Phenotypic Level Research Articles

Estimation of Nature and Magnitude of Correlation among Different Traits in Chickpea (Cicer arietinum L.)

The present investigation aimed to study correlations among different traits in chickpea, specifically indicated that the traits —days to 50% blooming, days to maturity, harvest index (%), plant height (cm), number of primary branches per plant, number of pods per plant, number of seeds per pod, 100-seedweight (g), and seed output per plant. Compared to the matching phenotypic correlation coefficient, the estimations of genotypic correlation were greater. It could be the consequence of the environment's altering influence on the genotypic level of character association. Harvest index, number of seeds per pod, number of major branches per plant, number of pods per plant, biomass per plant, and 100-seed weight at the genotypic level all showed a statistically positive connection with the seed output per plant. At the phenotypic level, the following variables demonstrated a positive and significant correlation with seed yield per plant: harvest index, number of seeds per pod, number of major branches per plant, number of pods per plant, and 100-seed weight. These correlations showed that enhancing the aforementioned traits can increase seed output.

Assessment of Character Association in Pole Type French Bean (Phaseolus vulgaris L.) Genotypes

The present investigation was carried out at Regional Agricultural Research Station (RARS), Vijayapura during Rabi 2022-23. The experiment was laid out in Randomized Complete Block Design (RCBD) with two replications. To study the association studies in 32 pole type French bean genotypes. The correlation studies revealed that pod yield per plant was found positively and significantly associated with number of pods per plant (rg=0.668 and rp=0.620), pod length (rg= 0.526 and rp =0.431), average 10 pod weight (rg= 0.657 and rp = 0.660), number of pods per cluster (rg=0.373 and rp= 0.344) and number of clusters per plant (rg =0.365 and rp= 0.345) at both genotypic and phenotypic level. The direct selection for these traits would be rewarding for improvement of pod yield per plant in pole type French bean.

Trait Interactions and Yield Enhancement in Linseed (Linum usitatissimum L.): Insights from Correlation and Path Analysis

Linseed (Linum usitatissimum L.) is a self-pollinated (2n = 30) annual Rabi season crop mainly cultivated for flax fiber and oil due to its commercial use. The present investigation was carried out to study an association analysis among the yield and yield attributes using 75 linseed genotypes including 10 checks in a randomized block design with three replications at Oilseeds Research Farm, Kalyanpur, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, Uttar Pradesh, (India) during Rabi season of 2019-20. The correlation analysis revealed that the traits number of secondary branches per plant followed the number of primary branches per plant and number of capsules per plant at both the genotypic and phenotypic levels. The results of the path coefficient analysis revealed that traits such as the number of secondary branches per plant, number of capsules per plant, number of seeds per capsule, and plant height exhibited a strong and positive direct effect on seed yield per plant at both the genotypic and phenotypic levels. The seed yield can be improved by selecting traits such as number of primary branches per plant, number of secondary branches, number of capsules per plant, and plant height. It is recommended that the breeder focus on these traits in linseed to enhance its commercial value for the farming community.

Studies on Path Coefficient Analysis and Correlation to Evaluate the Relationships between Yield and Its Components in Fenugreek (Trigonella foenum-graecum L.)

The present investigation was carried out for correlation and path coefficient analysis in Fenugreek (Trigonella foenum-graecum L.) The correlation of different traits with seed yield was examined both at phenotypic and genotypic levels and the study showed that genotypic correlation coefficient values were higher than the phenotypic values. This indicated that how much of phenotypic correlation coefficient are influenced by environment. The seed yield per plant was positive and significant with biological yield per plant, test weight and number of branches per plant at genotypic and phenotypic levels. The maximum direct positive effect on seed yield per plant was observed in biological yield per plant, harvest index, days to 50 per cent flowering, number of seed per pod, number of branches per plant and number of pods per plant. In the present investigation, genotypes viz., AFG-4 and RMT-303 were superior for seed yield per plant along with other traits like biological yield, test weight and number of pods per plant. These diverse genotypes can be used in future breeding programme of fenugreek.

Association of ABO phenotype, rhesus factor, platelet count and hemoglobin level with oral hygiene status and severity of chronic periodontitis

BackgroundThe development of periodontal diseases has multifactorial causes including genetic factors. Limited investigations have been conducted to explore the association between ABO blood groups and the development and progression of periodontal diseases. AimTo evaluate and assess the association of ABO Phenotype and Rhesus factor with oral hygiene status, severity of chronic periodontitis and blood parameters like hemoglobin level and Platelet count in localized and generalized chronic periodontitis. Material and methodsStudy was carried out on 100 patients, out of which 80 patients of Generalized Chronic Periodontitis and 20 patients of Localized Chronic Periodontitis. Patients were categorized into Mild, Moderate and Severe Periodontitis. ResultA highly significant association was found between severity of periodontitis and blood groups with blood group B and O were found to be at a greater risk to develop moderate to severe form of chronic periodontitis. Also subjects with blood group B and O showed worst oral hygiene among all the blood groups. Also patients suffering from chronic periodontitis showed a general trend towards lower limit of both hemoglobin level and platelet. ConclusionGenetic factors such as ABO blood group antigens may act as a risk influencer that plays a role in progression and severity of the chronic periodontitis, with blood group B and O being worst affected. Another observation was that a long standing case of chronic periodontitis can lead to anemia thus having systemic implications.

Multi-omics analysis uncovers the transcriptional regulatory mechanism of magnesium Ions in the synthesis of active ingredients in Sophora tonkinensis

Magnesium (Mg) plays a pivotal role as an essential component of plant chlorophyll and functions as a critical coenzyme. However, research exploring the regulatory mechanisms of magnesium ions on the synthesis of secondary metabolites is still in its early stages. Sophora tonkinensis is a widely utilized medicinal plant in China, recognized for its diverse secondary metabolites with active properties. This study investigates variations in these ingredients in tissue-cultured seedlings under varying magnesium concentrations. Simultaneously, an omics data analysis was conducted on tissue-cultured seedlings subjected to treatments with magnesium and low magnesium. These comprehensive omics analyses aimed to elucidate the mechanisms through which magnesium influences active components, growth, and development. Magnesium exerts a pervasive influence on various metabolic pathways, forming an intricate network. Research findings indicate that magnesium impacts diverse metabolic processes, including the absorption of potassium and calcium, as well as photosynthetic activity. Consequently, these influences lead to discernible changes in the levels of pharmacologically active compounds and the growth and developmental status.This study is the first to employ a multi-omics data analysis in S. tonkinensis. This methodology allows us to uncover the overarching impact of metabolic networks on the levels of various active ingredients and specific phenotypes.

Character association and path analysis for yield and its attributing traits among urdbean landraces

In the present study, character association and path analysis were studied among 23 urdbean genotypes for 11 quantitative traits. Correlation analysis divulged that seed yield/plant proclaimed a significant positive relationship between branches/plant, biological yield/plant, pods/plant, and pod length at both genotypic and phenotypic levels and also showed a direct effect on yield. Biological yield/plant, branches/plant and pods/plant had the most beneficial direct and indirect influences on the overall relationship between yield and other component attributes, indicating the high inter-dependent interaction among these traits. Therefore, these characteristics could be considered as optimum selection indices on a priority basis, which would be remarkable for improving genotype efficiency during genetic improvement.

Serum pentraxin-3 expression varies according to polycystic ovary syndrome phenotypes.

Pentraxin-3 (PTX-3) is a multibiological protein involved in cumulus cell expansion, fertilization, and implantation. This study was designed to analyze how circulating PTX-3 levels change in women with polycystic ovary syndrome (PCOS). A total of 50 Turkish participants, 35 of whom had PCOS and 15 of whom were fertile, were included in the study. Patients in the PCOS group were divided into 4 different phenotypes according to the NIH criteria (phenotypes A-D). The number of patients in phenotype A was the highest 13 (37.1%). In the calculations made without phenotyping, the serum ptx3 levels of the PCOS group were found to be significantly lower compared to the fertile control group (3.32 ± 0.73 ng/mL vs 4.97 ± 1.29 ng/mL; P < .001). The ptx3 value of phenotypes A and B was significantly lower than phenotype D (P = .008 and P = .009, respectively). When the phenotypes were compared with the fertile control group, the PTX-3 levels of phenotypes A and B were significantly lower than the fertile group. Although the ptx3 levels of phenotypes C and D were lower than the fertile group, the difference did not reach statistical significance. This is the first study to investigate serum ptx3 levels by phenotype in PCOS. While serum PTX-3 levels decreased in phenotypes A and B, ptx3 levels in phenotypes C and D were similar in fertile patients.

Effect of aortic valve phenotype and sex on aorta dilation in patients with aortic stenosis

BackgroundBicuspid aortic valve (BAV) is often associated with a concomitant aortopathy. However, few studies have evaluated the effect of the aortic valve (AV) phenotype on the rate of dilation of...

Molecular and cell phenotype programs in oral epithelial cells directed by co-exposure to arsenic and smokeless tobacco.

Chronic arsenic exposure can lead to various health issues, including cancer. Concerns have been mounting about the enhancement of arsenic toxicity through co-exposure to various prevalent lifestyle habits. Smokeless tobacco products are commonly consumed in South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the in vitro molecular and cellular responses to arsenic and/or smokeless tobacco, we performed temporal multi-omics analysis of the transcriptome and DNA methylome remodelling in exposed hTERT-immortalized human normal oral keratinocytes (NOK), as well as arsenic and/or smokeless tobacco genotoxicity and mutagenicity investigations in NOK cells and in human p53 knock-in murine embryonic fibroblasts (Hupki MEF). RNAseq results from acute exposures to arsenic alone and in combination with smokeless tobacco extract revealed upregulation of genes with roles in cell cycle changes, apoptosis and inflammation responses. This was in keeping with global DNA hypomethylation affecting genes involved in the same processes in response to chronic treatment in NOK cells. At the phenotypic level, we observed a dose-dependent decrease in NOK cell viability, induction of DNA damage, cell cycle changes and increased apoptosis, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. Live-cell imaging experiments indicated that the DNA damage likely resulted from induction of apoptosis, an observation validated by a lack of exome-wide mutagenesis in response to chronic exposure to arsenic and/or smokeless tobacco. In sum, our integrative omics study provides novel insights into the acute and chronic responses to arsenic and smokeless tobacco (co-)exposure, with both types of responses converging on several key mechanisms associated with cancer hallmark processes. The generated rich catalogue of molecular programs in oral cells regulated by arsenic and smokeless tobacco (co-)exposure may provide bases for future development of biomarkers for use in molecular epidemiology studies of exposed populations at risk of developing oral cancer.

Selection Strategy for Yield Improvement of Chickpea Genotypes (Cicer arietinum L.)

An investigation was undertaken to assess the genetic variability parameters, correlation and path analysis in 25 chickpea genotypes for 12 quantitative traits during the Rabi season of 2022-23 in a Randomized Block Design with three replications. Analysis of variance indicated high significant differences among the genotypes for all the traits. Considerable variability existed in the genotypes for all the characters studied. The study found that CG23, CG159, and CG199 were the most superior genotypes for grain yield per plant among 25 chickpea genotypes. High PCV, GCV, heritability and genetic advance as percent of mean were recorded for test weight and biological yield. Grain yield per plant showed positive significant association with number of pods, days to maturity, days to 50% pod initiation and number of primary branches. High and positive direct effect of grain yield per plant at both phenotypic and genotypic levels were depicted by harvest index. These characters may be taken into consideration for selection of quantitative characters for crop improvement.

Assessment of genetic diversity by phenological traits, field performance, and Start Codon Targeted (SCoT) polymorphism marker of seventeen soybean genotypes (Glycine max L.).

The Egyptian-farmed soybeans have a wide range of genetic diversity which is most important in plant improvement programs in order to develop new higher yielding soybean genotypes. The present study is designed to determine the genetic variability among seventeen genotypes of cultivated soybean (Glycine max L.) by examining the phenotypic level at the seedling stage, field performance over two years 2022/2023 and genetically using Start Codon Targeted (SCoT) markers. Results indicated that the SCoT markers, 100 seed weight, and tip angle (TA) traits were positively correlated with H2L12, DR 101, H15L5, and H117 genotypes. In addition, the number of branches per plant and plant height were associated with H113, H32, Crowford, H129, and D7512035. Furthermore, the length of the first internode (LFI), root width (RW), root length (RL), and shoot length (SL) were more associated with Giza 111, NC105, and Hutcheson. The hierarchical cluster analysis (HCA) and its associated heatmap explored the differences among the genotypes. It showed that all examined parameters were clustered into four distinct clusters. The obtained results showed that genotypes NC105, H30, D75_12035, and H2L12 have promising phenological and morphological traits besides tracking the inheritance of nearby genes surrounding the ATG translation start codon since they are in a monoclades. The obtained results will help the breeder plan appropriate selection strategies for improving seed yield in soybeans through hybridization from divergent clusters.

Estimation of genetic variability and association of yield and related traits in indigenous grain amaranth (Amaranthus hypochondriacus L.) genotypes

Twenty-five genotypes of grain amaranth (Amaranthus hypochondriacus L.) were tested during the rabi 2019-20, for genetic factors such as genetic variability, correlation, and path analysis. For each of the 13 characters under study, the results of the analysis of variance revealed a significant variation among the genotypes. Characteristics with high GCV and PCV were the leaf area, biological yield per plant, number of branches per plant, harvest index, plant height, stem diameter and grain yield per plant. The biological yield per plant, leaf area, number of branches per plant, harvest index, length of inflorescence, girth of inflorescence, stem diameter, plant height, grain yield per plant, days to 50% flowering, and days to maturity showed high estimates of heritability along with high genetic advance. Therefore, choosing such traits will be more beneficial. At the genotypic and phenotypic levels, there was a positive and highly significant correlation between the characters days to 50 per cent flowering, days to maturity, plant height, length of inflorescence, stem diameter, leaf area, biological yield per plant and grain yield per plant. Based on the results of the path co-efficient analysis high direct influence was observed between grain yield and the days to 50% flowering, plant height, inflorescence length and girth of inflorescence, number of branches per plant, and biological yield per plant. Keywords: Correlation, Grain amaranth, Genetic variability, Heritability, Path co-efficient analysis

Establishment of mouse alveolar macrophage extraction standard and its application in the evaluation of efficacy in lung metastasis of colorectal cancer

Introduction: Alveolar macrophages (AM) are involved in the development and progression of a variety of lung diseases. It is of great significance to explore the pathogenesis of diseases and evaluate the efficacy of drugs. However, there is no standard process for extracting primary AM. Nitidine chloride is an alkaloid extracted from Zanthoxylum nitidum (Roxb.) DC., which has an anti-tumour pharmacological effect. However, there is no evidence that nitidine chloride has a direct effect on CRC cell lung metastasis. The purpose of this study was to establish a standard for the extraction of primary AM from mice and to investigate the pharmacodynamics of nitidine chloride in mice with lung metastases to colorectal cancer. Methods: The standard for the extraction of mouse primary AM by lavage was established. Western blot and PCR were used to detect the regulatory mechanism of nitidine chloride in the treatment of lung metastasis in mice by macrophage phenotype and glycolysis level. Results: The results showed that sufficient quantity and quality of primary AM could be obtained by optimising extraction steps, and AM obtained by this method could accurately reflect disease progression. At the same time, nitidine chloride can effectively reduce colorectal cancer lung metastasis in mice. From the mechanism, nitidine chloride can inhibit the expression of M2 macrophage markers and the levels of mRNA and proteins of the glycolysis-limiting enzyme. Conclusions: Our results show that primary AM that accurately reflect disease and assess pharmacological effects can be obtained using our established criteria. The inhibitory effect of nitidine chloride on colorectal cancer lung metastasis may be attributed to its regulation of macrophage phenotype and glycolysis.

Formalizing the law of diminishing returns in metabolic networks using an electrical analogy.

The way biological systems respond to changes in parameter values caused by mutations is a key issue in evolution and quantitative genetics, as it affects fundamental aspects such as adaptation, selective neutrality, robustness, optimality, evolutionary equilibria, etc. We address this question using the enzyme-flux relationship in a metabolic network as a model of the genotype-phenotype relationship. The lack of a suitable mathematical tool from biochemical theory to investigate this relationship led us to use an analogy between electrical circuits and metabolic networks with uni-uni reactions. We show that a behaviour of diminishing returns, which is commonly observed at various phenotypic levels, is inevitable, irrespective of the complexity of the system. We also present a possible generalization to metabolic networks with both uni-uni and bi-bi reactions.

Roflumilast Attenuates Microglial Senescence and Retinal Inflammatory Neurodegeneration Post Retinal Ischemia Reperfusion Injury Through Inhibiting NLRP3 Inflammasome.

Retinal ischemia-reperfusion (RIR) injury is implicated in various retinal diseases, leading to retinal ganglion cells (RGCs) degeneration. Microglial senescence exacerbates inflammation, contributing to neurodegeneration. This study aimed to investigate the potential therapeutic role of Roflumilast (Roflu) in ameliorating microglial senescence and neuroinflammation following RIR injury. C57BL/6J mice underwent RIR surgery, and Roflu treatment was administered intraperitoneally. BV2 microglial cells were subjected to oxygen-glucose deprivation and reoxygenation (OGD/R) to simulate ischemic conditions in vitro. SA-β-gal staining was used to detect cellular senescence. Quantitative PCR and ELISA were used to examine the levels of senescence-associated secretory phenotype (SASP) factors. Hematoxylin and eosin (H&E) staining was performed on retinal sections to assess retinal morphology and thickness. Surviving RGCs were labeled and quantified in retinal whole-mounts using immunofluorescence (IF). Furthermore, Western blot and IF staining were used to quantify the proteins associated with the cell cycle and NLRP3 inflammasomes. Roflu treatment reduced microglial senescence, ROS production, and secretion of pro-inflammatory cytokines in OGD/R-exposed BV2 cells. It also restored cell proliferation capacity and reversed OGD/R-induced cell cycle arrest. In vivo, Roflu alleviated retinal senescence, preserved retinal thickness, and protected against RGCs death in the RIR mouse model. Mechanistically, Roflu inhibited the NLRP3 inflammasome activation and suppressed DNA damage signaling pathway in microglia. Roflu exerts neuroprotective effects by mitigating microglial senescence and inflammation via inhibition of the NLRP3 inflammasome in RIR injury. These findings suggest that Roflu may serve as a promising therapeutic strategy for retinal diseases associated with ischemic injury by targeting microglial senescence.

Polycystic Ovary Syndrome Accompanied by Hyperandrogenemia or Metabolic Syndrome Triggers Glomerular Podocyte Injury.

Objective: To determine whether the urinary excretion of podocyte degradation products varies according to PCOS phenotype and metabolic syndrome (MetS). Methods: The concentrations of podocalyxin (PDX) and nephrin, chronic markers of podocyte damage, and neutrophil gelatinase-associated lipocalin (NGAL), a marker of acute glomerular damage, were analyzed in the morning urine samples of 50 PCOS patients and 50 healthy controls matched by age and BMI. Albuminuria was assessed by calculating the urine albumin-creatinine ratio (uACR). Results: The PDX, nephrin and NGAL concentrations of PCOS participants were significantly higher than those of the control group. While PDX, nephrin and NGAL levels of classic phenotypes were similar, they were higher than ovulatory and non-hyperandrogenic phenotypes. Significant increases in urinary levels of each podocyte protein were detected in PCOS patients with MetS compared to patients without MetS. A positive significant correlation between podocyte proteins and BMI, systolic blood pressure, testosterone, glucose, HOMA-IR and uACR. After adjusting for age and BMI, podocyte proteins were an independent risk factor for microalbuminuria. The incidence of microalbuminuria in PCOS increased 6-fold compared to controls. The frequency of microalbuminuria was higher in classical phenotypes than in ovulatory phenotype. The frequency of microalbuminuria in PCOS patients with MetS was 6.5 times higher than in PCOS patients without MetS. Conclusions: In PCOS accompanied by hyperandrogenemia or metabolic syndrome, leakage of acute and chronic podocyte breakdown products into the urine becomes more pronounced.

Genomic and phenotypic polymorphism of Clostridium botulinum Group II strain Beluga through laboratory domestication

Laboratory domestication is the result of genetic and physiological changes of organisms acquired during numerous passages in vitro. This phenomenon has been observed in bacteria as well as in higher organisms. In an effort to understand the impact of laboratory domestication on the foodborne pathogen Clostridium botulinum and related microbial food safety research, we investigated multiple spore stocks of C. botulinum Group II Beluga from our collection, as that is a widely applied model strain used in laboratories over decades. An acquired nutrient auxotrophy was confirmed as thymidine dependency using phenotypic microarrays. In parallel, whole-genome re-sequencing of all stocks revealed a mutation in thyA encoding thymidylate synthase essential for de-novo synthesis of dTMP from dUMP in the auxotrophic stocks. A thyA-deficient Beluga variant stock was successfully complemented by introducing an intact variant of thyA and thymidine prototrophy was restored, indicating that the thymidine auxotrophy was solely due to the presence of a SNP in thyA. Our data suggested that this mutation, deleterious under nutrient-poor growth conditions in a chemically defined medium, has been present and maintained in laboratory stocks for nearly 30 years. Yet, the mutation remained unidentified since receiving the strain, most likely due to routine use of culture conditions optimized for growth performance. This work pinpoints the need for careful monitoring of model strains extensively used in laboratory settings at both phenotypic and genomic level. In applications like food safety challenge tests, compromised strains could cause incorrect predictions and thereby have deleterious consequences. To mitigate the risk of acquiring mutations, we recommend keeping passage numbers of laboratory strains low and to avoid single-colony passaging. In addition, relevant strains should be subjected to regular WGS checks and physiological validation to exclude DNA mutations with potential negative impacts on research data integrity and reproducibility.

Quantifying Genetic Diversity Based on Morphological and Molecular Analysis in Pearl millet [&lt;i&gt;Pennisetum glaucum&lt;/i&gt; (L.) R. Br.] Inbred Lines

The experiment was carried out with thirty pearl millet inbred lines at Research Farm of ICAR-AICRP on Pearl Millet, Project Coordinating Unit, Mandor-Jodhpur during kharif 2020 in randomized block design (RBD) with three replications. Morphological and molecular diversity was assessed in 30 pearl millet inbred lines by Mahalanobis D2 analysis and Simple Sequence Repeats (SSR) molecular marker, respectively. Total five clusters were formed from D2 analysis and seven clusters were generated from SSR markers data analysis. The character viz. panicle girth, number of effective tillers per plant and 1000 seed weight contributed maximum to morphological diversity. The clustering pattern based on SSR markers data revealed that genotypes at molecular level had high diversity as compared to that seen at phenotypic level. There was significant differences among the clustering pattern of D2 and SSR molecular marker analysis. The reason may be environmental influence on phenotypic level. This information can be used as selection criteria to have hybridization between diverse parents to exploit heterosis in pearl millet breeding program.

Genetic Variability, Character Association and Path Analysis for Yield and Yield Components in Foxtail Millet [Setaria italica (L.) P. Beauv.] Accessions under Multi Environments in Foothills of Nagaland

Background: Foxtail millet cultivation inIndia’s North Eastern Hill regionholds promise due to its adaptation to diverse environments and high-quality grain. The objective of this study was to assess the amount of variability present among the genotypes, association of traits and find out foxtail millet genotypes that produce high yield in diverse environments. Methods: The investigation was carried out during July 2022 to May 2023 in four different dates of sowing. Two environments maintained under rainfed condition and the remaining two environments are maintained under irrigated condition. The experiment was conducted in randomized complete block design with three replications in all environments. Result: Analysis of variance revealed statistically significant differences (at 5%) among the 30 genotypes for all yield variables under evaluation. Genotype ‘G1’ exhibited superior performance for both yield and yield-related traits. The present study revealed considerable genetic variation among the yield traits, with all traits demonstrating high heritability except for harvest index.Traits such as fodder yield per plant, panicle length, biological yield, flag leaf width, peduncle length, panicle width and grain yield per plant show high heritability coupled with high genetic advance. A strong correlation was observed between grain yield per plant and several traits including days to 50% flowering, days to maturity, plant height, panicle length, flag leaf length, peduncle length, biological yield and fodder yield per plant. This correlation was consistent at both the genotypic and phenotypic levels. Biological yield exhibited the strongest direct influence on grain yield per plant, followed by harvest index, flag leaf width and number of base tillers on genotypic and phenotypic levels.