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Context. Researchers have been accumulating information concerning the locations of genes and quantitative trait loci (QTLs) in cultivated oat (Avena sativa L.) for more than 100 years. Aims. The aim of this work was to create an inventory of genes and QTLs found in cultivated hexaploid oat and produce tools to make this resource more useful. Methods. By using the positions of perfectly matched, single nucleotide polymorphism markers, each centimorgan (cM) location along the consensus map was assigned to a location on the OT3098 v2 physical map found on the GrainGenes database website (https://wheat.pw.usda.gov/jb/?data=/ggds/oat-ot3098v2-pepsico). This information was then used to assign physical locations to the genes and QTLs in the inventory, where possible. Key results. A table comparing the major genetic maps of hexaploid oats to each other, to the 2018 oat consensus map, and to physical chromosomes was produced. Genome browser tracks aligning the consensus map regions and the locations of the genes and QTLs to OT3098 v2 were added to GrainGenes. Conclusions. Many oat genes and QTLs identified using genetic mapping could be assigned positions on physical oat chromosomes. However, many of these assigned regions are quite long, owing to the presence of large areas of reduced recombination. Specific examples of identified patterns of recombination between the genetic and physical maps and validated gene and QTL locations are discussed. Implications. These resources will assist researchers performing comparative genetic and physical mapping in oat.

Pterocarpus santalinus L.f. is an endangered tree species that is cherished worldwide for its valuable deep red-colored heartwood, which has multiple uses. This species exhibits a wide range of medicinal properties and offers immense potential for the discovery of bioactive compounds of pharmacological importance. The overharvesting of this species for heartwood has led to a gradual decline in its natural populations, thereby depleting its genetic resources and contributing to the loss of genetic diversity. Therefore, it is essential to assess genetic diversity, as such information allows for the effective conservation and utilization of genetic resources. In the present study, the genetic diversity and population structure among 40 germplasm accessions originating from 8 populations of P. santalinus were analyzed using six cross-species simple sequence repeats (SSR), 20 each of inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers. SSR markers revealed higher polymorphism (100 %), followed by ISSRs (82.81 %) and RAPDs (67.50 %), across all the accessions. The mean values of the polymorphic information content (PIC), effective multiplex ratio (EMR), and marker index (MI) were higher for SSRs (0.84, 9.17, and 7.7), followed by ISSRs (0.262, 4.474, and 1.251) and RAPDs (0.204, 3.268 and 0.970, respectively), indicating the superiority of SSRs in detecting polymorphisms in red sanders. Similarly, the estimates of Nei's gene diversity (H) and Shannon's information index (I) varied across the studied accessions, with the highest values for SSRs (H = 0.528, I = 0.923), followed by ISSRs (H = 0.287, I = 0.428) and RAPDs (H = 0.206, I = 0.307). However, the genetic statistic (Gst) or fixation statistic (Fst) and gene flow (Nm) values were higher for RAPDs (0.455 and 0.598) and ISSRs (0.446 and 0.620) than for SSRs (0.383 and 0.489, respectively), indicating significant genetic differentiation of the populations and moderate gene flow among the populations. Analysis of molecular variance (AMOVA) with SSR, ISSR, and RAPD markers revealed that a greater proportion of genetic variation resided within populations (74 %, 69 %, and 66 %, respectively) than among populations (26 %, 31 %, and 34 %, respectively). Hierarchical clustering on the basis of RAPDs grouped most of the accessions according to the population of origin; however, this clustering was different for the ISSR and SSR markers. STRUCTURE analysis divided the accessions into four, two, and three groups with SSR, ISSR, and RAPD markers, respectively, with admixtures detected in all the groups pointing toward shared genetic lineages and diverse genetic ancestry among the accessions of different populations. Overall, the populations of Gumudipoondi of Tamil Nadu and K.V. Bhavi of Andhra Pradesh were genetically more diverse than other populations, as revealed by genetic diversity estimates obtained with SSR and ISSR marker systems; therefore, the accessions of these populations must be prioritized for conservation and utilization in breeding programs for genetic improvement. [Display omitted] • Genetic diversity was assessed among 40 accessions of P. santalinus using 6 cross-species SSR, 20 each of ISSR and RAPD primers. • Cross-species SSRs were more efficient in detecting genetic diversity in the studied populations than ISSRs and RAPDs. • The populations of Gumidipoondi of Tamil Nadu (GTN) and K.V. Bhavi of Andhra Pradesh (KAP) exhibited higher genetic diversity than other populations according to SSR and ISSR marker analysis. • Analysis of molecular variance with SSR, ISSR and RAPD markers showed that genetic variations within populations (74 %, 69 % and 66 %) were greater than among populations (26 %, 31 % and 34 %). • STRUCTURE analysis using SSR, ISSR and RAPD markers divided the populations into four, two and three genetic groups, respectively, with admixtures detected in all genetic groups. [ABSTRACT FROM AUTHOR]

Molecular studies have contributed to the taxonomy of carrageenan-producing Kappaphycus spp. and Eucheuma denticulatum. However, unresolved species complexes and the lack of standardization in the use of genetic markers impede the identification of specimens and the delineation of a robust taxonomic framework. Here, nine molecular markers (cox1, cox2–3 spacer, cox2, cox3, COB, ITS, psbA, UPA and rbcL) were used to generate a multilocus phylogeny for 113 fresh eucheumatoid samples and four herbarium specimens. Analyses of species delineation and genetic distances confirmed the monophyly of currently accepted taxa. These analyses suggest that clades previously reported as K. striatus KS1 and KS2 are conspecific, and that E. denticulatum EDA 'spinosum' and EDB 'endong/cacing' are also conspecific. The results also unveiled possible new taxa from Hawaii and Indonesia. Each molecular marker and combinations thereof were assessed with regard to species identification, ease of amplification and sequencing, and haplotype characterization. All genetic markers recorded at least 94% success in the amplification and sequencing of fresh specimens, with cox1 being the most phylogenetically informative. Automatic partitioning, phylogenetic and tree-based assessments showed cox1, cox2–3 spacer, cox2 and rbcL were able to correctly identify species while cox1+ rbcL, COB+rbcL, cox2+ rbcL or cox1+ COB+rbcL trees best represented the phylogeny with consistently high nodal support. Among individual markers, cox1 identified the greatest number of haplotypes, while UPA, partial rbcL (750 bp), ITS, cox3 and cox2–3 spacer were able to retrieve information from herbarium specimens of 12–16 years of age. These molecular results provide a basis for a database essential for the taxonomic framework, cultivar development and germplasm conservation of eucheumatoids. Highlights: Mitochondria cox1, cox2–3 spacer, cox2 and plastid rbcL can be used for species identification and cox1 for haplotype detection of eucheumatoids. cox1+rbcL, COB+rbcL, cox2+rbcL or cox1+COB+rbcL are the most cost-effective molecular markers for phylogenetic inference. The most comprehensive up to date multilocus phylogeny of Kappaphycus spp. and Eucheuma denticulatum is presented. [ABSTRACT FROM AUTHOR]

The article "Exploring biodiversity of Uruguayan vascular plants through DNA barcoding" published in Frontiers in Genetics on October 15, 2024, discusses the use of DNA barcoding to study the biodiversity of Uruguayan vascular plants. The study aims to address the decline in biodiversity in Uruguay by establishing a DNA barcode national network. By analyzing 171 sequences from four loci for 50 vascular plant species, the researchers identified suitable markers for plant DNA barcoding and contributed to the Uruguayan Barcode of Life Initiative. The study highlights the importance of creating a comprehensive public database for species identification and biodiversity research. [Extracted from the article]

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part of the taxonomically challenging genus Desmidorchis, are well‐known for their ecological resilience and medicinal significance. This study sequences the first complete chloroplast genomes of these species, shedding light on their genomic characteristics and evolutionary relationships. The circular genomes of D. penicillata (161 776 bp) and D. retrospiciens (162 277 bp) display a quadripartite structure typical of Angiosperms. Gene content, order, and GC content are consistent, featuring 114 unique genes, including 80 protein‐coding, 30 transfer RNAs, and four ribosomal RNAs genes. Codon usage analysis underscores A/U‐rich preferences, while RNA editing sites, predominantly in ndhB and ndhD genes, suggest post‐transcriptional modifications. Analysis of long repeated sequences reveals a predominance of forward and palindromic repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are abundant, with high presence of mononucleotide, offering potential molecular markers. Comparative analysis with their relatives in subtribe Stapeliinae identifies mutational hotspots such as ycf1, ndhF, trnG(GCC)‐trnfM(CGA) and ndhG‐ndhI that could be potential DNA barcoding markers. The inverted repeat (IR) boundaries analysis revealed an expansion of IR on the small single copy region, leading to the formation of a pseudogene. Overall, substitution rate analysis indicated purifying selection, with a few genes (rpl22, clpP and rps11) showing signatures of positive selection. Additionally, the phylogenetic analysis positioned Desmidorchis within the Stapeliinae clade and strongly supported the sister relationship between D. penicillata and D. retrospiciens. This study provides comprehensive molecular data for future research in Desmidorchis. [ABSTRACT FROM AUTHOR]

Sugar beet is an economically significant crop, and the homozygosity of paired monogerm cytoplasmic male sterile (CMS) and maintainer lines directly influences the number of hybrid combinations that can be created. This study aimed to evaluate the genetic variation within monogerm sugar beet germplasm resources to establish a foundation for advancements in sugar beet breeding and the development of hybrid female parent lines. This study analyzed the genetic diversity of 86 distinct monogerm germplasm resources, including 38 paired monogerm CMS and maintainer lines, 5 individual maintainer lines, and 5 externally introduced sterile lines. The analysis employed 26 pairs of SSR primers and 35 pairs of InDel primers across nine sugar beet chromosomes. Several genetic parameters, and analyses such as structural analysis, genetic diversity analysis, and principal coordinate analysis, were used to evaluate the samples. The results indicated that these strains could be classified into two groups: Group I and Group II. Group I was further divided into three subgroups. Further, 18 pairs of original CMS and maintainer lines were successfully clustered, confirming that their nuclei had achieved homozygosity, making them suitable for use in the development of binary sterile lines. However, 20 other pairs still require further backcrossing to achieve homozygosity. The analysis of molecular variance (AMOVA) revealed that most of the genetic variation occurred within individuals, with relatively low genetic differentiation between groups. Significant genetic differentiation was observed between Subgroups 2 and 3, and between Subgroups 1 and 3. The results suggest that additional monogerm sterile and maintainer lines from these subgroups should be selected to configure binary sterile lines. This study offers a theoretical foundation for developing new sugar beet germplasm resources and cultivating hybrid mother plants. [ABSTRACT FROM AUTHOR]

Deciphering the genetic mechanisms underlying key agronomic and quality traits in potato (Solanum tuberosum L.) is essential for advancing varietal improvement. Phenotypic instability in early clonal generations and inbreeding depression, coupled with the complexity of tetrasomic inheritance, pose significant challenges in constructing mapping populations for the genetic dissection of complex traits. Genome-wide association studies (GWASs) offer an efficient method to establish trait–genome associations by analyzing genetic recombination and mutation events in natural populations. This review systematically examines the application of GWASs in identifying agronomic traits in potato, such as plant architecture, yield components, tuber shape, and resistance to early and late blight and nematodes, as well as quality traits including dry matter, starch, and glycoalkaloid content. Some key chromosomal hotspots identified through GWASs include chromosome 5 associated with tuber yield, starch content, and late blight resistance; chromosome 4 and 10 associations with tuber shape and starch content; chromosomes 1, 9, and 11 associated with plant height, tuber number, glycoalkaloid content, and pest resistance. It elucidates the advantages and limitations of GWASs for genetic loci identification in this autotetraploid crop, providing theoretical insights and a reference framework for the precise localization of key genetic loci and the discovery of underlying genes using GWASs. [ABSTRACT FROM AUTHOR]

Characterizing the genetic diversity of a species is crucial for understanding the factors that influence its local dispersion and population dynamics. Additionally, it provides insights into local processes that may affect the distribution of other species. Lineus sanguineus (Rathke, 1799) is a widely distributed species commonly found on fouling fauna along rocky shores. This species can reproduce asexually by fissiparity, and its pilidium larva facilitates dispersal, similar to other heteronemerteans. The present study utilized a population genetics approach combined with Ecological Niche Modeling analysis to evaluate L. sanguineus populations along the Brazilian coast. We used sequences from two mtDNA regions, 16S ribosomal RNA (16SrRNA) and cytochrome c oxidase subunit 1 (COI), and one nuclear region, Internal Transcribed Spacer 1 (ITS-1), from 85 specimens sampled in nine locations. Genetic diversity analysis revealed greater genetic variation for the ITS-1 marker compared to mtDNA, as evidenced by higher intrapopulation diversity values. There was no clear geographic pattern, and the AMOVA analysis revealed low to moderate genetic structuring and high connectivity among sampled localities, with most of the genetic variation contained within populations. The pairwise FST results indicate high genetic structuring between the Northeast and localities along the South and Southeast of Atlantic coastlines. This pattern suggests that Brazilian oceanic currents play an important role in species connectivity. The paleodistribution pattern demonstrated that the colonization could have occured from the South to the Northeast of the continent. These results reinforce that sexual reproduction and larval dispersion play a vital role in the connectivity of these Southwest Atlantic populations and that oceanographic currents, rafting and artificial transport facilitate these processes. [ABSTRACT FROM AUTHOR]

The present article describes the development of an improved Pinus taeda clonal seed orchard adapted to the edaphoclimatic conditions of Uruguay. Initially, 2068 hectares distributed in nine companies were prospected, and 124 plus trees were identified based on growth, straightness, and health traits. These trees were clonally propagated via grafting to establish a clonal seed orchard. For the genetic evaluation of the orchard, two progeny tests were carried out in the Rivera and Paysandú municipalities. Quantitative genetic analyses allowed us to identify a simple genotype–environment interaction and an expected genetic gain for volumes of 17%, 13%, and 8% for selection intensities of 12%, 25%, and 50%, respectively. Moreover, the genetic diversity of the 124 clones of the orchard was assessed using 10 microsatellite markers. The fingerprinting profiles allowed us to identify a total of 224 alleles. The polymorphism information content of the different markers was in the range of 0.594 to 0.895. The combined probability of identity and probability of identity among siblings had a discrimination power of 8.26 × 10–14 and 5.91 × 10–5, respectively. Analysis of the genetic structure demonstrated that the seed orchard population was not structured by the supplier. [ABSTRACT FROM AUTHOR]

To develop standardized in vitro thrombogenicity test methods for evaluating medical device materials, three platelet activation biomarkers, beta‐thromboglobulin (β‐TG), platelet factor 4 (PF4), soluble p‐selectin (CD62P), and a plasma coagulation marker, thrombin–antithrombin complex (TAT), were investigated. Whole blood, drawn from six healthy human volunteers into Anticoagulant Citrate Dextrose Solution A was recalcified and heparinized over a concentration range of 0.5–1.5 U/mL. The blood was incubated with test materials with different thrombogenic potentials for 60 min at 37°C, using a 6 cm2/mL material surface area to blood volume ratio. After incubation, the blood platelet count was measured before centrifuging the blood to prepare platelet‐poor plasma (PPP) and platelet‐free plasma (PFP) for enzyme‐linked immunosorbent assay analysis of the biomarkers. The results show that all four markers effectively differentiated the materials with different thrombogenic potentials at heparin concentrations from 1.0 to 1.5 U/mL. When a donor‐specific heparin concentration (determined by activated clotting time) was used, the markers were able to differentiate materials consistently for blood from all the donors. Additionally, using PFP instead of PPP further improved the test method's ability to differentiate the thrombogenic materials from the negative control for β‐TG and TAT. Moreover, the platelet activation markers were able to detect reversible platelet activation induced by adenosine diphosphate (ADP). In summary, all three platelet activation markers (β‐TG, PF4, and CD62P) can distinguish thrombogenic potentials of different materials and detect ADP‐induced reversible platelet activation. Test consistency and sensitivity can be enhanced by using a donor‐specific heparin concentration and PFP. The same test conditions are applicable to the measurement of coagulation marker TAT. [ABSTRACT FROM AUTHOR]

Selection is a fundamental part of the plant breeding process, enabling the identification and development of varieties with desirable traits. Thanks to advances in genetics and biotechnology, the selection process has become more precise and efficient, resulting in faster breeding progress and better adaptation of crops to environmental challenges. Genetic parameters related to gene additivity and epistasis play a key role and can influence decisions on the suitability of breeding material. In this study, 188 rapeseed doubled haploid lines were assessed in field conditions for resistance to Leptosphaeria spp. Through next-generation sequencing, a total of 133,764 molecular markers (96,121 SilicoDArT and 37,643 SNP) were obtained. The similarity of the DH lines at the phenotypic and genetic levels was calculated. The results indicate that the similarity at the phenotypic level was markedly different from the similarity at the genetic level. Genetic parameters related to additive gene action effects and epistasis (double and triple) were calculated using two methods: based on phenotypic observations only and using molecular marker observations. All evaluated genetic parameters (additive, additive-additive and additive-additive-additive) were statistically significant for both estimation methods. The parameters associated with the interaction (double and triple) had opposite signs depending on the estimation method. [ABSTRACT FROM AUTHOR]

Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species' adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products. [ABSTRACT FROM AUTHOR]

Soybean, one of the most important oil seed crops known for its high-quality oil and protein content, is widely grown and consumed worldwide. However, the crop is severely affected by various biotic and abiotic factors, of which diseases are by far the most important, resulting in significant yield losses each year. The major diseases affecting soybean production include soybean rust, soybean mosaic virus, anthracnose, charcoal rot, Sclerotinia stem rot (white mold), seedling diseases, sudden death syndrome, frogeye leaf spot, and Stem canker. Development of soybean varieties resistant to these diseases using modern biotechnology techniques is a viable option to increase genetic potential and boost soybean production. This paper, hence, aims to explore the application of functional genomics in improving resistance to various diseases in soybean. Therefore, this paper provides a comprehensive overview of the progress made in improving soybean resistance to major diseases by using the various approaches of modern biotechnological tools such as molecular markers, QTL/gene mapping, omics technology, freely available online databases, genome editing, genetic modification, and marker-assisted breeding. This review also highlights future directions that may be important for genomics-based research programs to improve disease resistance in soybean while increasing production.Article Highlights: Summarizes main discoveries and findings. Offers in-depth explorations of various genetic loci. Identifies direction for future progress. [ABSTRACT FROM AUTHOR]

The reticulated iris is one of the most attractive wild ornamentals and bulbous irises and is widely distributed throughout the mountains of the Iraqi Kurdistan region. Because little is known about the genetic diversity and population structure of this plant species in Iraq, this study was undertaken to fill that gap. In the present study, 10 start codon-targeted (SCoT) polymorphic and 10 sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and population structure of 50 wild reticulated iris accessions from five different sites in Iraqi Kurdistan. Overall, the SCoT and SRAP markers produced 135 and 87 polymorphic bands, respectively. The average number of polymorphic bands (TPB), number of observed alleles (Na), Shannon's information index (I), effective number of alleles (Ne), expected heterozygosity or gene diversity (He), polymorphic information content, and unbiased expected heterozygosity (uHe) were 13.7, 1.54, 0.35, 1.40, 0.23, 0.31, and 0.25, respectively, for the SCoT markers and 8.7, 1.54, 0.36, 1.40, 0.24, 0.32, and 0.25, respectively, for the SRAP markers. According to the unweighted pair group method with arithmetic mean (UPGMA) dendrogram and structure analysis, SCoT markers grouped 50 reticulated iris accessions into two main clades with some subclades, SRAP markers separated these accessions into four main clades, and the combination of both markers divided all accessions into five main clades. The analysis of molecular variance revealed 80.00, 76.00, and 78.38% variability within populations using SCoT, SRAP, and SCoT+SRAP markers, respectively. Except for the private band numbers for the SCoT, SRAP, and SCoT+SRAP markers, population 3, population 1, and population 3 had the highest diversity indices, respectively. The highest genetic similarity among populations was revealed by the SRAP markers between population 2 and population 3, with 92% similarity. The findings of this study demonstrate the efficacy of these markers for determining genetic variation in iris accessions, in addition to their use in conserving germplasm and genome diversity. [ABSTRACT FROM AUTHOR]

The complexity of citrus phylogeny and taxonomy, influenced by polyembryony, genetic diversity, and extended generation cycles, necessitates assessing genetic relationships for improved production and disease resilience. DNA polymorphism markers are pivotal in genotyping and resolving phenotypic varietal ambiguities through accurate and objective genetic relatedness and distinctiveness assessments. In this study, 27 accessions of kagzi and ornamental lime were evaluated at morphological (based on IPGRI citrus descriptor), biochemical, and molecular levels using DNA-based markers, namely, random amplified polymorphic DNA (RAPD), start codon targeted (SCoT) polymorphism, and simple sequence repeats (SSR). Morphological analysis unveiled significant variation in leaf lamina attachment, shape, margins, fruit characteristics, and texture across all parameters. Biochemical research noted minimal differences, with total soluble solids (TSS) ranging from 5.7° to 8.0° Brix and titratable acidity (TA) from 0.36 to 0.50%. Notably, ornamental lime accessions exhibited higher TSS:TA ratios of 16.00. Molecular markers (RAPD, SCoT, and SSR) corroborated these findings, yielding 115, 74, and 64 amplicons, respectively, with polymorphic percentages varying from 33.33 to 100%. Polymorphic information content ranged from 0.20 to 0.90 for RAPD, 0.41 to 0.99 for SCoT, and 0.07 to 0.67 for SSR markers. Analysis of molecular variance (AMOVA) substantiated significant genetic differences among the kagzi and ornamental lime accessions (RAPD PhiPT = 0.267, SCoT PhiPT = 0.351, SSR PhiPT = 0.107). Furthermore, STRUCTURE software 2.3.4 revealed a ΔK value of two (K = 2), indicating two distinct genetic pools within the accessions, possibly attributable to bud mutations generating varying morphological traits within the same plant. Molecular marker-based germplasm characterization can mitigate confusion linked to morphological characteristics and multiple cultivar registrations. [ABSTRACT FROM AUTHOR]

Genetic diversity within germplasm holds significant importance in the context of okra breeding programs. However, the limited knowledge regarding the genetic diversity of okra in Palestine poses a challenging obstacle to enhancing the local cultivar. Characterization of Palestinian okra landraces using phenotypic or molecular approaches is limited. Crop characterization usually provides knowledge on diversity within and among crop accessions, which is crucial for breeding efforts and the conservation of germplasm. This study was carried out to evaluate genetic variation in seven okra local landraces. Seven Palestinian okra landraces were grown. DNA was extracted and subjected to polymerase chain reaction (PCR) using 27 random amplified polymorphic DNA (RAPD) markers. The banding pattern for each primer was scored. The data matrix was created to facilitate cluster analysis employing the unweighted pair group method with arithmetic mean (UPGMA) method. From the 15 RAPD markers tested, 92 DNA fragments were identified in total, of these fragments, 76% were polymorphic and 24% were monomorphic, in addition, at least two and no more than eleven DNA fragments were identified. The average resolving power recorded was 2.8. The dendrogram derived from RAPD data categorized the genotypes into two primary clusters. Cluster-I consisted of a single genotype (PARC-OKRA-1). In contrast, Cluster-II further subdivided the genotypes into two subclusters, sub-cluster-II.a represented one genotype accession (UB 405-19), and sub-cluster-II.b included five genotypes (UB 457-19, UB 280-15, UB 457-14, UB 280-12, and UB 457-20). The generated similarity matrix indicated that the similarity coefficients among okra genotypes, as determined by 15 RAPD markers, ranged from 0.226 to 0.678. The present study represents the first application of molecular markers to assess genetic diversity within Palestinian okra landraces. The detection of a high level of polymorphism among RAPD markers demonstrated the efficacy of RAPD markers for identifying polymorphism in Palestinian okra genotypes. [ABSTRACT FROM AUTHOR]

Knowledge of the genetic diversity and population structure of species can facilitate conservation and guide management programs. However, the type of molecular markers used can affect estimates of genetic divergence and population structure. Here three types of molecular markers were used to estimate the genetic diversity and population structure of Euterpe edulis, a palm endemic to the Atlantic Forest and economically and ecologically important. The objective was to estimate the parameters of genetic diversity and population structure for two other types of molecular markers (SNP and SilicoDArT) in addition to the commonly used one (SSR) to the species. We used single nucleotide polymorphism (SNP), SilicoDArT, and microsatellite (SSR) markers in 138 E. edulis individuals sampled from 15 sites. Euterpe edulis individuals were grouped into 11 clusters using SNPs and SilicoDArT and six groups using SSR data. The SNP and SilicoDArT data showed less divergence between the individuals within each cluster in comparison to the results derived from the SSR data. The probability of reassigning individuals to their cluster of origin revealed an average association with the original clusters was 0.92 for SNPs (n = 100), 0.71 for SSR (n = 8), and 0.99 for SilicoDArT (n = 445). The genetic divergence is high among sites using SNP markers, whereas SSRs showed the largest genetic divergence is found within each site. The overall heterozygosity values for each site in the eight SSR (He = 0.69; Ho = 0.59) markers were almost four times higher than those values inferred using SNPs (data 7833 SNP, He = 0.15; Ho = 0.13; data 100 SNP, He = 0.14; Ho = 0.12). Within each site, we found low inbreeding rates using both markers (SNP and SSR). In addition, population structure analysis identified two strongly supported geographical groups, one northern and one southern Brazilian Atlantic Forest group, for both markers. This study contributes to the understanding of the population genetics and population structure of E. edulis and may have important implications for its conservation. In addition, our results suggest that SNP and SilicoDArT markers are more effective for evaluating population structure, but SSR is more capable of detecting diversity among individuals for this species. [ABSTRACT FROM AUTHOR]

The cultivated apple (Malus domestica Borkh.) is an economically important fruit crop in countries worldwide, including Bosnia and Herzegovina (BIH).The gene bank activities in BIH were initiated in the 1930s and continued until the war in the 1990s, when much of the documentation was lost. Since then, uncoordinated efforts were made to establish apple collections in different regions, but a comprehensive analysis of genetic resources was lacking. This prompted the current study where we present the first thorough overview of the national genetic resources of BIH apples. Thus, we analyzed 165 accessions in the apple gene bank at the Institute for Genetic Resources (IGR) established at Banja Luka using the 20 K apple Infinium® single nucleotide polymorphism (SNP) array. We combined the results with previously published data on the germplasm collections at Srebrenik and Goražde, genotyped using the Axiom® Apple 480 K SNP array. In total, 234 accessions were included in the study of which 220 were presumed to be local cultivars and 14 were known international reference cultivars. We identified numerous genotypic duplicates within and between collections and suggested preferred names to be used in the future. We found the BIH germplasm to have relatively few parent-offspring relationships, particularly among local cultivars, which might reflect the country's history and patterns of apple cultivar introduction. A number of cultivars unique to BIH and a weakly defined genetic group were identified via STRUCTURE analysis, representing interesting targets for future research and preservation efforts. [ABSTRACT FROM AUTHOR]

Background: Antioxidant properties of rice provide various health benefits due to its ability to inhibit cellular oxidation. Antioxidant content of rice is known to be linked with the pericarp pigmentation. The Rc gene of rice (Os07g0211500) codes for a basic helix-loop-helix (bHLH) protein, acting as a transcriptional factor in regulating proanthocyanidin biosynthesis. The current study was carried out to evaluate the variation of antioxidant properties in a selected panel of rice accessions and assess the possibility of using haplotypes defined based on the Rc gene to predict pericarp pigmentation and antioxidant content in rice. Results: Thirty-two rice accessions were evaluated for grain pericarp colour and antioxidant properties; total phenolic content (TPC), total flavonoids (TFC), proanthocyanidins (PAC) and radical scavenging activity (RSA). The parameters TPC, TFC and PAC showed significant positive correlation with RSA (r > 0.69; P < 0.01). The study panel showed a wide variation for antioxidant properties and rice accessions such as Sudu Heenati, Deweraddiri, Madathawalu, Masuran, Ld 368, At 311, Kalu Heenati, Bw 272-6B, Pokkali, At 362 and Wanni Dahanala exhibited profound potential with respect to antioxidant properties. Based on three-target sites previously reported as critical for the function of the coded bHLH protein (an A/C SNP at 1,353-bp, a 1-bp insertion/deletion at 1,388-bp, and a 14-bp insertion/deletion at 1,408-1,421-bp positioned in the mRNA corresponding to the exon 6 of rice Rc gene), three haplotypes were defined (H1-H3). Pigmentation of the rice pericarp could be successfully explained based on the defined haplotypes (H1 (C/G/+): red, and H2 (A/G/+) and H3 (C/G/-): white), and the H1 haplotype corresponded to a significantly (P < 0.05) higher TPC, TFC, PAC and RSA compared to the other haplotypes. Conclusions: The studied rice accessions showed a significant variation with respect to antioxidant properties. Haplotype H1 defined based on the three-target sites in the exon 6 of Rc gene can detect rice accessions with red pigmented pericarp and high antioxidant properties effectively. Hence, its use can be recommended as an alternative to biochemical assays for screening during rice breeding programs. [ABSTRACT FROM AUTHOR]

Background: Cadmium (Cd) is one of the most important stress factors in plants, with its high mobility in soils, ease of uptake by plants and toxicity at low concentrations. Aluminum (Al) is another phytotoxic metal, the accumulation of which is a crucial agricultural complication for plants, especially in acidic soils. Methods and results: In this study, Bryophyllum daigremontianum clone plantlets were obtained from bulbiferous spurs of a mother plant and separated into four different groups and watered with Hoagland solution and mixtures containing 0, 50, 100, and 200 µM of AlCl3 and CdCl2 each for 75 days. Control groups were maintained under the same conditions without Al and Cd treatment. To simulate acidic soil conditions typical of environments where Al toxicity is prevalent, the soil pH was adjusted to 4.5 by spraying the sulphuric acid (0.2%) with 2-day intervals after each irrigation day. After harvesting, growth parameters such as shoot length and thickness, root, shoot and leaf fresh and dry weights were measured, along with physiological parameters like mineral nutrient status, total protein, and photosynthetic pigment concentrations (chlorophyll a, b, a/b, total chlorophyll, and carotenoid) in both control and experimental groups of B. daigremontianum clones. In response to Al and Cd applications, the plant height, shoot thickness and carotenoid levels were declined, whereas the increments were found in leaf/shoot/root fresh weight, root dry weight, and total protein content. Moreover, differences in genomic alterations were investigated using 21 ISSR and 19 RAPD markers, which both have been used extensively as genetic markers to specify phylogenetic relationships among different cultivars as well as stress-dependent genetic alterations. RAPD primers were used due to their arbitrary sequences and the unknown genome sequence of the plant material used. In contrast, ISSR primers were preferred for a genome-wide genotoxic effect scan via non-arbitrary and more common genetic markers. Distinct types of band polymorphisms detected via RAPD and ISSR markers include band loss, and new band formation under a combination of Al and Cd stress. 17 ISSR and 14 RAPD primers generated clear electrophoretic bands. Conclusion: The study revealed that combined application of Al and Cd affect B. daigremontianum clones in terms of growth, physiology and genotoxicity related to the increasing concentrations. [ABSTRACT FROM AUTHOR]

Simple Summary: This research highlights the differences in genetic mutations between primary tumors and their subsequent spine metastases. These distinctions are relevant to neurosurgeons because effective surgical planning and goals rely on factors such as patient prognosis, which is impacted by tumor genetic markers. Certain genetic markers may be more or less favorable, thus impacting the predicted patient treatment course and prognosis. The authors aim to present an overview of these complex molecular characteristics for neurosurgical oncology providers. The content of this review is intended to assist neurosurgeons' decision-making when caring for spinal oncology patients and to illustrate the importance of multidisciplinary management of this complex patient population. For many spine surgeons, patients with metastatic cancer are often present in an emergent situation with rapidly progressive neurological dysfunction. Since the Patchell trial, scoring systems such as NOMS and SINS have emerged to guide the extent of surgical excision and fusion in the context of chemotherapy and radiation therapy. Yet, while multidisciplinary decision-making is the gold standard of cancer care, in the middle of the night, when a patient needs spinal surgery, the wealth of chemotherapy data, clinical trials, and other medical advances can feel overwhelming. The goal of this review is to provide an overview of the relevant molecular biomarkers and therapies driving patient survival in lung, breast, prostate, and renal cell cancer. We highlight the molecular differences between primary tumors (i.e., the patient's original lung cancer) and the subsequent spinal metastasis. This distinction is crucial, as there are limited data investigating how metastases respond to their primary tumor's targeted molecular therapies. Integrating information from primary and metastatic markers allows for a more comprehensive and personalized approach to cancer treatment. [ABSTRACT FROM AUTHOR]

Genetic markers are powerful tools for understanding genetic diversity and the molecular basis of traits, ushering in a new era of molecular breeding in crops. Over the past 50 years, DNA markers have rapidly changed, moving from hybridization-based and second-generation-based to sequence-based markers. Simple sequence repeats (SSRs) are the ideal markers in plant breeding, and they have numerous desirable properties, including their repeatability, codominance, multi-allelic nature, and locus specificity. They can be generated from any species, which requires prior sequence knowledge. SSRs may serve as evolutionary tuning knobs, allowing for rapid identification and adaptation to new circumstances. The evaluations published thus far have mostly ignored SSR polymorphism and gene evolution due to a lack of data regarding the precise placements of SSRs on chromosomes. However, NGS technologies have made it possible to produce high-throughput SSRs for any species using massive volumes of genomic sequence data that can be generated fast and at a minimal cost. Though SNP markers are gradually replacing the erstwhile DNA marker systems, SSRs remain the markers of choice in orphan crops due to the lack of genomic resources at the reference level and their adaptability to resource-limited labor. Several bioinformatic approaches and tools have evolved to handle genomic sequences to identify SSRs and generate primers for genotyping applications in plant breeding projects. This paper includes the currently available methodologies for producing SSR markers, genomic resource databases, and computational tools/pipelines for SSR data mining and primer generation. This review aims to provide a 'one-stop shop' of information to help each new user carefully select tools for identifying and utilizing SSRs in genetic research and breeding programs. [ABSTRACT FROM AUTHOR]

Introduction: Camellia anthracnose is caused by multiple Colletotrichum species, resulting in severe yield losses of oil-tea Camellia. Colletotrichum fructicola is one of the major anthracnose pathogens of oil-tea Camellia worldwide. However, developing unique molecular markers for the rapid and accurate detection of Colletotrichum fructicola from diverse Colletotrichum species, as well as early monitoring and effective control of the disease, remains largely unexplored. Methods: C. fructicola-specific genes were obtained using a BLAST search of the sequences of predicted genes in C. fructicola against the genome sequences of Colletotrichum fungal pathogens. In this study, Colletotrichum fructicola- specific molecular markers were developed for rapid and accurate detection of C. fructicola among Camellia anthracnose causing fungal pathogens. Results: Using genomic DNA-based end-point PCR and qPCR, three C. fructicola-specific genes with the ability to distinguish C. fructicola from other oil-tea Camellia anthracnose-related Colletotrichum species, including Colletotrichum camelliae, Colletotrichum gloeosporioides, and Colletotrichum siamense, and oil-tea Camellia fungal pathogens belonging to the genus Neopestalotiopsis, Pestalotiopsis, and Alternaria, were validated as molecular markers. In addition, these three molecular markers were highly sensitive to detecting C. fructicola using DNA extracted fromthe inoculated leaves of oil-tea Camellia. Discussion: These findings enable us to rapidly and uniquely detect the Camellia anthracnose disease caused by Colletotrichum fructicola, which will equip farmers with an effective tool for monitoring Camellia anthracnose disease in the field and taking timely control measurements in advance. [ABSTRACT FROM AUTHOR]

This study aimed for a better understanding of the niche specification of bacteria carrying the tfd-genes for aerobic 2,4-dichlorphenoxyacetic acid (2,4-D) degradation in the rice paddy ecosystem. To achieve this, a dedicated microcosm experiment was set up to mimic the rice paddy system, with and without 2,4-D addition, allowing spatial sampling of the different rice paddy compartments and niches, i.e., the main anaerobic bulk soil and the aerobic surface water, surface soil, root surface and rhizosphere compartments. No effect of 2,4-D on the growth and morphology of the rice plant was noted. 2,4-D removal was faster in the upper soil layers compared to the deeper layers and was more rapid after the second 2,4-D addition compared to the first. Moreover, higher relative abundances of the 2,4-D catabolic gene tfdA and of the mobile genetic elements IncP-1 and IS1071 reported to carry the tfd-genes, were observed in surface water and surface soil when 2,4-D was added. tfdA was also detected in the root surface and rhizosphere compartment but without response to 2,4-D addition. While analysis of the bacterial community composition using high-throughput 16S rRNA gene amplicon sequencing did not reveal expected tfd-carrying taxa, subtle community changes linked with 2,4-D treatment and the presence of the plant were observed. These findings suggest (i) that the surface soil and surface water are the primary and most favorable compartements/niches for tfdmediated aerobic 2,4-D biodegradation and (ii) that the community structure in the 2,4-D treated rice paddy ecosystem is determined by a niche-dependent complex interplay between the effects of the plant and of 2,4-D. [ABSTRACT FROM AUTHOR]

The severity of pancreatic ductal adenocarcinoma (AP), the few available treatments and the diversity of therapeutic responses highlight the crucial need to find molecular markers aiming to personalize treatments. Recent research has identified promising molecular signatures, based on transcriptomic analyzes and chemotherapy sensitivity testing. Clinical trials are currently evaluating their effectiveness in guiding the treatment of patients with AP. At the same time, the development of non-invasive methods to predict response to treatments, in particular by exploring blood biomarkers, is necessary. These advances offer considerable potential for a more precise and individualized approach to the treatment of this disease. [ABSTRACT FROM AUTHOR]

ttarakhand has a rich plant biodiversity, many of which have high medicinal properties. Medicinal plants have been used against insects, diseases, and herbivorous mammals through the production of chemical compounds. Various reasons like overexploitation, overgrazing, unsustainable development, etc. lead to their extinction and make them threatened species. The International Union for Conservation of Nature (IUCN) was established to prioritize species conservation, assess threat status, and develop suitable strategies due to the vast diversity of species. The genetic diversity of these threatened species can be determined using various markers. Molecular marker technology aids in analyzing genetic diversity, population structure, and species adaptation, enabling conservation measures and assessing genetic stability in conserved species. In this article, we have reviewed the genetic diversity of six threatened plants of Uttarakhand (Picrorhiza kurroa, Aconitum heterophyllum, Nardostachys jatamansi, Dactylorhiza hatagirea, Zanthoxylum armatum, Saussurea costus) in India as well as in other countries. A review highlighting the use of recent molecular markers like ISSR, SSR, RAPD, etc. to determine genetic diversity. Most of the medicinal plants show diversity less than 0.5, which indicates that the plants are at extreme risk of extinction. The diversity is calculated based on polymorphism percentage. The analysis of genetic diversity between species using ISSR, nextgeneration sequencing, AFLP, and microsatellite markers reveals low genetic diversity in A. heterophyllum, P. kurroa, N. jatamansi, Z. armatum, D. hatagirea, and S. costus. [ABSTRACT FROM AUTHOR]

Introduction: Gluten quality is one of the most important traits of the common wheat (Triticum aestivum L.). In Chinese wheat production, Yannong series cultivars/derivative lines possess unique characteristics and play an important role in both yield and quality contribution. Methods: To dissect their genetic basis of the gluten quality, in this study, allelic variations of high-molecular-weight glutenin subunit (HMW-GS) and lowmolecular- weight glutenin subunit (LMW-GS) in 30 Yannong series wheat cultivars/derivative lines and three check cultivars were evaluated using the allele-specific molecular markers, and six crucial quality indexes were also further measured and analyzed. Results: The results demonstrated that the frequencies of HMW-GSs By8, Dx5 + Dy10 and Dx5 + Dy10 + Dy12 in these 30 genotypes and three check cultivars accounted for 87.9%, 24.2% and 9.1%, respectively. For the allelic variations of LMW-GSs, Glu-A3a, Glu-A3b, Glu-A3c, Glu-A3f, and Glu-A3g were identified in 18, 9, 13, 11, and 2 genotypes, respectively; Glu-B3d, Glu-B3g and Glu-B3f were identified in 13, 23 and 4 genotypes, respectively. Notably, Yannong 999, containing By8 + Dx5 + Dy10, and Jinan 17 containing By8 + Dy12 both meet the national standard for high-quality wheat and belong to the category of first-class high-quality strong gluten wheat. Discussion: These findings can provide reference for wheat quality improvement and popularization in the production. [ABSTRACT FROM AUTHOR]

The leaf rust (Puccinia triticina f. sp. tritici), stripe rust (Puccinia striiformis f. sp. tritici), and stem rust (Puccinia graminis f. sp. tritici) are major fungal constraints affecting wheat production worldwide. Identifying and deploying wheat varieties with diverse resistance are the best ways to manage all the rusts. Therefore, a continuous search goes on to identify diverse germplasm with effective rust resistance that expresses at different stages of plant growth (seedling and adult plant). A set of 22 rust resistant wheat genotypes and 4 checks (controls), viz., Avocet‐Yr10, Avocet ‐Yr15, Agra Local, and respective positive checks were studied for characterising rust resistance genes using host–pathogen interactions complemented by molecular markers. Among 22 elite genotypes, 05 genotypes amplified 191 bp fragment with marker PSY1E1, confirmed the presence of gene Lr19/Sr25. These genotypes also expressed resistance to most virulent leaf rust pathotypes, 77‐5 and 77‐9 in host–pathogen interaction test (HPI). Seven genotypes showed the presence of Lr34/Yr18/Sr57/Pm38/Ltn1 in homozygous state, whereas G4 showed its presence in heterozygous condition. Among 22 genotypes, 16 genotypes possessed Yr10. Five genotypes (22.7%) exhibited two gene combinations, Lr19/Sr25, and Yr10 as revealed through the detection of 191 bp fragment with marker PSY1E1 and 260 bp fragment with co‐dominantly inherited microsatellite marker Xpsp3000, respectively. All five genotypes (G2, G3, G8, G9, and G18) also expressed brown glumes controlled by the gene Rg1 tightly linked to Yr10 on the 1BS chromosome. Broad spectrum rust resistance present in these lines in good agronomic backgrounds could be used as potent genetic donors for diverse and durable rust resistance breeding programmes in wheat. [ABSTRACT FROM AUTHOR]

To explore the structural features of Artemisia parviflora chloroplast genome and its systematic position, high-throughput sequencing technology were employed for genome sequencing and bioinformatics tools for analyzing. The results were as follows: (1) The chloroplast genome of A. parviflora was 151 047 bp, with a typical circular double-stranded tetrad structure, and the GC content was 37.5%. (2) Total 115 unique genes were annotated, including 81 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. (3) Sixty-eight simple sequence repeats (SSRs) and 37 long repeat sequences were detected. (4) The codon usage bias was weak in the A. parviflora chloroplast genome, and natural selection mainly contributed to the codon usage bias. High-frequency codons tend to ended with A/U. (5) There was no obvious expansion or contraction of the inverted repeat (IR) regions. Five high variation regions (trnH-psbA, rpl16-rps3, ycf15-trnL-UAG, ndhA, and ycf1) were identified which could be used as potential molecular markers for identifying subgen. Dracunculus species. (6) Phylogenetic analysis revealed the systematic position of A. parviflora within subgen. Dracunculus and elucidated the phylogenetic relationships among the various subgenera of Artemisia. This study provides the reference for future molecular marker development and phylogenetic research of Artemisia species. [ABSTRACT FROM AUTHOR]

Heat as an abiotic stress significantly impairs the sustainable productivity of wheat (Triticum aestivum L.). To determine the tolerance of genotypes to heat stress, a comprehensive approach should be used that integrates simultaneous phenotyping and genotyping analyses. The aim of this study is to identify local heat-tolerant genotypes using simple sequence repeat (SSR) markers and evaluate the selected genotypes under field conditions for their tolerance to heat stress. Of the 12 SSR markers that showed polymorphism, eight were associated with six important traits. The use of hierarchical cluster analysis (HC) based on SSR markers led to the identification of 13 genotypes that showed varying results and were grouped into three distinct heat tolerance classes: tolerant (T), moderately tolerant (MT), and sensitive (S). The results showed that heat stress had a significant effect on 19 traits under this study, with significant variation in tolerance to heat stress between genotypes. The tolerant genotypes exhibited a range of average thousand-kernel weight (TKW) values between 40.56 and 44.85, while the sensitive genotype (Yecora Rojo) had an average TKW of 35.45. Furthermore, the tolerant genotypes showed two to three times higher levels of antioxidants compared to the sensitive genotypes when exposed to heat stress. Among the traits analyzed, six showed a favorable combination of high heritability (>60%) and genetic gain (>20%). Through the integration of principal component analysis and stepwise multiple linear regression, it was determined that six traits (grain yield, 1000-kernel weight, plant height, intercellular carbon dioxide, flag leaf area, and grain filling duration) revealed differences between the 13 genotypes. HC analysis of the six traits resulted in the same division of genotypes into three main categories as observed in an HC analysis based on SSR markers. It is worth noting that Saudi wheat, including KSU106, KSU105, and KSU115 as local genotypes, in addition to the 16HTWYT-22 genotype, showed higher heat tolerance compared to the other genotypes tested, indicating its potential suitability for agriculture in Saudi Arabia. These results contribute to breeding programs focused on developing heat-tolerant wheat varieties and accelerate progress in wheat productivity improvement programs. [ABSTRACT FROM AUTHOR]

Oxidative stress (OS) and apoptosis are critical factors in placental development and function. Their interplay influences trophoblast proliferation, differentiation, and invasion, as well as vascular development. An imbalance between these processes can lead to pregnancy-related disorders such as preeclampsia, intrauterine growth restriction, and even spontaneous abortion. Our study seeks to elucidate the associations between preventive antioxidant/protective OS response factors—glutathione (GSH), MutT Homolog 1 (MTH1), and apoptotic regulation modulators—tumor protein p53 and B-cell lymphoma (Bcl-2) transcripts, in the context of spontaneous abortion (30 samples) versus elective termination of pregnancy (20 samples), using immunohistochemistry (IHC) to determine their proteomic expression in chorionic villi within abortive fetal placenta tissue samples. Herein, comparative statistical analyses revealed that both OS response factors, GSH and MTH1, were significantly under-expressed in spontaneous abortion cases as compared to elective. Conversely, for apoptotic regulators, p53 expression was significantly higher in spontaneous abortion cases, whereas Bcl-2 expression was significantly lower in spontaneous abortion cases. These findings suggest that a strong pro-apoptotic signal is prevalent within spontaneous abortion samples, alongside reduced anti-apoptotic protection, depleted antioxidant defenses and compromised oxidative DNA damage prevention/repair, as compared to elective abortion controls. Herein, our hypothesis that OS and apoptosis are closely linked processes contributing to placental dysfunction and spontaneous abortion was thus seemingly corroborated. Our results further highlight the importance of maintaining redox homeostasis and apoptotic regulation for a successful pregnancy. Understanding the mechanisms underlying this interplay is essential for developing potential therapies to manage OS, promote placentation, and avoid unwanted apoptosis, ultimately improving pregnancy outcomes. Antioxidant supplementation, modulation of p53 activity, and the enhancement of DNA repair mechanisms may represent potential approaches to mitigate OS and apoptosis in the placenta. Further research is needed to explore these strategies and their efficacy in preventing spontaneous abortion. [ABSTRACT FROM AUTHOR]

Wheat (Triticum aestivum L.) is a crucial cereal crop, contributing around 20% of global caloric intake. However, challenges such as diminishing arable land, water shortages, and climate change threaten wheat production, making yield enhancement crucial for global food security. The heading date (HD) is a critical factor influencing wheat's growth cycle, harvest timing, climate adaptability, and yield. Understanding the genetic determinants of HD is essential for developing high-yield and stable wheat varieties. This study used a doubled haploid (DH) population from a cross between Jinmai 47 and Jinmai 84. QTL analysis of HD was performed under three phosphorus (P) treatments (low, medium, and normal) across six environments, using Wheat15K high-density SNP technology. The study identified 39 QTLs for HD, distributed across ten chromosomes, accounting for 2.39% to 29.52% of the phenotypic variance. Notably, five stable and major QTLs (Qhd.saw-3A.7, Qhd.saw-3A.8, Qhd.saw-3A.9, Qhd.saw-4A.4, and Qhd.saw-4D.3) were consistently detected across varying P conditions. The additive effects of these major QTLs showed that favorable alleles significantly delayed HD. There was a clear trend of increasing HD delay as the number of favorable alleles increased. Among them, Qhd.saw-3A.8, Qhd.saw-3A.9, and Qhd.saw-4D.3 were identified as novel QTLs with no prior reports of HD QTLs/genes in their respective intervals. Candidate gene analysis highlighted seven highly expressed genes related to Ca2+ transport, hormone signaling, glycosylation, and zinc finger proteins, likely involved in HD regulation. This research elucidates the genetic basis of wheat HD under P stress, providing critical insights for breeding high-yield, stable wheat varieties suited to low-P environments. [ABSTRACT FROM AUTHOR]

Genetic similarity determines the extent to which two genotypes share common genetic material. It can be measured in various ways, such as by comparing DNA sequences, proteins, or other genetic markers. The significance of genetic similarity is multifaceted and encompasses various fields, including evolutionary biology, medicine, forensic science, animal and plant breeding, and anthropology. Genetic similarity is an important concept with wide application across different scientific disciplines. The research material included 21 rapeseed genotypes (ten interspecific Brassicaceae hybrids of F2 generation and 11 of their parental forms) and 146 alleles obtained using 21 ISSR molecular markers. In the presented study, six measures for calculating genetic similarity were compared: Euclidean, Jaccard, Kulczyński, Sokal and Michener, Nei, and Rogers. Genetic similarity values were estimated between all pairs of examined genotypes using the six measures proposed above. For each genetic similarity measure, the average, minimum, maximum values, and coefficient of variation were calculated. Correlation coefficients between the genetic similarity values obtained from each measure were determined. The obtained genetic similarity coefficients were used for the hierarchical clustering of objects using the unweighted pair group method with an arithmetic mean. A multiple regression model was written for each method, where the independent variables were the remaining methods. For each model, the coefficient of multiple determination was calculated. Genetic similarity values ranged from 0.486 to 0.993 (for the Euclidean method), from 0.157 to 0.986 (for the Jaccard method), from 0.275 to 0.993 (for the Kulczyński method), from 0.272 to 0.993 (for the Nei method), from 0.801 to 1.000 (for the Rogers method) and from 0.486 to 0.993 (for the Sokal and Michener method). The results indicate that the research material was divided into two identical groups using any of the proposed methods despite differences in the values of genetic similarity coefficients. Two of the presented measures of genetic similarity (the Sokal and Michener method and the Euclidean method) were the same. [ABSTRACT FROM AUTHOR]

Background: Lung cancer is a leading cause of cancer deaths in the United States. An increasing understanding of relevant non-small cell lung cancer (NSCLC) biomarkers has led to the recent development of molecular-targeted therapies and immune checkpoint inhibitors that have revolutionized treatment for patients with advanced and metastatic disease. The purpose of this review is to provide surgeons with a state-of-the-art understanding of the current medical and surgical treatment trends and their implications in the future of management of NSCLC. Materials and Methods: A systematic search of PubMed was conducted to identify English language articles published between January 2010 and March 2024 focusing on molecular markers, tumor targeting, and immunotherapy in the diagnosis and treatment of NSCLC. Case series, observational studies, randomized trials, guidelines, narrative reviews, systematic reviews, and meta-analyses were included. Results: There is now increasing data to suggest that molecular-targeted therapies and immune therapies have a role in the neoadjuvant setting. Advances in intraoperative imaging allow surgeons to perform increasingly parenchymal-sparing lung resections without compromising tumor margins. Liquid biopsies can noninvasively detect targetable mutations in cancer cells and DNA from a blood draw, potentially allowing for earlier diagnosis, personalized therapy, and long-term monitoring for disease recurrence. Conclusions: The management of NSCLC has advanced dramatically in recent years fueled by a growing understanding of the cancer biology of NSCLC. Advances in medical therapies, surgical techniques, and diagnostic and surveillance modalities continue to evolve but have already impacted current treatment strategies for NSCLC, which are encompassed in this review. [ABSTRACT FROM AUTHOR]

Worldwide, breast cancer (BC) is one of the most common cancers in women and is responsible for the highest number of cancer-related deaths among women, with a special clinical behavior and therapy response. Triple-negative breast cancer (TNBC) is seen as a highly invasive BC, characterized by a short survival, higher mortality, recurrence, and metastasis when it is compared to the other BC subtypes. The molecular subtyping of TNBC based on mRNA expression levels does not accurately reflect protein expression levels, which impacts targeted therapy effectiveness and prognostic predictions. Most TNBC cases exhibit a high frequency of homologous recombination (HR) DNA repair deficiency (HRD) signatures and are associated with a complex genomic profile. Biomarker research in TNBC includes investigating genetic mutations, gene expression patterns, immune system-related markers, and other factors that can provide valuable information for diagnosis, treatment selection, and patient outcomes. Additionally, these biomarkers are often crucial in the development of personalized and precision medicine approaches, where treatments are customized to each patient's unique characteristics. This ongoing research is essential for improving the management and outcomes of TNBC, which is a challenging and heterogeneous form of breast cancer. The findings of this research have practical implications for refining treatment strategies, particularly in selecting appropriate systemic therapies and integrating traditional treatment modalities like surgery and radiotherapy into comprehensive care plans for TNBC patients. [ABSTRACT FROM AUTHOR]

Rich nutrients, climate resilience, and the economic importance of millets are believed to ensure food security for future generations. Millets have the habit of growing against abiotic stresses (particularly drought stress). Millets show much better climate resilience and nutrient supplementation properties compared to other major cereals. Understanding the molecular mechanisms of genes that respond to stresses and nutrient transport will help understand the tolerance mechanism and improve against both stresses. Genome sequences are currently available for two major (sorghum and pearl millet) and eight minor millets (foxtail millet, finger millet, kodo millet, barnyard millet, proso millet, job's tear, fonio millet, and tef). Five minor millets (little millet, kodo millet, brown top millet, guinea millet, and raishan) do not have genome sequences to date. Transcriptome studies help to identify differentially expressed genes (DEGs), mine genes induced in a particular stress and develop several molecular markers for all plants, including millets. Some millets have reports on transcriptome datasets for plants exposed to various biotic and abiotic stresses and for nutritional traits. Unfortunately, the transcriptome datasets of millets have not been adequately leveraged to explore genes associated with traits such as climate resilience, nutrient enrichment, and crop improvement. This underutilization stems from a lack of high-resolution studies and limited exploration within the field. As a result, the potential insights and genetic understanding offered by these datasets remain largely untapped. Through this review, we plan to elucidate the current status of transcriptome resources on millets and draw future insights on the utilization of these resources. This review will motivate researchers to utilize the available transcriptome resources for millet improvement. [ABSTRACT FROM AUTHOR]

Jackfruit, primarily cultivated in Nayarit, Mexico, has four notable genotypes: "Agüitada", "Rumina", "Licenciada", and "Karlita", which require thorough characterization. This study aimed to provide a comprehensive characterization of these genotypes through an integration of morphological, physiological, physicochemical, phytochemical, and DNA fingerprinting analyses. Measurements were taken from physiological maturity to senescence. SSR and SRAP markers were employed for DNA fingerprinting, and a complete randomized design followed by multivariate analysis was used to observe variable relationships. The results revealed that "Rumina" had the largest leaf size, while "Karlita" had the largest fruit size and the highest respiration rate (117.27 mL of CO2·kg−1·h−1). "Licenciada" showed the highest ethylene production (265.45 µL·kg−1·h−1). "Agüitada" and "Licenciada" were associated with orange bulbs, whereas "Rumina" and "Karlita" were associated with yellow ones. Additionally, "Agüitada" demonstrated higher levels of soluble phenols and carotenoids, indicating greater antioxidant capacity. The Jaccard index suggested moderate genetic diversity among the genotypes, and the dendrogram revealed two genetic clusters. "Licenciada" emerged as a promising genotype, combining high genetic diversity with desirable physicochemical traits. This study highlights the need to broaden future genetic analyses to include a wider range of jackfruit genotypes from various regions, offering a more comprehensive understanding of genetic diversity. [ABSTRACT FROM AUTHOR]

The genetic diversity and structure of 17 populations of J. curcas, including 92 accessions from different provenances (tropical and subtropical), were investigated and effectively evaluated using twelve inter-simple sequence repeats (ISSRs) and seven pairs of florescence-amplified fragment-length polymorphism (AFLP) primers. Genetic diversity, at the overall level among populations of J. curcas based on the ISSR markers, showed that the observed number of alleles (Na) was 1.593, the effective number of alleles (Ne) was 1.330, Nei's gene diversity (H) was 0.200, Shannon's information index (I) was 0.303, and the percentage of polymorphic loci was 59.29%, indicating moderate genetic diversity between and within the different populations of J. curcas. Based on the genetic diversity analysis of AFLP markers, there were 1.464 (Na) and 1.216 (Ne) alleles, Nei's gene diversity (H) was 0.132, Shannon's information index (I) was 0.204, and the percentage of polymorphic loci was 46.40%. The AMOVA analysis showed that this large variance was due to differences within the populations, with genetic distinctions and limited gene flow among those from varied regions. The 17 populations were clustered into five main groups via UPGMA clustering analysis based on Nei's genetic distance, and the genetic relationships among the populations exhibited no significant correlations with geographical provenances. The genetic variation among Chinese populations of J. curcas distributed in dry-hot valley areas was remarkable, and the American germplasm presented with distinct genetic differentiation. [ABSTRACT FROM AUTHOR]

Yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), is one of the most damaging wheat diseases because of their widespread distribution and ability to produce new races that can attack cultivars that were previously resistant. In this study characterization of 48 wheat genotypes was done using 51 primers comprised of stripe rust gene-specific markers and found that WH730 and WH1142 possess the highest number of rust resistant genes while WH1263 bears the lowest Yr genes. These identified resistant Yr genes were exhibited at different frequencies. The resistant genes like, Yr6, Yr18, Yr46, Yr53 and Yr61 were absent in all the 48 studied wheat genotypes. Yr35 and Yr51 had the highest frequency (95.3 and 91.6%, respectively), while Yr16 related to xwmc177 and xwmc18 had lower frequencies (8.0 and 10.4%, respectively). Genetic diversity analysis using 61 molecular markers, and population structure analysis grouped the population into three clusters. Association study of morph-physiological traits showed that the marker xgdm160 was strongly associated with two traits i.e. days to anthesis and days to heading at P value 0.0031 and 0.0048 (P < 0.01), respectively, and showed the highest phenotypic variance (R2). These assessed markers might help develop novel genotypes with numerous genes of resistance against yellow rust races in wheat genotypes by marker-assisted pyramiding. [ABSTRACT FROM AUTHOR]

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Spring bread wheat (Triticum aestivum) is a major crop in Russia and in Kazakhstan. The rust pathogens, leaf rust caused by the fungus Puccinia triticina, stem rust incited by P. graminis and yellow rust caused by P. striiformis, are the significant biotic factors affecting wheat production. In this study, 40 new promising spring wheat genotypes from the Kazakhstan-Siberia Network for Spring Wheat Improvement (KASIB) were tested for resistance to leaf, stem and yellow rust at the seedling stage, and for identification of rust resistance genes using molecular markers. In addition, the collection was tested for leaf rust resistance and grain yields in the South Urals agroclimatic zone of Russia in 2023. As a result, 16 accessions with seedling resistance to leaf rust, 21 to stem rust and 4 to yellow rust were identified. Three breeding accessions were resistant to all rust species, and nine to P. triticina and P. graminis. Wheat accessions resistant to leaf rust at the seedling stage were also resistant in the field. Molecular analysis showed the presence of cataloged resistance genes, Lr1, Lr3a, Lr9, Lr10, Lr19, Lr20, Lr24, Lr26, Sr15, Sr24, Sr25, Sr31, Sr38, Yr9 and Yr18; uncatalogued genes Lr6Agi1 and Lr6Agi2 from Thinopyrum intermedium and LrAsp from Aegilops speltoides; and 1AL.1RS translocation. The current analysis showed an increase in leaf and stem rust resistance of new KASIB genotypes and their genetic diversity due to the inclusion of alien genetic material in breeding. [ABSTRACT FROM AUTHOR]

Cellular aging is considered as one of the main factors implicated in female infertility. We evaluated the expression of senescence-associated secretory phenotype (SASP) markers and additional molecular factors in an in vitro model of cellular aging. We induced genotoxic stress (UVB/UVA ray irradiation) in primary human endometrial cells obtained from female subjects of young reproductive age (<35 years of age). We assessed the expression levels of IL-6, IL-8, IL-1α, MMP3, SIRT-1, SIRT-6, TERF-1, and CALR at the mRNA level by RT-qPCR and at the protein level by immunofluorescence and confocal microscopy in primary human endometrial cells upon induction of genotoxic stress and compared them to untreated cells. Statistically significant differences were found for the expression of SIRT-1, SIRT-6, and TERF, which were found to be decreased upon induction of cell senescence through genotoxic stress, while IL-6, IL-8, IL-1α, MMP3, and p16 were found to be increased in senescent cells. We propose that these molecules, in addition to SAS-linked factors, could represent novel markers, and eventually potential therapeutic targets, for the aging-associated dysfunction of the female reproductive system. [ABSTRACT FROM AUTHOR]

New-generation molecular approaches and methods are currently being developed to accurately identify species and establish species boundaries. Various approaches to species delimitation are utilized to evaluate the species richness of poorly studied and highly diverse taxa. DNA barcoding has proven to be a powerful tool for species identification and delimitation. While DNA barcoding studies have been conducted in the family Heteroderidae, there has been a lack of research on species delimitation. Therefore, in 2024, a study was undertaken at the University of Limpopo to compare species delimitation analyses within the Meloidogyne genus based on the cytochrome c oxidase I (COI) region. In this study, ASAP species delimitation approaches were employed. A total of 73 sequences from South Africa were utilised (GenBank), representing four species (Meloidogyne sp, M. incognita, M. javanica, and M. enterolobii). The phylogenetic analyses grouped all the species into two major clades, with M. enterolobii being distinctly separate. In conclusion, the ASAP results showed no significant differences among the species. Therefore, the COI marker is not a suitable marker for Meloidogyne species. [ABSTRACT FROM AUTHOR]

Identification of Meloidogyne species is difficult using classical techniques alone, as some species have similar characteristics. Meloidogyne incognita is a plant-parasitic nematode that is one of the four most common species worldwide and has numerous hosts, including tomato (Solanum lycopersicum L.). This nematode is regarded as the most significant contributing factor to the reduction in tomato yield. Therefore, the present investigation was conducted in 2024 at the University of Limpopo to identify M. incognita. The COI mtDNA was sequenced and amplified from female nematodes, following which the blast result showed that the South African population exhibited a high similarity (100% identity) to those populations studied in China (MH743221 and MH743220). Utilizing the Maximum Likelihood method for phylogenetic analysis, it was demonstrated that our population and the other populations of M. incognita form a robust clade (87% bootstrap values). [ABSTRACT FROM AUTHOR]

The decline in the yield of tomato (Solanum lycopersicum L.) is largely attributed to the prevalence of nematodes belonging to the Meloidogyne species, commonly known as root-knot nematodes. The Meloidogyne species of nematodes are regarded as the most significant contributing factor to the reduction in tomato yield. Therefore, the present investigation was conducted in 2023 at the University of Limpopo to reveal that Meloidogyne javanica (Treub) Chitwood was the identified cause of the nematode. The ITS rDNA was sequenced and amplified from female nematodes, following which the blast result showed that the South African population exhibited a high similarity (99% identity) to those populations studied in the United States (AF387094 and U96305) and China (AY438555). A comparison to the USA population (AF387094), revealed four nucleotide differences. Utilizing the maximum likelihood method for phylogenetic analysis, it was demonstrated that our population and the other populations of M. javanica form a robust clade (91% bootstrap values). [ABSTRACT FROM AUTHOR]

Background and Objectives: The relationship between hepatitis C virus (HCV) infection and melanoma remains poorly understood. This study aimed to investigate the association between HCV and melanoma, assess outcomes in patients with both conditions, and explore potential molecular mechanisms connecting the two diseases. Materials and Methods: We conducted a retrospective cohort study of 142 melanoma patients, including 29 with HCV-related cirrhosis, and analyzed their clinical outcomes. For external validation, we used the TriNetX Global Collaborative Network database, comprising 219,960 propensity-matched patients per group. An in silico analysis was performed to identify the molecular pathways linking HCV and melanoma. Results: In the retrospective cohort, HCV-positive melanoma patients showed an increased risk of early relapse (41.4% vs. 18.6%, p = 0.014), recurrence (65.5% vs. 39.8%, p = 0.020), and mortality (65.5% vs. 23.0%, p < 0.001) compared to HCV-negative patients. TriNetX data analysis revealed that HCV-positive patients had a 53% lower risk of developing melanoma (RR = 0.470, 95% CI: 0.443–0.498, p < 0.001). However, HCV-positive melanoma patients had higher all-cause mortality (HR = 1.360, 95% CI: 1.189–1.556, p < 0.001). An in silico analysis identified key molecular players, including IL-6 and CTLA4, in the HCV-melanoma network. Conclusions: While HCV infection may be associated with a lower risk of melanoma development, HCV-positive patients who develop melanoma have poorer outcomes. The identified molecular pathways provide potential targets for future research and therapeutic interventions. [ABSTRACT FROM AUTHOR]

Abstract Odontogenic tumors are a group of tumors that originate from the tissues associated with tooth development and are classified into benign or malignant based on their behavior and characteristics. Tumor markers are substances that can be found in the blood, urine, or tissues of individuals with cancer. They are the substances produced either by tumor cells itself or by the body in response to tumor growth, can sometimes be used in the diagnosis, prognosis, and monitoring of various types of tumors. However, the use of tumor markers in odontogenic tumors is not as common as it is in other types of cancers, and their utility in this context is limited. Tumor markers are not the main tools for diagnosing cancer; instead, they serve as supplementary laboratory tests to aid in the diagnosis. Researchers continue to investigate potential biomarkers to improve our understanding of these tumors and their behavior. With this concept in mind, the objective of this study is to elucidate the key diagnostic markers essential for diagnosing odontogenic tumors.

Abstract Soybean, one of the most important oil seed crops known for its high-quality oil and protein content, is widely grown and consumed worldwide. However, the crop is severely affected by various biotic and abiotic factors, of which diseases are by far the most important, resulting in significant yield losses each year. The major diseases affecting soybean production include soybean rust, soybean mosaic virus, anthracnose, charcoal rot, Sclerotinia stem rot (white mold), seedling diseases, sudden death syndrome, frogeye leaf spot, and Stem canker. Development of soybean varieties resistant to these diseases using modern biotechnology techniques is a viable option to increase genetic potential and boost soybean production. This paper, hence, aims to explore the application of functional genomics in improving resistance to various diseases in soybean. Therefore, this paper provides a comprehensive overview of the progress made in improving soybean resistance to major diseases by using the various approaches of modern biotechnological tools such as molecular markers, QTL/gene mapping, omics technology, freely available online databases, genome editing, genetic modification, and marker-assisted breeding. This review also highlights future directions that may be important for genomics-based research programs to improve disease resistance in soybean while increasing production.