Use Of Molecular Markers Research Articles

Genetic structure of wolf populations in North Eurasia: the effect of exclusion of closely related individuals from analysis

We describe the results of analysis of genetic structure and spatial autocorrelation in the populations of grey wolf (Canis lupus Linnaeus, 1758) on the territory of the Russian Federation and the Republic of Kazakhstan, based on 20 autosomal microsatellite markers. With the use of molecular markers, we uncovered hidden genealogical patterns reaching as far as 700–1600 km and having the most pronounced effect on distances up to 150 km. Our research has shown that identification and exclusion of closely related genotypes has limited effect on the results of analysis of intrapopulation genetic diversity. Meanwhile, such procedure is recommended for researching population structure, as it allows for streamlining some statistical approaches. Results of our work demonstrate integral effect of natal migration, working against the differentiation effect of philopatry. Finally, we also show that the exclusion of closely related individuals can lead to underestimation of values of genetic distances between populations.

Evolution of Molecular Biomarkers and Precision Molecular Therapeutic Strategies in Glioblastoma.

Glioblastoma is the most commonly occurring malignant brain tumor, with a high mortality rate despite current treatments. Its classification has evolved over the years to include not only histopathological features but also molecular findings. Given the heterogeneity of glioblastoma, molecular biomarkers for diagnosis have become essential for initiating treatment with current therapies, while new technologies for detecting specific variations using computational tools are being rapidly developed. Advances in molecular genetics have made possible the creation of tailored therapies based on specific molecular targets, with various degrees of success. This review provides an overview of the latest advances in the fields of histopathology and radiogenomics and the use of molecular markers for management of glioblastoma, as well as the development of new therapies targeting the most common molecular markers. Furthermore, we offer a summary of the results of recent preclinical and clinical trials to recognize the current trends of investigation and understand the possible future directions of molecular targeted therapies in glioblastoma.

Evaluating tomato lines resistance to Late Blight and molecular genetic screening with the use of molecular markers

Relevance. Tomato late blight caused by Phytophthora infestans can cause almost 100% yield loss in open ground in cool and humid conditions. At the same time, the genetic characteristics of P. infestans allow it to overcome the genetic resistance of host plants over time, which requires breeders to look for new genes for resistance to late blight and to obtain new varieties that have several resistance genes at once.Material and methods. 12 tomato lines, or a total of 335 plants, were obtained from the N.N. Timofeev breeding station collection and planted in an artificially infected background. For molecular genetic screening, 12 plants from the Kr6 line were used. The markers linked to the late blight resistance genes Ph-3, R1, and R3a were utilized.Results. On an artificial infectious background, phenotypic evaluation of tomato resistance to late blight showed 1 line of plants free of pathogen damage, 5 lines of plants fully afflicted by late blight, and 6 lines with only partial plant damage. According to molecular genetic investigation the resistant plants were heterozygotes for the Ph-3 gene. Furthermore, the R1 gene was present in most of the plants under study; but, without the Ph-3 gene, this gene did not provide plant resistance against late blight.Conclusions. The results of this research led to the selection of tomato plants for further breeding that were resistant to late blight. It was shown that markers linked to the Ph-3 and R1 genes might be used for marker-mediated selection. Furthermore, it has been established that tomato plants are more effectively protected against P. infestans when several resistance genes are present.

7355 A Case of High-Risk Thyroid Tumor Markers Found in Subcutaneous Thyroid Implants in a Patient with Benign Thyroid Pathology

Abstract Disclosure: J. Fedorko: None. S. Fatima: None. A.P. Amblee: None. C.A. Poku: None. Background: While fine needle aspiration (FNA) remains the primary diagnostic tool for thyroid malignancies, the utilization of molecular markers has become increasingly common in the workup of thyroid nodules. They play a useful role in distinguishing between malignant and benign pathology when cytology is indeterminate and in formulating treatment plans. The vast majority of research for these genetic markers is conducted in cases with thyroid malignancy. However, there have been numerous cases where these genetic markers were identified in benign thyroid tissue. Case: A 73-year-old male with left hemithyroidectomy (benign left nodule) presented 6 years later with new superficial neck nodules along the midline, left thyroid bed and R thyroid lobe. FNA of the right thyroid nodule was benign. Three months later the patient underwent an excision of the midline neck nodules which revealed thyroid tissue arranged in nests of fibrotic tissue without definite features of papillary thyroid carcinoma. Molecular analysis (Thyroseq) was positive for HRAS, E1F1AX and TERT mutations thus metastatic follicular carcinoma was suspected. The patient underwent complete thyroidectomy. Pathology revealed normal thyroid tissue and a diagnosis of thyroid neck implants was made. Given the benign pathology, the plan was for close follow-up with neck imaging every 6 months. Discussion: Thyroid tissue implants can rarely be caused by previous surgical interventions, especially partial thyroidectomy. There is literature documenting similar clinical cases in which subcutaneous thyroid implants are found in patients after undergoing total or subtotal thyroidectomy. In one case series, there were cases in which thyroid implants were discovered 26 years post-surgery, with most of the cases reporting benign pathology. Given our patient’s presentation and clinical history, the possibility remains that his subcutaneous tissue findings were caused by his prior partial thyroidectomy. A recent article reviewed 60 publications and >8000 patients for the prevalence of high-risk tumor markers (RAS mutation, RET/PTC, and PAX8/PPAR-gamma chromosomal rearrangements) in benign thyroid tissue. They concluded that prevalence findings were highly variable, warning providers to exercise caution when using these genetic markers to guide diagnosis and treatment decisions. Conclusion: While certain high-risk genetic tumor markers are increasingly used to help identify thyroid malignancies, it is important to keep in mind that these genetic markers are not exclusively found in cancerous tissue, and should not be used as the sole diagnostic tool for diagnosis and treatment. While it is imperative that metastatic disease is ruled out, it is essential to consider other pathologies when evaluating recurrent thyroid and neck masses in patients with a history of benign thyroid lesions. Presentation: 6/3/2024

A search for tomato disease resistance genes using molecular markers to create new genotypes

Background. The creation of tomato cultivars and hybrids with a complex of resistance genes is the main task of a breeder. This process can be accelerated through the use of molecular markers at the stages of initial forms selection and the offspring analysis. There is a large amount of information in the literature about DNA markers of resistance genes. Their significant part was recommended for the use in marker-assisted breeding. The purpose of our work was to screen a collection of tomato varieties and hybrids using molecular markers of genes for resistance to the most common diseases of open-ground tomato (late blight, root nematodes, tomato bronzing virus (TSWV)) and to identify gene sources for breeding work. The following markers were selected for research: Sw-5-2 (Sw-5b gene of resistance to TSWV), Mi23 (Mi1.2 gene of resistance to the root-knot nematode), 2 markers NC-LB-9-78 and NC-LB-9-79 (late blight resistance gene Ph-3). During the work, a collection of 46 accessions of tomato cultivars and hybrids was analyzed. Results. The molecular genetic analysis has yielded clear, reproducible fragments that corresponded to the expected ones. All the used markers were codominant. Analysis of the studied collection accessions found the analyzed genes to be polymorphic. The cultivars and hybrids F1 of tomato identified as promising for the use in breeding have resistance to root nematodes (F1 hybrids: A-01, ‘Imitator’, ‘Manon’, cultivars ‘Elegiya’ and ‘Buoy-Tur’), to tomato spotted wilt virus (TSWV) (F1 hybrids: A-01, ‘Manon’ and cultivar ‘Buoy-Tur’), and also to late blight (hybrids F1: А-01, ‘Azhur’, ‘Barin’, ‘Vlastelin stepej’, ‘Zhirdyaj’, Luchshij SeDeK, ‘Manon’ and cultivars: ‘Buoy-Tur’, ‘Zefir v shokolade’, ‘Zolotaya kaplya’, ‘Krasavec’, ‘Lodochka’, ‘Metelitsa’, ‘Alice's Dream’, ‘Sibirskij tigr’, ‘Slavyanskij shedevr’, ‘Elegiya’). It is advisable to use these accessions as sources of resistance genes. Based on the obtained data, five initial forms were selected for breeding and assessed for the intracultivar polymorphism of the studied genes. Cultivars ‘Krasavec’ and ‘Sibirskij tigr’ were used as parent forms. Their hybridization was carried out and hybrid forms homozygous for the dominant allele of the Ph-3 gene were obtained. Conclusions. The use of molecular markers in the conducted study allowed screening the collection of tomato varieties and hybrids for the presence of resistance genes to the most common diseases. Based on the obtained data, parental pairs were selected, hybridization carried out, and hybrid forms with the late blight resistance gene obtained.

Advances in Artemisinin Resistance: Mechanisms, Detection, and Novel Therapeutic Approaches

Artemisinin-based combination therapies (ACTs) have been instrumental in reducing global malaria mortality over the past two decades. However, the rise of artemisinin resistance, particularly in Southeast Asia and parts of Africa, threatened these gains. Artemisinin resistance was characterized by delayed parasite clearance and is primarily driven by mutations in the kelch13 (K13) gene, which reduce the drug’s efficacy. This review explored the mechanisms behind artemisinin resistance, including genetic mutations, parasite stress responses, and reduced ring-stage sensitivity. Detection strategies, such as the use of molecular markers like K13 mutations and in vitro phenotypic assays, were discussed in detail. To combat resistance, novel therapeutic approaches were emerging, including the optimization of ACTs, the use of triple-drug regimens, host-directed therapies, and gene-editing technologies. The article highlighted the need for new antimalarial drugs, improved diagnostic tools, and global collaboration to address this growing challenge. We conducted the review by analyzing recent literature and summarizing advances in both resistance mechanisms and therapeutic strategies. Finally, future directions were outlined, emphasizing the importance of research, regulatory frameworks, and investment to mitigate the spread of resistance and ensure effective malaria control. Keywords: Artemisinin resistance, K13 mutations, malaria treatment, combination therapies, gene editing, host-directed therapies.

Identification of Capsicum species from Colombia by DNA barcoding and high resolution melting (HRM) analysis

AbstractDNA barcoding allows the use of molecular markers to differentiate the species of an interest group. This is especially useful when morphological characters are insufficient due to high similarity between species. The genus Capsicum contains some species that are difficult to determine by taxonomic means, in particular the annuum complex. Thus, the objective of this study was to investigate the discriminatory ability of two molecular markers in Colombian Capsicum accessions, including three wild species belonging to the Andean clade of the genus. A total of 95 Capsicum accessions, representing eight species, were genotyped by high resolution melting analysis (HRM) using the Waxy and C2_At5g04590 markers. Waxy could discriminate the Andean clade species (C. rhomboideum, C. dimorphum and C. lycianthoides), C. baccatum, C. pubescens and C. chinense, while C2_At5g04590 could discriminate C. frutescens, C. annuum var. annuum and C. annuum var. glabriusculum. Hence, a combination of the two markers could be used for discrimination of the eight species including the wild variety of C. annuum: C. annuum var. glabriusculum. Most nucleotide substitutions and indels were found in the sequences of the three Andean species, indicating that the Andean clade has a high genetic diversity compared to the other species. The incorporation of more wild species and varieties in this study allowed to correct the power of both markers to discriminate Capsicum species, besides the registration of new haplotypes.

Выявление патогенов картофеля с использованием различных методов диагностики

Abstract. Potato diseases have far reaching implications for the agricultural industry as they not only reduce productivity and quality of potato crop but also negatively affect the livelihood of farmers. The purpose of the studies detection and identification of potato phytopathogens by visual assessment, real time polymerase chain reaction (PCR) and molecular genetic screening for phytopathogen resistance genes. Methods. Visual evaluation of each potato variety for major fungal, viral and bacterial diseases was carried out during the period of full sprouting, at plant height of 15–20 cm and in the phase of full flowering. The percentage of plants affected by diseases in relation to the total number of inspected plants was calculated. Diagnosis of resistance of potato samples to diseases was carried out on the basis of PCR. DNA markers of phytopathogen resistance genes YES3-3A, RYSC3, Ry186, TG 689, Gro1-4-1, Gpa2-2, PVX were used for molecular screening of potato. Infection of samples by PCR-RV (real-time) was determined using reagent kits of Syntol LLC Potato Virus X and Potato Virus Y, Potato spindle tuber viroid-PB, Clavibacter michiganensis subsp. sepedonicus-PB, Dickeya spp-PB. Results. According to the results of visual evaluation, the absence of symptoms of wrinkle mosaic in 20% of hybrids, mottle mosaic in 40%, mosaic leaf curl in 96 %, leaf curl in 72 hybrids, black leg in 100%, phytophthorosis in 88% of hybrids, alternaria in 84 %, rhizoctoniosis in 96 % of hybrids were observed. According to the results of PCR-RV analysis in 21 samples detected virus Y. The scientific novelty consists in the diagnosis of potato viruses using traditional visual assessment with the use of molecular markers that allow to identify correlation relationship between trhis methods.

Molecular Marker Applications in the Selection of Elite Genotypes for Plant Stress Tolerance and Genetic Fidelity

Molecular markers play a crucial role in accelerating crop production for sustainable agriculture by identifying resistant traits and enhancing genetic diversity. In this review, we examine the impact of the molecular markers on advancing our understanding of stress tolerance mechanisms in plants, addressing the pressing imperative to bolster global food production to meet the escalating demands of the growing population. Additionally, the application of molecular markers to evaluate the genetic accuracy of plants due to genetic changes caused by somaclonal variation during <em>in vitro</em> propagation is mentioned. Specifically, we highlight emerging technologies like MAS, MARS, MABC, GWAS, GS, DH production, speed breeding, and genome editing, which offer promising opportunities to enhance stress tolerance and genetic integrity in crop cultivars, aiding in addressing global food security challenges. The literature search focused on studies published in the last ten years. We utilized a combination of specific and broad keywords such as genetic stability, <em>in vitro</em> propagation, molecular markers, abiotic-biotic stress, and plant biotechnology. In conclusion, this review analyzes the use of molecular markers in assessing the stress tolerance and genetic fidelity of <em>in vitro</em> grown plants.

Role of molecular markers in identifying genetic disorders

Molecular markers are critical tools in identifying genetic disorders, allowing for precise diagnosis, risk assessment, and personalized treatment approaches. They are classified into various categories, including single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), and restriction fragment length polymorphisms (RFLPs), each serving distinct roles in genetic diagnostics. SNPs are widely used in genome-wide association studies (GWAS) to identify genetic predispositions to complex diseases, while STRs are valuable in diagnosing disorders like Huntington's disease. RFLPs, though less commonly used today, remain important in specific diagnostic contexts. The application of molecular markers spans a wide range of genetic disorders, from monogenic conditions such as cystic fibrosis (CF) to complex diseases like hereditary breast and ovarian cancer syndrome and fragile X syndrome. These markers enable early detection and targeted interventions, improving patient outcomes. However, several challenges hinder their widespread adoption, including difficulties in interpreting genetic data, limited access to genetic screening, and ethical concerns related to privacy and genetic discrimination. Future directions in the use of molecular markers for genetic screening involve integrating advanced technologies like next-generation sequencing and combining molecular data with other omics approaches to provide a more comprehensive understanding of genetic disorders. Addressing the challenges of data interpretation, accessibility, and ethical issues will be crucial in expanding the utility of molecular markers in clinical practice. The advancements in molecular marker technology and their applications in detecting specific genetic disorders hold promise for improving diagnostic accuracy and personalized treatment strategies. However, ensuring that these technologies are accessible and ethically implemented will be key to their success in transforming healthcare. The ongoing evolution of molecular markers and genetic screening technologies suggests a future where early diagnosis and personalized medicine become standard care for genetic disorders.

Identification of QTLs and candidate genes for water-soluble protein content in soybean seeds

Soybean represents a vital source of premium plant-based proteins for human nutrition. Importantly, the level of water-soluble protein (WSP) is crucial for determining the overall quality and nutritional value of such crops. Enhancing WSP levels in soybean plants is a high-priority goal in crop improvement. This study aimed to elucidate the genetic basis of WSP content in soybean seeds by identifying quantitative trait loci (QTLs) and set the foundation for subsequent gene cloning and functional analysis. Using 180 F10 recombinant inbred lines generated by crossing the high-protein soybean cultivar JiDou 12 with the wild variety Ye 9, our researcher team mapped the QTLs influencing protein levels, integrating Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene expression profiling to identify candidate genes. During the 2020 and 2022 growing seasons, a standard bell-shaped distribution of protein content trait data was observed in these soybean lines. Eight QTLs affecting protein content were found across eight chromosomes, with LOD scores ranging from 2.59 to 7.30, explaining 4.15–11.74% of the phenotypic variance. Notably, two QTLs were newly discovered, one with a elite allele at qWSPC-15 from Ye 9. The major QTL, qWSPC-19, on chromosome 19 was stable across conditions and contained genes involved in nitrogen metabolism, amino acid biosynthesis, and signaling. Two genes from this QTL, Glyma.19G185700 and Glyma.19G186000, exhibited distinct expression patterns at maturity, highlighting the influence of these genes on protein content. This research revealed eight QTLs for WSP content in soybean seeds and proposed a gene for the key QTL qWSPC-19, laying groundwork for gene isolation and enhanced soybean breeding through the use of molecular markers. These insights are instrumental for developing protein-rich soybean cultivars.

Characterization of Lithuanian Tomato Varieties and Hybrids Using Phenotypic Traits and Molecular Markers.

The aim of this study was to evaluate phenotypic traits and genetic diversity of the 13 tomato (Solanum lycopersicum L.) varieties and 6 hybrids developed at the Institute of Horticulture Lithuanian Research Centre for Agriculture and Forestry (LRCAF IH). For the molecular characterisation, seven previously published microsatellite markers (SSR) were used. A24 and 26 alleles were detected in tomato varieties and hybrids, respectively. Based on the polymorphism information content (PIC) value, the most informative SSR primers for varieties were TMS52, TGS0007, LEMDDNa and Tom236-237, and the most informative SSR primers for hybrids were SSR248 and TMS52. In UPGMA cluster analysis, tomato varieties are grouped in some cases due to genetic relationships, as the same cluster cultivars 'Viltis' (the parent of cv. 'Laukiai') and 'Aušriai' (the progeny of cv. 'Jurgiai') are present. The grouping of all hybrids in the dendrogram is related to the parental forms, and it shows the usefulness of molecular markers for tomato breeding, as they can be used to trace the origin of hybrids and, eventually, varieties accurately. The knowledge about the genetic background of Lithuanian tomato cultivars will help plan targeted crosses in tomato breeding programs.

Classification and prediction of drought and salinity stress tolerance in barley using GenPhenML

Genetic and agronomic advances consistently lead to an annual increase in global barley yield. Since abiotic stresses (physical environmental factors that negatively affect plant growth) reduce barley yield, it is necessary to predict barley resistance. Artificial intelligence and machine learning (ML) models are new and powerful tools for predicting product resilience. Considering the research gap in the use of molecular markers in predicting abiotic stresses, this paper introduces a new approach called GenPhenML that combines molecular markers and phenotypic traits to predict the resistance of barley genotypes to drought and salinity stresses by ML models. GenPhenML uses feature selection algorithms to determine the most important molecular markers. It then identifies the best model that predicts atmospheric resistance with lower MAE, RMSE, and higher R2. The results showed that GenPhenML with a neural network model predicted the salinity stress resistance score with MAE, RMSE and R2 values of 0.1206, 0.0308 and 0.9995, respectively. Also, the NN model predicted drought stress scores with MAE, RMSE and R2 values of 0.0727, 0.0105 and 0.9999, respectively. The GenPhenML approach was also used to classify barley genotypes as resistant and stress-sensitive. The results showed that the accuracy, accuracy and F1 score of the proposed approach for salinity and drought stress classification were higher than 97%.

The Kirkhouse Trust: Successes and Challenges in Twenty Years of Supporting Independent, Contemporary Grain Legume Breeding Projects in India and African Countries.

This manuscript reviews two decades of projects funded by the Kirkhouse Trust (KT), a charity registered in the UK. KT was established to improve the productivity of legume crops important in African countries and in India. KT's requirements for support are: (1) the research must be conducted by national scientists in their home institution, either a publicly funded agricultural research institute or a university; (2) the projects need to include a molecular biology component, which to date has mostly comprised the use of molecular markers for the selection of one or more target traits in a crop improvement programme; (3) the projects funded are included in consortia, to foster the creation of scientific communities and the sharing of knowledge and breeding resources. This account relates to the key achievements and challenges, reflects on the lessons learned and outlines future research priorities.

Development and application of molecular markers in fisheries, aquaculture, and industry of representative temperate and tropical sea cucumbers: a review

Sea cucumber has emerged as a crucial economic species in aquaculture in China because of its remarkable nutritional and medicinal value. However, wild sea cucumber populations have experienced a decline due to overfishing and environmental factors, underscoring the urgent need for genetic resource conservation and biotechnology innovation within the sea cucumber aquaculture and breeding industry. The development of the sea cucumber industry is still impeded by challenges and difficulties. Nevertheless, significant progress has been made through the utilization of molecular markers, which have effectively addressed a number of fisheries and aquaculture issues. In recent years, diverse types of molecular markers including mitochondrial DNA, microsatellites, and SNP markers have been developed and extensively applied in various aspects of sea cucumber research. These markers play vital roles in genetic sex identification, germplasm resource evaluation, population structure assessment, as well as marker-assisted breeding in marine ranching and sea cucumber aquaculture and breeding industry. This review provides an overview of the fundamental principles, functions, and characteristics associated with various markers employed across various sea cucumber species while also discussing their applications within different aspects of the sea cucumber fisheries, aquaculture, and breeding industry.

Phenotypic characterization of cryptic species in the fungal pathogen Histoplasma.

Histoplasmosis is an endemic mycosis that often presents as a respiratory infection in immunocompromised patients. Hundreds of thousands of new infections are reported annually around the world. The etiological agent of the disease, Histoplasma, is a dimorphic fungus commonly found in the soil where it grows as mycelia. Humans can become infected by Histoplasma through inhalation of its spores (conidia) or mycelial particles. The fungi transition into the yeast phase in the lungs at 37°C. Once in the lungs, yeast cells reside and proliferate inside alveolar macrophages. Genomic work has revealed that Histoplasma is composed of at least five cryptic phylogenetic species that differ genetically. Three of those lineages have received new names. Here, we evaluated multiple phenotypic characteristics (colony morphology, secreted proteolytic activity, yeast size, and growth rate) of strains from five of the phylogenetic species of Histoplasma to identify phenotypic traits that differentiate between these species: Histoplasma capsulatum sensu stricto, Histoplasma ohiense, Histoplasma mississippiense, Histoplasma suramericanum, and an African lineage. We report diagnostic traits for three species. The other two species can be identified by a combination of traits. Our results suggest that (i) there are significant phenotypic differences among the cryptic species of Histoplasma and (ii) those differences can be used to positively distinguish those species in a clinical setting and for further study of the evolution of this fungal pathogen.IMPORTANCEIdentifying species boundaries is a critical component of evolutionary biology. Genome sequencing and the use of molecular markers have advanced our understanding of the evolutionary history of fungal pathogens, including Histoplasma, and have allowed for the identification of new species. This is especially important in organisms where morphological characteristics have not been detected. In this study, we revised the taxonomic status of the four named species of the genus Histoplasma, H. capsulatum sensu stricto (ss), H. ohiense, H. mississippiense, and H. suramericanum, and propose the use of species-specific phenotypic traits to aid their identification when genome sequencing is not available. These results have implications not only for evolutionary study of Histoplasma but also for clinicians, as the Histoplasma species could determine the outcome of disease and treatment needed.

Studies of Molecular Marker in Sunflower (Helianthus annus L.)

Helianthus annus L., known as sunflower, is belong to Asteraceae family. This family is one of the biggest angiosperm plant families in between dicotyledons and cultivated sunflower is an important oil plant all around the world. Chloroplast DNA analysis reveals that the origin of the genus dates back to 4.75 to 22.7 million years ago. Sunflower seeds contain 18% protein, 15% cellulose, 9% water, 14% minerals and carbohydrates. In general, sunflower seeds contain 35% to 50% oil by weight. The oil content of sunflower had been specified from 36.9% to 50.2%. These features have made sunflower an important plant worldwide. In principle, the breeding of sunflowers aims to improve the oil content and to get a plant resistant to disease. All breeding methods both classical and biotechnological methods try to contribute these aims. With the help of technology DNA markers have provided useful information about polymorphism, genetic relatedness, and diversity. Technology advances in breeding, especially the use of molecular markers, offer new strategies to obtain high-yielding and resistant plants through DNA sequences located at a known location on the chromosome. Sunflower has been a model plant in Asteraceae family in molecular marker studies because of its economic importance. Many molecular marker studies have been conducted against biotic and abiotic stress conditions, increase oil content and nutritional value, and water consumption etc. Considering its economic value, current studies on the plant will shed light on future studies and improvements can be observed in many yield criteria such as water consumption, harvest efficiency, resistance to pests.

Determining the Relationships Between Genotype and Phenotype Using Molecular Genetic Tools in Chickens

Context: Chicken meat is one of the rich sources of protein and is considered one of the most commonly consumed meats in the world. Enhancing poultry production and its products is achievable through chicken breeding. Effective breeding projects for future genetic improvement require an understanding of the genetic potential of a given population. Evidence Acquisition: Articles were selected based on novel molecular markers related to economic traits of chicken in Animal quantitative trait loci (QTL) database, Ensemble genome browser, CorrDB, ChickVD, Galbase, and Google Scholar. These databases contain QTLs, markers, and reference genomes of chicken. Galbase provides research communities with updated possibilities to conduct thorough functional genomics research on chickens. ChickVD manages high-quality sequence variation data, variation analysis in relation to chicken genes, cDNAs, genetic markers, and QTLs. CorrDB compiles all available chicken genetic and phenotypic trait correlation data to aid in the analysis of genetic networks and facilitate systems biology research. Animal Quantitative Trait Loci Database (Animal QTLdb) gathers and compiles all existing data on trait mapping, including QTL (phenotype/expression, eQTL), candidate gene, association data (GWAS), and copy number variations (CNV) for livestock animal genomes. This comprehensive database facilitates the easier identification and comparison of discoveries within and across species. Ensemble genome browser is a powerful tool for analyzing vertebrate genomes, offering valuable insights into comparative genomics, evolutionary processes, sequence variations, and transcriptional regulation. Results: Valuating the relatedness of the studied broilers and layers is important for maintaining and improving the genetic reserves of the same population. Candidate genes (CGs) are used to determine genes related to economic traits in chickens. Molecular genetic techniques such as whole-genome re-sequencing (WGRS) can identify single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (indels), structural variations (SV), CNV, and simple sequence repeats (SSRs) and their chromosomal regions in terms of QTL. Recently, the pan-genome (PG) has become one of the most important tools to study genome variation and changes in important traits. The use of molecular markers and CGs can aid in evaluating the genetic relationships between phenotype and genotype of broilers and layers. Conclusions: This review introduces molecular genetic methods and new approaches to identify novel genes related to important biological pathways and significant production and reproductive traits.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus.

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.

Enhancement of aquaculture performance of cobia, Rachycentron canadum (Linnaeus 1766): A review

Cobia, Rachycentron canadum, is a marine fish with recognized potential for aquaculture due to its fast growth rate, high fecundity, disease resistance, and quality flesh. However, much progress has been made to overcome problems associated with aspects of cobia production, including broodstock management, fingerling production, larval-rearing, grow-out, and disease management, though, an effort is needed to ensure its sustainability. Broodstock conditioning protocols for continuous spawning as well as induced spawning via hormonal injection resulted in all-year-round seed production in cobia, but detailed information on the cost-effective dosages of various spawning hormones for maximum fecundity and larval survival needs to be investigated. Selective breeding, the application of genetics in trait selection, and the use of molecular markers could produce more viable strains to mitigate high mortality, particularly in colder climates. In addition, considering the fact cobia are carnivorous fish with a high protein requirement, it will be necessary to investigate fishmeal alternatives to reduce feeding costs. Low salinity pond culture may become a reality in the future if the cobia metabolism-physiology of nutrition at various levels of salinity is well understood. The present paper provides information on some of the options for optimizing the aquaculture performance of Rachycentron canadum.