternal allele could be detected in maternal plasma samples with gestation periods ranging from 27 to 40 weeks. To conclude, the DIP-linked length polymorphic markers may serve as a convenient method for detecting the presence of a minor donor in unbalanced mixtures and show promise for noninvasive prenatal diagnosis.

Harnessing genetic diversity in Sudanese sorghum wild relatives for stay-green drought tolerance via microsatellite (SSR) marker assessment

AbstractSudan is the birthplace of sorghum, and vast genetic diversity exists among its wild relatives. To assess the genetic potential of Sudan wild sorghum accessions, we used 41 stay-green-specific microsatellite (SSR) markers to analyze the genetic variability and population structure of 256 accessions. Overall, 17 SSR markers were polymorphic, with 55 alleles on average 3.3 per locus. The polymorphic information content (PIC) ranged from 0.49 to 0.57, with an overall mean of 0.53, indicating the potential of these markers for capturing the genetic construction of wild sorghum. Linkage disequilibrium analysis identified the two most informative markers, Xcup05 and Xtxp212. Accordingly, the Nei gene diversity of the populations varied from 0.032 to 0.127, with an overall mean of 0.083. Molecular variance analysis (AMOVA) demonstrated that 99% and 1% of the genetic variations were within and among populations (Fst = 0.066; P 0.001), respectively. However, gene flow (Nm) values varied from 0.058 in populations 1 and 2 to 1.018 in populations 2 and 3. Neighbor-joining trees identified from 21 Sudanese wild sorghum accessions clustered closely to the universally drought-tolerant landrace B35. Structural analysis generated the highest Delta K value (58.2) at K = 2, revealing two distinct subpopulations. While this work provides valuable information about the potential of sorghum wild relatives from Sudan as sources for stay-green drought tolerance, further research should be directed toward identifying the exact mechanisms and genes underlying this stay-green trait using advanced molecular omics techniques. In conclusion, this study highlights the potential role of Sudanese sorghum accessions as reservoirs of ready-to-use stay-green genes for the design of climate-resilient sorghum cultivars in drought-prone areas of Sudan and beyond. However, these wild relatives would require extensive pre-breeding and validation efforts before their genes can be effectively incorporated into elite cultivars.

Key role of laboratory diagnostics of cardiovascular system injury in COVID‑19

This literature review examines data characterizing the clinical significance of the most informative laboratory markers, which make it possible not only to promptly identify the pathology of the cardiovascular system, but also to assess the risk of adverse outcomes of coronavirus infection. The most studied markers are hsTnI, NT-proBNP, D-dimer. Promising laboratory markers that require comprehensive study include osteopontin, stimulating growth factor ST2, Gal-3, copeptin, endothelin-1. With all the variety of pathological conditions that are accompanied by an increase in the concentrations of these markers, they can be considered as indicators that undoubtedly deserve close attention when assessing patients with COVID-19.

Genetic Diversity and Population Structure Analysis of Soybean [Glycine max (L.) Merrill] Genotypes Using Agro-Morphological Traits and SNP Markers

Background/Objectives: Understanding the genetic diversity of soybean genotypes can provide valuable information that guides parental selection and the design of an effective hybridization strategy in a soybean breeding program. In order to identify genetically diverse, complementary, and prospective parental lines for breeding, this study set out to ascertain the genetic diversity, relationships, and population structure among 35 soybean genotypes based on agro-morphological traits and Single Nucleotide Polymorphic (SNP) marker data. Methods/Results: Cluster analysis, based on agro-morphological traits, grouped the studied genotypes into four clusters. The first two principal components accounted for 62.8% of the total phenotypic variation, where days to 50% flowering, days to 95% maturity, grain yield, shattering score, and lodging score had high and positive contributions to the total variation. Using the SNP marker information, mean values of 0.16, 0.19, 0.067, and 0.227 were obtained for minor allele frequency (MAF), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. Using different clustering approaches (admixture population structure, principal component scatter plot, and hierarchical clustering), the studied genotypes were grouped into four major clusters. Conclusions:The agro-morphological and molecular analysis results indicated the existence of moderate genetic diversity among the studied genotypes. The traits identified to be significantly related to yield provide valuable information for the genetic improvement of soybeans for yield.

Morphological and molecular characterization of some Chrysanthemum (Dendranthema grandiflora) cultivars

The diversity and genetic relationships among seven commercial chrysanthemum cultivars were analyzed using morphological and molecular markers. Vegetative growth, flowering, flower yield, and flower quality parameters were evaluated to assess genetic variability across the cultivars. Cultivars Crystal Red, Kodiack, and Crystal White exhibited superior vegetative growth, while Abrun, Crystal Red, and Kodiack displayed better flowering characteristics, particularly in terms of the number of inflorescences per plant and mass of colored flowering. Crystal White, Coca Bleach, and Crystal Red cultivars demonstrated the highest inflorescence stalk length, while cvs. Crystal Red, Crystal Yellow, Crystal Pink, and Kodiack Yellow recorded the maximum number of ray floret inflorescences. Other quality parameters such as inflorescence diameter and ray floret length were found to be optimal in Kodiack, Crystal White, Crystal Pink, Coca Bleach, and Crystal Yellow cultivars. Simple Sequence Repeat (SSR) markers were employed to distinguish and identify standard-type chrysanthemum cultivars, utilizing twelve SSR markers from the chrysanthemum SSR database. The results suggest that these SSR markers hold promise for identifying additional chrysanthemum cultivar types and assessing genetic relationships among them. Association studies combining morphological and molecular data offer a valuable approach to identifying informative markers for plant breeding purposes.

Sympathetic activity markers in patients with resistant hypertension with renal dysfunction

Aim. To study the informativeness of sympathetic activity markers and perirenal adipose tissue (PRAT) in assessing renal function decline in patients with resistant hypertension (RH).Material and methods. The study included 63 patients with RH of both sexes aged 40-80 years. The main group included 19 patients with chronic kidney disease (CKD). The control group consisted of 44 patients with RH without CKD. All patients were assessed for uric acid, blood lipid profile, beta-adrenergic reactivity of erythrocyte mem­branes, free metanephrine and normetanephrine in plasma and 24-hour urine. The renal function was assessed by the glomerular filtra­tion rate calculated using the CKD-EPI equation. Twenty-four hour blood pressure monitoring was performed on the brachial artery of one arm at intervals of 15 minutes during the day and 30 minutes at night. Kidney size and PRAT were calculated based on the magnetic reso­nance imaging.Results. In both groups of patients, a significant increase in blood normetanephrine and beta-adrenergic reactivity of erythrocyte mem­branes relative to the reference values was shown. Blood and 24-hour urine metanephrine were within the reference intervals. No differences were found between the sympathetic activity indices in the main and control groups. In the main group patients, the PRAT thickness was greater (p=0,013), and the kidney diameter was smaller (p=0,046) than in the control group patients.Conclusion. CKD in RH patients is not accompanied by additional significant changes in sympathetic regulation, assessed by the blood and 24-hour urine catecholamine levels, the degree of beta-adrenergic receptor desensitization and variability of blood pressure. PRAT increase according to magnetic resonance imaging in patients with RH is associated with a decrease in renal filtration function.

Percutaneous Wearable Biosensors: A Brief History and Systems Perspective

AbstractWearable biosensors are envisioned to disrupt both delivery and accessibility of healthcare by providing real‐time, continuous monitoring of informative and predictive physiological markers in convenient, user‐friendly, and portable designs. In recent years, there has been myriad demonstrations of biosensor‐integrated clothing and skin‐borne biosensor patches, enabled by device miniaturization, reduced power consumption, and new biosensing chemistries. Despite these impressive demonstrations, most consumer‐grade wearables have been limited to biophotonic and biopotential sensing methods to extrapolate information such as pulse, blood oxygenation, and electrocardiograms. The only commercial example of wearable electrochemical sensing methods is for glucose monitoring. However, there is a growing interest in developing percutaneous biosensors for monitoring in interstitial fluid (ISF), which offers direct access to popular analytes such as glucose, lactate, and urea, as well as new targets like hormones, antibodies, and even medications. Herein, a brief context for the current status of wearable biosensors is provided and assess the major engineering successes and pitfalls of percutaneous biosensors over the past five years, with a view to identifying areas for further developments that will enable deployable, clinical‐ or consumer‐grade systems.

Prospective study on immune function in renal transplant patients during perioperative period: A prospective cohort study.

Delayed graft function (DGF) is a type of acute renal failure that is closely linked to the immune system. The objective of this study is to investigate immune trends during the perioperative period of renal transplantation and compare the variations between patients with DGF and immediate graft function (IGF). A total of 48 kidney transplant patients were enrolled. Parameters including stimulated adenosine triphosphatase concentrations (sATP), nonstimulated ATP concentrations, white blood cells, and lymphocyte count were assessed. Patients were categorized into the DGF or IGF group. Clinical information and changes in immune markers were compared. Receiver operating characteristic analysis was performed to determine the sensitivity and specificity in predicting DGF. Additionally, separate immune function analyses were conducted for the 3 infection cases. Following induction immunosuppressive therapy, white blood cells, and neutrophil count showed a significant initial increase followed by a gradual decline. Lymphocyte count, nonstimulated ATP concentrations, and sATP exhibited an initial significant decrease followed by a slow recovery. Immune markers between the DGF and IGF groups were significantly different at day 4 after renal transplantation. Only sATP levels at day 4 after renal transplantation (area under the curve = 0.731, sensitivity = 0.864, specificity = 0.684) demonstrated predictive value for DGF occurrence. Among the 3 infection cases, 2 cases exhibited persistently decreased sATP levels and died within the first month and 6 months, while the remaining case showed a recovery of sATP levels at D9 and survived. These findings indicate that sATP level can potentially serve as a biomarker reflecting the impact of immunosuppressants. Poor recovery of sATP may be associated with DGF, infection, or even mortality.

Variable habitat use supports fine-scale population differentiation of a freshwater piscivore (northern pike, Esox lucius) along salinity gradients in brackish lagoons.

In mobile animals, selection pressures resulting from spatio-temporally varying ecological factors often drive adaptations in migration behavior and associated physiological phenotypes. These adaptations may manifest in ecologically and genetically distinct ecotypes within populations. We studied a meta-population of northern pike (Esox lucius) in brackish environments and examined intrapopulation divergence along environmental gradients. Behavioral phenotypes in habitat use were characterized via otolith microchemistry in 120 individuals sampled from brackish lagoons and adjacent freshwater tributaries. We genotyped 1514 individual pike at 33highly informative genetic markers. The relationship between behavioral phenotype and genotype was examined in a subset of 101 pikes for which both phenotypic and genomic data were available. Thermosaline differences between juvenile and adult life stages indicated ontogenetic shifts from warm, low-saline early habitats towards colder, higher-saline adult habitats. Four behavioral phenotypes were found: Freshwater residents, anadromous, brackish residents, and cross-habitat individuals, the latter showing intermediary habitat use between brackish and freshwater areas. Underlying the behavioral phenotypes were four genotypes,putative freshwater, putativeanadromous, and two putativelybrackish genotypes. Through phenotype-genotype matching, three ecotypes were identified: (i) a brackish resident ecotype, (ii) a freshwater ecotype expressing freshwater residency or anadromy, and (iii) a previously undescribed intermediary cross-habitat ecotype adapted to intermediate salinities, showing limited reliance on freshwater. Life-time growth of all ecotypes was similar, suggesting comparable fitness. Bycombining genetic data with lifelong habitat use and growth as a fitness surrogate, our study revealed strong differentiation in response to abiotic environmental gradients, primarily salinity, indicating ecotype diversity in coastal northern pike is higher than previously believed.

The diagnostic value of leptin for the detection of liver steatosis in postmenopausal obese women

Introduction. More than half of post-reproductive age women are overweight and obese, which puts them at high risk of developing non-alcoholic fatty liver disease (NAFLD). In the abdominal type of obesity, adipose tissue dysfunction and impaired leptin secretion develop.Aim. To evaluate the possibilities and diagnostic characteristics of leptin for the determination of liver steatosis in pre-obese and obese women in the early postmenopausal period.Materials and methods. 76 women in the early postmenopausal period were examined, including 63 patients with NAFLD and overweight and obesity with an average age of 50.50 ± 2.16 years and 13 practically healthy women with an average age of 49.29 ± 2.64 years, who underwent an ultrasound examination of the liver, calculation of the HSI index (Hepatic Steatosis Index) and determination of the level of leptin in the blood.Results. Abdominal type of obesity was detected in 84% of patients, the gynoid type was 16%, and the body mass index averaged 33.5 ± 1.3 kg/m2. According to the ultrasound examination and the HSI index, all patients had liver steatosis. Their leptin levels significantly exceeded the control data (p < 0.001) and directly correlated with the severity of steatosis according to the HSI index (r = 0.321; p = 0.010). The threshold value of the serum leptin level in patients with NAFLD was 13 ng/ml with sensitivity and specificity of 90.5% and 92.3%, respectively.Conclusion. Leptin is a highly informative marker of NAFLD in women with pre-obesity and obesity in the early postmenopausal period, the value of which is higher or equal to 13 ng/ml allows to verify steatosis, less than this value – to exclude it in this category of persons with high diagnostic effectiveness.

Distribution extension of a vent scale worm Branchinotoglumabipapillata (Polychaeta, Polynoidae) in the Indian Ocean.

Branchinotogluma Pettibone, 1985 is the most species-rich genus within the subfamily Lepidonotopodinae Pettibone, 1983, comprising 18 valid species from chemosynthesis-based ecosystems in the Pacific and Indian Oceans. Here, we report a new distributional record of Branchinotoglumabipapillata Zhou, Wang, Zhang & Wang, 2018, at the hydrothermal vent sites on the northern Central Indian Ridge (nCIR). This record represents the northernmost occurrence of B.bipapillata in the Indian Ocean. We conducted a comparative study of the nCIR population and other documented populations using distributional information, morphological traits, and genetic markers (two mitochondrial [COI, 16S rRNA] and one nuclear [18S rRNA] genes). While most morphological characters of B.bipapillata were consistent with those found in the Southwest Indian Ridge (SWIR), variations were noted in the segment with the last branchiae. Molecular data revealed that all populations of B.bipapillata form a single clade, indicating a wide distribution from the SWIR to nCIR, covering ~4,000 km across various ridges in the Indian Ocean. This study presents extensive distribution of a vent species with well-connected populations throughout the Indian Ocean, distinguishing it from many other vent species affected by the dispersal barrier in the Indian Ocean.

Pure wild forest reindeer (Rangifer tarandus fennicus) or hybrids? A whole-genome sequencing approach to solve the taxonomical status

AbstractIn Finland, the geographic distribution of domestic reindeer (Rangifer tarandus tarandus) and Finnish wild forest reindeer (Rangifer tarandus fennicus) partly overlap in the vicinity of the southern border of the reindeer herding area. Additionally, domestic reindeer are occasionally kept as pets within the distribution range of the wild forest reindeer. Hybridisation of these two subspecies is one of the major threats for the wild forest reindeer population. Concerns about potential hybridisation served as the catalyst also for this study, which we aimed to clarify the taxonomic status of presumed wild forest reindeer individuals intended as founder individuals for a reintroduction project. To do this, we resequenced genomes of four Rangifer tarandus individuals with unknown taxonomical status and investigated their ancestries by comparing the genomic data with the existing resequenced data of the Finnish domestic reindeer and Finnish wild forest reindeer. The genetic relationship investigations indicated that all individuals we analysed were pure wild forest reindeer, making them suitable as founder individuals for the reintroduction project. Thus, our study provided critical knowledge for practical conservation action, where it was essential to recognise each individual’s origin. In the future, it will also offer novel insights into the spread of native wild forest reindeer to new geographic regions in Finland. For subsequent studies, additional resequenced genomic data of Rangifer individuals will be needed to develop an ancestry information marker panel of single nucleotide polymorphisms for rapid and cost-effective identification of hybrid individuals of these subspecies.

GWAS for root yield and its contributing traits in Withania somnifera (L.) dunal: First report

Ashwagandha [Withania somnifera (L.) Dunal] is a significant medicinal plant, with limited information on its genetic variability. This study evaluateed genetic diversity among 96 ashwagandha genotypes with the aim of developing strategies to improve root yield and secondary metabolites. A joint ANOVA indicated significant variability within the evaluated panel. Key traits, such as root girth, fresh root yield and dry root yield showed positive and significant correlations at both tested years. Molecular markers (SRAP, ISSR, and SSR) were used to assess genetic diversity. Amplified PCR products ranged from 210 bp (SRAP-22) to 1350 bp (SRAP-19), with PIC value ranged from 0.332 (SSR 20) to 0.494 (ISD 11), indicated moderate informativeness of markers. Genetic diversity analysis using Dice's coefficient formed six clusters, identifying two genotypes (86 and 87) as highly diverse. Population structure analysis revealed five clusters with an Fst range of 0.21–0.36, indicating allele flow among genotypes. The highest genetic differentiation was observed between clusters G2 and G4 (Fst = 0.1253). On the basis of structure analysis, genotypes in cluster G5 exhibited similar genetic make-up. A genome-wide association study (GWAS) identified a 490 bp locus of the SRAP 49 marker as highly effective and informatice. This locus was broadly associated with fresh root yield (FW) and dry root yield (DW) across individual and pooled environments. The positive correlation between these traits suggests simultaneous improvement is feasible. This study highlights the importance of genetic diversity for enhancing root yield and provides valuable insights for the genetic improvement of ashwagandha.

Genetic Diversity Analysis and Fingerprint Construction for 87 Passionfruit (Passiflora spp.) Germplasm Accessions on the Basis of SSR Fluorescence Markers

A comprehensive genetic diversity analysis of 87 Passiflora germplasm accessions domesticated and cultivated for several years in the karst region of Guizhou, China, was conducted utilizing simple sequence repeat (SSR) fluorescent markers. These Passiflora species, renowned for their culinary and medicinal value, could bring significant economic and ecological benefits to the region. This study aimed to assess the genetic resources of these species and facilitate the selection of superior cultivars adapted to the karst environment. Our analysis revealed an abundance of SSR loci within the Passiflora transcriptome, with single-base repeats being the most prevalent type. Through rigorous primer screening and amplification, we successfully identified 27 SSR primer pairs exhibiting robust polymorphisms. Further interrogation at eight microsatellite loci revealed 68 alleles, underscoring the high level of genetic diversity present in the cultivated accessions. The average expected heterozygosity was 0.202, with the ssr18 locus exhibiting the highest value of 0.768, indicating significant genetic variation. The mean polymorphic information content (PIC) of 0.657 indicates the informativeness of these SSR markers. Comparative analyses of the cultivated and potential wild progenitors revealed distinct genetic variations among the different Passiflora types. Genetic structure and clustering analyses of the 87 accessions revealed seven distinct groups, suggesting gene flow and similarities among the resources. Notably, a DNA fingerprinting system was established using eight SSR primer pairs, effectively distinguishing the selected cultivars that had adapted to the karst mountainous region. This study not only deepens our understanding of Passiflora genetic resources in the karst environment but also provides a valuable reference for conservation, genetic improvement, and cultivar selection. The rich genetic diversity of the Passiflora germplasm underscores their potential for sustainable utilization in breeding programs aimed at enhancing the economic and ecological viability of these valuable plant species.

Cluster-Based White Matter Signatures and the Risk of Dementia, Stroke, and Mortality in Community-Dwelling Adults.

Markers of white matter (WM) injury on brain MRI are important indicators of brain health. Different patterns of WM atrophy, WM hyperintensities (WMHs), and microstructural integrity could reflect distinct pathologies and disease risks, but large-scale imaging studies investigating WM signatures are lacking. This study aims to identify distinct WM signatures using brain MRI in community-dwelling adults, determine underlying risk factor profiles, and assess risks of dementia, stroke, and mortality associated with each signature. Between 2005 and 2016, we measured WMH volume, WM volume, fractional anisotropy (FA), and mean diffusivity (MD) using automated pipelines on structural and diffusion MRI in community-dwelling adults aged older than 45 years of the Rotterdam study. Continuous surveillance was conducted for dementia, stroke, and mortality. We applied hierarchical clustering to identify separate WM injury clusters and Cox proportional hazard models to determine their risk of dementia, stroke, and mortality. We included 5,279 participants (mean age 65.0 years, 56.0% women) and identified 4 distinct data-driven WM signatures: (1) above-average microstructural integrity and little WM atrophy and WMH; (2) above-average microstructural integrity and little WMH, but substantial WM atrophy; (3) poor microstructural integrity and substantial WMH, but little WM atrophy; and (4) poor microstructural integrity with substantial WMH and WM atrophy. Prevalence of cardiovascular risk factors, lacunes, and cerebral microbleeds was higher in clusters 3 and 4 than in clusters 1 and 2. During a median 10.7 years of follow-up, 291 participants developed dementia, 220 had a stroke, and 910 died. Compared with cluster 1, dementia risk was increased for all clusters, notably cluster 3 (hazard ratio [HR] 3.06, 95% CI 2.12-4.42), followed by cluster 4 (HR 2.31, 95% CI 1.58-3.37) and cluster 2 (HR 1.67, 95% CI 1.17-2.38). Compared with cluster 1, risk of stroke was higher only for clusters 3 (HR 1.55, 95% CI 1.02-2.37) and 4 (HR 1.94, 95% CI 1.30-2.89), whereas mortality risk was increased in all clusters (cluster 2: HR 1.27, 95% CI 1.06-1.53, cluster 3: HR 1.65, 95% CI 1.35-2.03, cluster 4: HR 1.76, 95% CI 1.44-2.15), compared with cluster 1. Models including clusters instead of an individual imaging marker showed a superior goodness of fit for dementia and mortality, but not for stroke. Clustering can derive WM signatures that are differentially associated with dementia, stroke, and mortality risk. Future research should incorporate spatial information of imaging markers.

A new leaf pubescence gene, Hl1th , introgressed into bread wheat from Thinopyrum ponticum and its phenotypic manifestation under homoeologous chromosomal substitutions.

Blue-grain lines were created on the basis of the spring bread wheat variety Saratovskaya 29 (S29) with chromosome 4B or 4D replaced with chromosome 4Th from Thinopyrum ponticum. The leaf pubescence of the two lines differs from S29 and from each other. In this work, we studied the effect of these substitutions on the manifestation of this trait. To quantify pubescence, the LHDetect2 program was used to determine trichome length and number on the leaf fold microphotographs. The key gene Hl1 on chromosome 4B and another unidentified gene with a weak effect determine the leaf pubescence of the recipient S29. Their interaction leads to the formation of trichomes of up to 300 microns in length. Replacement of both copies of chromosome 4B with two copies of wheatgrass chromosome 4Th modifies leaf pubescence in line S29_4Th(4B) so that the leaf pubescence characteristic of S29 becomes more sparse, and trichomes of up to 600- 700 μm in length are formed. Additionally, we described modification of pubescence in the substitution line S29_4Th(4D) where chromosome 4D that does not carry any pubescence gene was replaced. Under this substitution, trichomes of up to 400 μm in length were formed and the average length of trichomes on the underside of the leaf was reduced. The replacement of the Hl1 gene in the lines was also confirmed by the allelic state of the linked microsatellite marker Xgwm538. Thus, as a result of the studies, a new leaf pubescence gene introgressed from Th. ponticum into bread wheat was identified. We designated it as Hl1th. For the purpose of selection, we propose to use the unlicensed informative microsatellite markers Xgwm538 and Xgwm165, allowing chromosomes 4A, 4B, 4D and 4Th to be distinguished.

Identification of false smut – resistant donors in Rice (Oryza sativa L.) and analysis of their morpho-molecular diversity for resistance breeding

False smut disease of rice caused by the pathogen Ustilaginoidea virens is a growing threat to the rice farmers as it affects both quality and quantity. Development of resistant variety becomes difficult, since very few resistant donors were available for false smut resistant breeding programme. Therefore, to identify potential donors for resistance breeding a total of 60 genotypes were screened at hotspot location (Gudalur) during kharif 2023 which led to identification of 12 highly resistant genotypes and the notable ones are Koolavalai, Periya chandikar, Kapikar selection and Earapalli. Genetic variability studies indicated the presence of additive gene action for all the agronomic and disease related traits. Principal component analysis revealed the first 5 principal components collectively contributing 78.79 % of the total variance with disease-related traits contributing significantly to divergence. Ten clusters were delineated using Mahalanobis D2 statistics with clusters IX and V showing higher inter cluster distance (3453.64). Forty-one polymorphic markers were used to analyse the genotypes and The Unweighted Pair Group method with Arithmetic Mean (UPGMA) clustering by Jaccard distance formed 6 clusters. The Bayesian clustering classified the entire population into 2 subpopulations. False smut linked marker RM336 and RM218 were found to be the most informative marker with high Polymorphism Information Content (0.71, 0.69) and Heterozygosity Index (0.76, 0.73). The resistant genotypes such as IG71, Thulasi vasanai sambha, Arupatham vellai, Kaltikar and Chinna aduku nel can be used in the future breeding programmes to develop the resistant cultivar and to identify the candidate genes governing resistance.

Identifiable Information Value of Standard Autosomal STR in Indigenous Populations of Russia for Determination of First-Degree Relatedness

The effects of the demographic history of mankind have led to the fact that the indigenous peoples of Dagestan and Siberia are inferior in terms of genetic diversity to the populations of Europe, which affects the level of identification informativeness of standard forensic autosomal markers in these populations. In our study, we evaluated the effectiveness of two standard sets of autosomal STRs (13 CODIS, 20 CODIS, Combined DNA Index System) for the genetic testing of parent-child relatedness in four highly inbred populations of the Russian Federation and the Russian population, using two types of reference frequencies. The results of the study confirmed the assumption that the level of identification informativity of standard autosomal markers in highly inbred populations of Siberia and Dagestan is lower than in the Russian population. The total information content of markers of the new CODIS standard exceeds the threshold values required in the order of the Ministry of Health and Social Development of the Russian Federation (No. 346n). At the same time, the probability of a false positive result increases with an increase in the inbreeding coefficient in the population.

Group sequential testing of a treatment effect using a surrogate marker.

The identification of surrogate markers is motivated by their potential to make decisions sooner about a treatment effect. However, few methods have been developed to actually use a surrogate marker to test for a treatment effect in a future study. Most existing methods consider combining surrogate marker and primary outcome information to test for a treatment effect, rely on fully parametric methods where strict parametric assumptions are made about the relationship between the surrogate and the outcome, and/or assume the surrogate marker is measured at only a single time point. Recent work has proposed a nonparametric test for a treatment effect using only surrogate marker information measured at a single time point by borrowing information learned from a prior study where both the surrogate and primary outcome were measured. In this paper, we utilize this nonparametric test and propose group sequential procedures that allow for early stopping of treatment effect testing in a setting where the surrogate marker is measured repeatedly over time. We derive the properties of the correlated surrogate-based nonparametric test statistics at multiple time points and compute stopping boundaries that allow for early stopping for a significant treatment effect, or for futility. We examine the performance of our proposed test using a simulation study and illustrate the method using data from two distinct AIDS clinical trials.

Detection of putative loci affecting milk yield in Turkish Awassi sheep using microsatellite markers.

On the basis of comparisons between bovine and ovine genome mapping information, the aim of the study was to analyze the genetic diversity of selected DNA microsatellites from the bovine genome and to investigate their correlation with the average daily milk yield in Awassi sheep. 18 informative microsatellite markers were selected from the significant QTL regions affecting milk yield identified in the bovine genome in previous studies. The selected microsatellite markers were then amplified by PCR as reciprocal amplifications on the genomic DNA of Awassi sheep, with standard daily milk yield records. Thus, in this study, 18 microsatellite markers associated with milk yield in the bovine genome were examined for both determination of genetic polymorphism within the flock and the effects of marker loci on average daily milk yield in Awassi sheep. Allele frequencies of markers were determined based on the results of fragment analysis. The analysis of variance showed that the 123bp allele at the marker locus BMS1341 on BTA2 significantly influenced the average daily milk yield of Ivesi sheep (P < 0.01). On the other hand, the BMS381 locus with a 115bp allele on BTA2, the MCM140 locus with a 185bp allele on BTA6, the BMS2721 locus with a 155bp allele, the BM1237 locus with 174 and 180bp alleles on BTA7, and finally, the BMS1967 locus with a 117bp allele, the BM4208 locus with 176 and 182bp alleles, and the INRA locus with a185 bp allele on BTA8 showed moderately significant effects on the average daily milk yield of Ivesi ewes (P < 0.05).