Genetic Variation Research Articles

Genetic and linguistic comparisons reveal complex sex-biased transmission of language features

The history of people’s movements and interactions shapes both genetic and linguistic variation. Genes and languages are transmitted separately and their distributions reflect different aspects of human history, but some demographic processes can cause them to be similarly distributed. In particular, forms of societal organization, including movements in and out of a community, may have shaped the transmission of both genes and languages. If children were more likely to learn their mother’s language than their father’s when their parents were from populations that spoke different languages or dialects, then language variation might show a closer association with maternally transmitted genetic markers than autosomal ones; this association could be further reinforced if children reside with predominantly maternal kin. We analyze the worldwide relationship between linguistic and genomic variation, leveraging the sex-biased transmission of X chromosomes to assess whether language has tended to be preferentially transmitted along the male or female line. In addition, we measure the effects of postmarital residence with female kin, matrilineal descent, and endogamy on the covariation of mitochondrial DNA and languages, using mtDNA because genomic data were available for very few populations with these ethnographic traits. We find that while there is little evidence for a consistent or widespread sex bias in the transmission of language, such biased transmission may have occurred locally in several parts of the world and might have been influenced by population-level ethnographic characteristics, such as female-based descent or residence patterns. Our results highlight the complex relationships between genes, language, ethnography, and geography.

Genotypic variation in nitrogen fixation characteristics in faba bean (Vicia faba L.) under contrasting phosphorus fertilizer regimes

AbstractAssessment of the genetic variability is an important step in improving nitrogen (N2) fixation potential of faba bean (Vicia faba L.) genotypes. The study was conducted to evaluate the genotypic variation for symbiotic N2 fixation traits of faba bean under contrasting phosphorus (P) fertilizer regimes. Twenty and 12 genotypes in the field and greenhouse, respectively, were planted under two P fertilizer regimes (P− and P+ corresponding to 0 and 46 kg/ha) using a randomized complete block design with three replications. Analysis of variance indicated highly significant (p < 0.01) variation among genotypes for all N2 fixation traits under both P regimes, indicating the availability of genotypic variation. Genotypes Obse, Dosha, Didea, Gebelcho, Gora, Moti, and Hachalu had better performance for N2 fixation traits and higher grain yield (GY) across all study conditions. Performances of all N2 fixation traits, except nitrogen harvest index, were better under P+ than under P−. P fertilizer application in the field resulted in 12.3, 12.9%, 18.9%, and 24.2% increase in the number of nodules per plant, nodule dry weight per plant (NDWP), N2 yield (NY), and the amount of N2 fixed (NF), respectively. In the greenhouse, 18.9%, 22.5%, and 27.2% increment was obtained for NDWP, NY, and NF, respectively, due to fertilizer application. Biplot analysis revealed that NF, NY, percentage of nitrogen derived from atmosphere (%Ndfa), shoot nitrogen concentration (ShN), and GY were the traits responsible for large genetic variation for N2 fixation. NF had higher heritability and formed a significant positive correlation with most nitrogen fixation traits, suggesting the potential of the trait to be improved through breeding.

Dissecting genetic variation for agro-morphological traits of elevated temperature under CO2-temperature gradient chamber and validation of markers linked to heat tolerance of rice (Oryza sativa L.)‏ cultivars of north-eastern Himalayan Region

Dissecting genetic variation for agro-morphological traits of elevated temperature under CO2-temperature gradient chamber and validation of markers linked to heat tolerance of rice (Oryza sativa L.)‏ cultivars of north-eastern Himalayan Region

Biochemical composition of Armenian chili pepper varieties: insights for functional food applications

Background: Capsicum annuum L. (pepper) is economically significant in many countries, including Armenia, where it helps conserve the vegetable gene pool and supports public health. Its rich biochemical composition makes it a key dietary component, particularly for its antioxidant properties, which combat free radicals. The biochemical makeup of peppers vary by genotype and maturity, leading breeders to develop varieties with both agronomic and nutritional benefits. Chili peppers are especially valued for their high carotene and ascorbic acid content, earning them the title of "multi vitamin concentrate," along with other vitamins and bioactive compounds that enhance their health benefits. Objective: This study examines the biochemical profiles of various Armenian chili pepper varieties, highlighting their nutritional value and potential in agricultural systems. By analysing these unique varieties, the research aims to advance knowledge of their health benefits and promote sustainable farming practices. Methods: The study examined six locally bred chili pepper varieties—'Artsiv', 'Punj', 'Kon', 'Deghin kakach', 'Oranj kakach', and 'Kaytsak'. Ascorbic acid, carotenoids, and phenols were measured at both the technical and biological ripening stages using spectrophotometry. Dry matter was determined by the thermogravimetric method, and sugar content by Bertrand’s method. Pungency was assessed using the Scoville heat units’ method, and statistical analysis was performed using ANOVA. Results: The study of six Armenian chili pepper varieties showed differences in fruit shape, color, ripening times, and productivity. 'Deghin kakach', 'Oranj kakach', and 'Kon' produce conical fruits that change to yellow, orange, and red, respectively, while 'Punj', 'Kaytsak', and 'Artsiv' have elongated fruits that ripen red. Early varieties like 'Punj', 'Artsiv', and 'Kaytsak' mature 11–17 days earlier. 'Oranj kakach' was the most productive (19.4 t/ha), while 'Kaytsak' had the lowest yield. 'Artsiv', 'Punj', and 'Kaytsak' were hot, while the others were moderately hot. Carotenoid content rose during ripening, ascorbic acid ranged from 115.0 to 175.6 mg/100 g, with 'Punj' highest, and total phenolics peaked in 'Deghin kakach'. Conclusion: Armenian chili pepper varieties are rich in bioactive compounds—phenols, ascorbic acid, carotenoids, and capsaicin— suitable for functional foods. During ripening, carotenoids increased by up to 583.64%, ascorbic acid by 97.4%, and phenols by 96.43%. ‘Punj’ had the highest ascorbic acid, ‘Oranj kakach’ the most carotenoids, and ‘Deghin kakach’ the most phenols, highlighting the potential of ripening to boost the health benefits of these peppers. Keywords: hot pepper, vitamin C, carotenoids, phenols, phenological stages, productivity

Juvenile and total reproductive values for sexual reproduction under any genetic system

Abstract Reproductive value (RV) is the expected contribution of genes by an individual or class of individuals to the gene pool in the distant future, and it plays a crucial role in understanding adaptation in long-term evolution. Class RVs are linked to the genetic system and to life history: for diploid genetics, Grafen derived expressions for relative RVs of female and male juveniles, and for the absolute RVs of all females and of all males. Subsequently, Gardner presented a derivation for relative RVs of juvenile females and males under haplodiploidy. Here we generalise these results to any genetic system for biparental sexual reproduction, such that RV is explicitly linked to parameters of the genetic system and life history. The earlier results by Grafen and Gardner arise as special cases. Finally, we derive expressions for absolute juvenile and total reproductive values of both sexes under any genetic system.

Genetic Variation in Yield and Fruit Weight Among Strawberry (Fragaria ×ananassa) Cultivars and the Interaction With Year and Location Effect

ABSTRACTStrawberry (Fragaria ×ananassa) is an important crop in the United States. In this study, we analysed strawberry trials established across 7 years and two locations. Our objective was to estimate genetic parameters and predict breeding values for yield. Linear mixed models were used for unbalanced data across years and locations and study the genotype by year and location interactions. The results suggested significant differences between cultivars for fruit weight but not for total and marketable yield. Fruit weight was controlled by genetic factors, shown by the high heritability of cultivar means (0.93), whereas marketable yield and total yield showed lower heritability estimates (0.48 and 0.63, respectively), indicating a substantial environmental influence. For fruit weight, cultivars exhibited stability across years and locations, supported by the high additive genetic correlations observed for cultivar‐by‐year (r = 0.90) and cultivar‐by‐location interactions (r = 0.98). Fruit weight and total yield were genetically independent as suggested near zero additive genetic correlation (−0.06 ± 0.416) between two traits, and they should be considered for an index selection in the strawberry breeding strategy.

Phenotypic variation and association of agronomic traits in tepary bean genotypes under drought-stress and non-stress conditions

Genetic variation for economic traits associated with drought adaptation is a prerequisite for developing climate-smart crop varieties, including tepary bean (Phaseolus acutifolius A. Gray). This study aimed to assess the magnitude of genetic variation and the relationship of agronomic traits among 45 tepary bean genotypes under drought-stress (DS) and non-stress (NS) conditions and to identify key traits to aid in the selection of genotypes for drought-tolerance breeding. The study was conducted across three locations in 2019/2020 and 2021/2022 seasons using a 9 × 5 alpha lattice design with two replications. Significant (p < 0.05) genotypic variation was observed for assessed traits under DS and NS conditions. Under DS and NS conditions, seed yield was significantly and positively correlated with the number of pods per plant (NPP) (r = 0.50 and r = 0.57, respectively) and above-ground shoot biomass (r = 0.34 and r = 0.29, respectively). This implied that simultaneous selection for these traits may improve seed yield gains. Highly statistically significant positive direct effects on seed yield were recorded for NPP under both DS and NS conditions. The following genotypes were high yielding and suitable for cultivation in drought-prone environments: G40138, G40042, G40148, G40136, G40150, G40144A, G40066A, G40020, G40022, G40069, G40068, G40063, G40129, G40133 and G40134.

Assessment of Dietary Patterns in Thyroid Patients in Zawia City, Libya

Hormonal abnormalities, especially those related to follicle-stimulating hormone (FSH). This study seeks to examine the relationships of BMI, dietary patterns, seafood intake, FSH levels, and genetic variables in patients with thyroid conditions. This cross-sectional study encompassed 94 patients with thyroid conditions. BMI was categorized into four classifications (&lt;17, 17–19, 20–25, &gt;25), and dietary patterns were divided into conventional, balanced, specific diets, and others. Seafood consumption was classified as daily, weekly, seldom, infrequently, or never. FSH levels were categorized into five ranges. Statistical analysis was conducted to evaluate the correlations among these characteristics. A significant correlation was seen between BMI and FSH levels (p = 0.000041), with people exhibiting a BMI &lt;17 demonstrating elevated FSH levels (&gt;15 in 10 participants). Individuals with a BMI exceeding 25 demonstrated reduced FSH levels (ranging from 1 to less than 5 in 18 subjects). Seafood consumption significantly influenced FSH levels (p = 0.002334), with weekly consumers exhibiting a wide range of FSH values, whereas infrequent or non-consumers demonstrated elevated FSH levels (&gt;15 in 5 subjects). Concerning dietary patterns, 60.63% adhered to a conventional diet, whereas 67% of patients have a familial history of thyroid disorders. Furthermore, 48.2% of subjects had second-degree obesity. This study highlights the intricate relationship among BMI, dietary habits, seafood intake, and hormonal regulation in patients with thyroid conditions. These factors, in conjunction with genetic predispositions, must be taken into account in the management of thyroid problems to enhance patient outcomes.

Assessment of Terminal Heat Stress Tolerance in Doubled Haploids Derived from Synthetic Hexaploid Wheat (Triticum aestivum L.) Using Genetic Variability and PCA-based Cluster Analyses

A comprehensive study was conducted on germplasm derived from two synthetic wheats and two hexaploid wheats i.e., SHW14102 x BWL4444, SHW14102 x BWL3531, and SHW3761 x BWL4444 to identify the potential doubled haploids that can withstand high temperatures, particularly at the reproductive stage during crop seasons viz., 2020–2021 and 2021–2022. The doubled haploid lines were selected based on phenotypic characteristics using genetic variability analysis. In the preliminary field trial evaluation, 100 lines were selected based on high phenotypic uniformity for further testing against terminal heat stress conditions and high yield potential. Among these, 17 lines had relatively higher values for days to biomass yield, grain yield, thousand-grain weight, and harvest index and relatively lower values for maturity, and grain filling duration based on principal component and cluster analyses. Principal component analysis (PCA) based cluster analysis exhibited that, clusters II and III had clear separation compared to cluster I. All three clusters were analyzed according to their means and standard deviations. The mean values for GYP (385.07), BMYP (1162.37), and TGW (38.13) were relatively higher in cluster 1 than in other clusters. Cluster 2 exhibited a higher value for DH (89.14), SL with awns (18.21), and GFD (18.19) while cluster 3 showed a higher value for HI (41.02). Thus, it was concluded that cluster I demonstrated superior performance in grain yield per plant, biomass yield per plant, and thousand-grain weight, indicating its overall higher productivity compared to the other clusters under terminal heat stress conditions and suggesting them as potential germplasm for future breeding programs.

Cryptic Diversity in Scorpaenodes xyris (Jordan & Gilbert 1882) (Scorpaeniformes: Scorpaenidae) Throughout the Tropical Eastern Pacific.

The tropical eastern Pacific (TEP) is a biogeographic region with a substantial set of isolated oceanic islands and mainland shoreline habitat barriers, as well as complex oceanographic dynamics due to major ocean currents, upwelling areas, eddies, and thermal instabilities. These characteristics have shaped spatial patterns of biodiversity between and within species of reef and shore fishes of the region, which has a very high rate of endemism. Scorpaenodes xyris, a small ecologically cryptic reef-dwelling scorpionfish, is widely distributed throughout the TEP, including all the mainland reef areas and all the oceanic islands. This wide distribution and its ecological characteristics make this species a good model to study the evolutionary history of this type of reef fish across the breadth of a tropical biogeographical region. Our evaluation of geographic patterns of genetic (mitochondrial and nuclear) variation shows that S. xyris comprises two highly differentiated clades (A and B), one of which contains four independent evolutionary subunits. Clade A includes four sub-clades: 1. The Cortez mainland Province; 2. The Revillagigedo Islands; 3. Clipperton Atoll; and 4. The Galapagos Islands. Clade B, in contrast, comprises a single unit that includes the Mexican and Panamic mainland provinces, plus Cocos Island. This geographical arrangement largely corresponds to previously indicated regionalization of the TEP. Oceanic distances isolating the islands have produced much of that evolutionary pattern, although oceanographic processes likely have also contributed.

Genetic diversity of Dalbergia melanoxylon Guill. &amp; Perr. populations in the Ferlo zone (Senegal) using nuclear and chloroplast microsatellite markers

AbstractDalbergia melanoxylon Guill. &amp; Perr. is a highly valued species in the Ferlo region, and its wood is used for various purposes by local populations, including firewood, service wood, and timber. This multifunctionality has weakened its populations, and it has been identified as threatened in previous research. The aim of this study was to investigate the genetic variability of three populations (LC, VC, and YC) along a north–south rainfall gradient, to support the species’ sustainable management and conservation. Eighteen microsatellite markers were used, including eight nuclear (nSSR) and 10 chloroplast (cpSSR) markers, to test their transferability to D. melanoxylon and study the genetic variability. The results showed that all nSSRs and cpSSRs were transferable, however, only five nSSRs and one cpSSR were polymorphic and used in the downstream analysis. Based on the nSSRs, comparatively high, but non-significantly different, genetic variation was found in all populations (LC: He = 0.650, VC: He = 0.674, YC: He = 0.706), however, indications of inbreeding were detected. For the single polymorphic cpSSR, three haplotypes were identified. Haplotype diversity (Hd) varied in LC (Hd = 0.536), VC (Hd = 0.577), and YC (Hd = 0.674). Low to moderate genetic differentiation was observed between populations (Fst nSSR = 0.019 and Fst cpSSR = 0.133) suggesting recent fragmentation of populations that has not yet impacted genetic variation but could become more pronounced in future generations. This finding underscores the need for further research on effective management and conservation strategies for D. melanoxylon populations in the Ferlo region.

Role of CD38 in mediating the effect of Bacillus on acute pancreatitis: a study of mediated Mendelian randomization

BackgroundSome studies suggest a potential link between intestinal flora and acute pancreatitis (AP). However, the causal relationships between specific intestinal flora and AP, and the possible mediating role of immune cell traits, remain unclear.MethodsA genome-wide association study (GWAS) involving 5,959 participants was conducted to identify genetic instrumental variables associated with 473 intestinal flora taxa. Summary statistics for AP were obtained from the UK Biobank. Immune cell traits were also identified using large-scale GWAS summary data. We employed a two-sample bidirectional Mendelian randomization (MR) approach to investigate the causal relationships between intestinal flora, immune cell traits, and AP, with inverse variance weighting (IVW) as the primary statistical method. Sensitivity analyses, including the MR-Egger intercept test, Cochran’s Q test, MR-PRESSO test, and leave-one-out test, were conducted to assess the robustness of our findings. Additionally, we explored whether immune cell traits mediate the pathway from intestinal flora to AP.Results11 positive and 11 negative causal relationships were identified between genetic susceptibility in intestinal flora and AP. Furthermore, 19 positive and 9 negative causal relationships were observed between immune cell traits and AP. Notably, CD38 mediated the causal relationship between Bacillus C and AP.ConclusionsThis study is the first to uncover novel causal relationships between various intestinal flora and acute pancreatitis, emphasizing the mediating role of immune cell traits in the pathway from intestinal flora to AP. It also provides new evidence supporting the conditional pathogenicity of the Bacillus genus.

Genetic variation perspective reveals potential drug targets for subtypes of endometrial cancer.

The study aims to identify potential drug targets for endometrial cancer (EC) subtypes through a Mendelian randomization (MR) approach, assessing their clinical relevance. We utilized genetic instruments for 4,907 plasma proteins from the deCODE Genetics study dataset, and data with EC (n = 12,906) from a genome-wide study (GWAS) meta-analysis in European populations for MR analyses. Complementary analyses included protein-protein interactions (PPI) network analysis, therapeutic efficacy evaluation, differential gene expression assessment, and prognosis evaluation. The expression levels of key drug targets were quantitatively measured at both the transcriptional and translational stages utilizing reverse transcription quantitative PCR (RT-qPCR) and immunohistochemistry (IHC). Additionally, we analyzed various clinicopathological features. Five drug targets for EC (CBR3, GSTO1, HHIP, IGF2R, and MMP10), seven for endometrioid subtypes (ACAP2, CBR3, GSTO1, HHIP, IGF2R, MMP10, and TLR2), and seven for non-endometrioid subtypes (CST3, DNAJB14, FSTL5, GMPR2, IFI16, MAPK9, and NEO1) were identified. Among these, IGF2R (OR = 1.165; 95% CI 1.067-1.272; p = 1.046 × 10- 2) and CST3 (OR = 0.523; 95% CI 0.339-0.804; p = 7.010 × 10- 3) were highlighted as key drug targets with causal evidence both at transcriptional and translational levels. This study preliminarily confirms that IGF2R and CST3 may serve as novel targets for the treatment of EC, providing a foundational reference for innovative clinical approaches to this disease.

Global Invasion of Thrips parvispinus (Karny) (Thysanoptera: Thripidae) Across Three Continents Associated With Its One Haplotype

ABSTRACTThrips parvispinus (Karny) is an exotic pest that has invaded many regions around the world in the last three decades. It was first detected in Florida in 2020 on ornamental plants (Hoya and Anthurium) in greenhouses and subsequently on ornamental plants in residential landscapes (Gardenia) in 2021. However, its first report on open vegetable field crops (Capsicum) in Florida was in 2022. We conducted field surveys and genetic analysis to answer three questions: (1) Is the population of T. parvispinus that invaded Florida the same as the one that has spread globally in the last few decades? (2) Is the host expansion to Capsicum in Florida a new population or the extension of the existing population reported on ornamental plants? and (3) What are the native and invaded distribution ranges of T. parvispinus? We analysed the genetic variation in the mitochondrial gene cytochrome oxidase I (COI) to address these questions. The global genetic diversity analysis of T. parvispinus revealed 18 haplotypes (populations) worldwide based on available data, but only one population (Hap1) invaded three continents: Africa, Europe, and North America. Based on available data, the highest haplotype diversity was observed in India, suggesting India may be part of the presumed native range (South and Southeast Asian countries) of T. parvispinus. Our survey of retail plant stores across 10 Florida counties indicated that plant trade is the source of T. parvispinus in open vegetable field crops and ornamental landscape plants. The outcome of this study will assist with regulatory and management decisions of T. parvispinus in Florida and elsewhere.

Population pharmacokinetic study of the effect of polymorphisms in the ABCB1 and CES1 genes on the pharmacokinetics of dabigatran

PurposeThe impact of genetic polymorphisms in the ABCB1 and CES1 genes on dabigatran plasma concentrations remains a subject of debate, and the purpose of this study was to quantitatively assess the effects of genetic polymorphisms on dabigatran esters in healthy Chinese subjects employed a population pharmacokinetic (PopPK) approach.MethodsIn total, 1,926 pharmacokinetic (PK) samples from 123 healthy individuals who were given 150 mg of dabigatran orally during a fasting state or postprandially were analyzed using the PopPK model. A two-compartment model with first-order absorption was found to adequately describe the PK data.ResultsThe results showed that covariates food intake and ABCB1 SNP rs4148738 were shown to have statistically significant impacts. Specifically, in postprandial administration increased lag time (ALAG) and clearance (CL) by 2.65% and 0.51%, respectively, and decreased absorption rate constant (KA) by 0.24%. Additionally, in subjects with CT genotype ABCB1 (rs4148738), the central ventricular volume of distribution (V2) was increased by 0.38%.ConclusionIn summary, the PopPK model developed in this study was robust and effectively characterized the pharmacokinetics of dabigatran in healthy Chinese adults, demonstrating that both food and ABCB1 genetic variation significantly influence the absorption and plasma concentration levels of dabigatran.

Host and geographically related genetic variation in species of Cloacina (Nematoda: Strongyloidea) from western and eastern grey kangaroos, Macropus fuliginosus and M. giganteus (Marsupialia: Macropodidae).

Host and geographically related genetic variation in species of Cloacina (Nematoda: Strongyloidea) from western and eastern grey kangaroos, Macropus fuliginosus and M. giganteus (Marsupialia: Macropodidae).

Unraveling the DNA methylation landscape in dog blood across breeds.

DNA methylation is a covalent bond modification that is observed mainly at cytosine bases in the context of CG pairs. DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment, in mammals. Genetic factors also impact DNA methylation, and the genetic diversity among various dog breeds provides a valuable platform for exploring this topic. Compared to those in the human genome, studies on the profiling of methylation in the dog genome have been less comprehensive. Our study provides extensive profiling of DNA methylation in the whole blood of three dog breeds using whole-genome bisulfite sequencing. The difference in DNA methylation between breeds was moderate after removing CpGs overlapping with potential genetic variation. However, variance in methylation between individuals was common and often occurred in promoters and CpG islands (CGIs). Moreover, we adopted contextual awareness methodology to characterize DNA primary sequences using natural language processing (NLP). This method could be used to effectively separate unmethylated CGIs from highly methylated CGIs in the sequences that are identified by the conventional criteria. This study presents a comprehensive DNA methylation landscape in the dog blood. Our observations reveal the similar methylation patterns across dog breeds, while CGI regions showed high variations in DNA methylation level between individuals. Our study also highlights the potential of NLP approach for analyzing low-complexity DNA sequences, such as CGIs.

Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments.

Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds-Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations. We identified 3,893 CNV regions (CNVRs) covering 19.15Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60kb to 488.0kb, with an average size of 4.92kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation (GBE1 and SOD1), heat stress adaptation (HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations (BoLA and KRT33A). In addition, variance stabilizing transformation (VST) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits. Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.

Extent and patterns of morphological and molecular genetic diversity and population structure of Nigerian Taro cultivars.

Genetic diversity is crucial for conservation efforts as well as breeding programs targeted at the development of improved varieties. Taro, a climate-resilient crop, plays a vital role in the nutritional and economic livelihoods of many households in Nigeria, but its yield is very low due to inadequate genetic improvement efforts. A diversity assessment of Nigerian taro is therefore required to create a premise for its improvement in yield, quality and disease tolerance. In this study, the genetic diversity and population structure of 490 taro cultivars comprising two main gene pools: Dasheen (215) and Eddoe (275), collected from farmers and marketers across seven states in Nigeria was assessed using 3047 Diversity Array Technology single nucleotide polymorphism (DArT-SNP) markers. A subset of 114 taro cultivars, comprising 30 Dasheens and 84 Eddoes were further phenotyped using 24 agro-morphological descriptors. Both phenotypic and molecular characterization revealed higher genetic diversity among the Eddoes than Dasheens. Estimates of gene flow (Nm = 0.353) revealed intermixing of cultivars among the States of collection, with the highest gene flow occurring between cultivars from Anambra and Ondo states and the lowest between Anambra and Kwara states. Population structure and Ward's minimum variance hierarchical cluster based on DArT-SNPs identified four groups, one comprising Dasheen and three comprising Eddoe cultivars. Hierarchical clustering based on phenotypic traits delineated three clusters. Variation between gene pools (49%) was higher than within gene pools (32%). Variation among States of collection was high (41%), while variation among individuals within gene pools (18%) and States of collection (19%) was relatively low. Correlation between phenotypic and genotypic diversity assessments was low (r = 0.01), indicating that both approaches were necessary for assessing genetic diversity in taro. However, genotypic assessment provided better information about genetic diversity of the taro cultivars. This is the first study that represented germplasm collection across the major taro growing regions of Nigeria. The findings from this study based on agro-morphological characterization and DArT-SNP genotyping are critical for genetic characterization, conservation and breeding of taro in Nigeria, mainly initiating hybridization between the two genepools after careful assessment of ploidy levels of the accessions collected in this study. This will facilitate in developing improved taro varieties with desirable traits, such as higher yield, better disease resistance, and improved nutritional quality.

Pan-cancer analysis of STAT3 indicates its potential prognostic value and correlation with immune cell infiltration in prostate cancer.

Targeting the STAT3 signaling pathway is a promising therapeutic approach for cancer patients. However, the association between STAT3 expression, the tumor immune microenvironment, and genetic variation remains unclear across human cancers, especially prostate cancer. We used R software and other tools to analyze pan-cancer and mutation data from publicly available databases statistically. A comprehensive investigation was performed to assess the genetic heterogeneity and clinical relevance of STAT3 in various malignancies, with a specific focus on its role in the immune landscape and prognostic significance in prostate cancer. The findings were validated through immunohistochemistry (IHC) and multiplex immunofluorescence (mIF). STAT3 expression is abnormal in the majority of cancer tissues, which is strongly correlated with these patients' prognosis. Eight measures of tumor heterogeneity and six measures of tumor stemness of multiple tumor types showed a strong correlation with STAT3 expression. Furthermore, in individuals with prostate cancer, STAT3 expression indicated the degree of immune cell infiltration and the advancement of the disease. IHC analysis revealed that STAT3 was down-regulated in prostate tumor tissues, while mIF analysis demonstrated that STAT3 signaling (p-STAT3) was extensively active in tumor tissues and positive lymph node tissues. STAT3 may serve as a valuable prognostic biomarker and therapeutic target across various cancers, with particular relevance to prostate cancer.