Phenotypic Level Research Articles

Domestication During Restoration: Unintentional Selection During Eight Generations of Wild Seed Propagation Reduces Herkogamy, Dichogamy and Heterozygosity in Clarkia pulchella.

Seed production on native seed farms has increased to meet the rising demand for plant material for restoration. Although these propagation efforts are necessary for restoration, cultivating wild populations may also result in unintentional selection and elicit evolutionary changes that mimic crop domestication, essentially turning these efforts into artificial domestication experiments. Here, we investigated whether phenotypic and genomic changes associated with domestication occurred in the wildflower Clarkia pulchella Pursh (Onagraceae) by comparing the wild source populations to the farmed population after eight generations of cultivation. At the phenotypic level, the farmed population shifted towards a floral morphology associated with self-pollination, with a significant decrease in both dichogamy and herkogamy. At the genomic level, > 6500 SNPs revealed that mean expected heterozygosity of the farmed population was significantly lower than the wild populations, despite the fact that the farmed population originated from a pool of multiple wild populations. Both the shift towards a selfing phenotype and the loss of diversity are expected consequences of domestication, although the phenotypic shifts in particular occurred much more rapidly than has been observed for other domestication traits. We discuss these results in the context of plant domestication and the implications for retaining the genetic integrity of wild populations during the process of seed production for restoration.

Correlation and Path Coefficient Analysis of Onion (Allium cepa L.) for Green Foliage Yield

The present investigation was carried out during the year 2023-24 in the experimental field of Department of Vegetable Science at Pt. KLS College of Horticulture and Research Station, Rajnandgaon under Mahatma Gandhi University of Horticulture and Forestry, Sankra-Patan, Durg (C.G.). The experiment, consisting of 11 varieties of onion was laid under Randomized Block Design (RBD) with three replications. High magnitude of phenotypic coefficient of variance were observed for green foliage yield per hectare (33.71%), green foliage yield per plot (33.46%) and diameter of bulb (22.74%). High magnitude of genotypic coefficient of variance were observed for green foliage yield per hectare (32.31%) and green foliage yield per plot (32.02%). The estimates of heritability were recorded high for dry matter percentage of leaves (97.97%). High value of genetic advance as percentage of mean was recorded for green foliage yield per hectare (63.79%). Green foliage yield per hectare had highly significant and positive correlation both at genotypic and phenotypic level with green foliage yield per plant (0.787 and 0.649), dry matter percentage of leaves (0.794 and 0.748), plant height (0.746 and 0.577), length of leaves (0.659 and 0.589), collar girth (0.814 and 0.533), dry matter percentage of bulbs (0.721 and 0.693) and moisture percentage of bulbs (0.740 and 0.646). Path coefficient analysis revealed positive and direct effect of green foliage yield per hectare was recorded via length of leaves followed by dry matter percentage of leaves, moisture percentage of bulbs, plant height, collar girth, dry matter percentage of bulbs, leaves width, moisture percentage of leaves, green foliage yield per plant and no. of leaves per plant.

Character Association and Path Analysis of Garlic (Allium sativum L.) for Yield and Its Attributes

This research sought to determine the associations between bulb yield and other traits and to measure their effects of yield attributes on bulb yield of garlic genotypes. The experiment was laid out in randomized complete block design (RCBD) with three replications using twenty garlic genotypes with one standard check variety (HL) at Kulumsa Agricultural Research center, during 2020-2021. Yield and agronomic traits were determined. The data from two years were analyzed separately because the homogeneity of error variances of both seasons were not similar. In both seasons the association analyses indicated that the bulb yield was positively and significantly associated with plant vigor (0.9762), plant height (0.9057), neck thickness (0.5918), leaf width (0.7527), number of clove per bulb (0.766), cloves weight (0.9621), bulb polar diameter (0.9247), pseudo stem length (0.7885), clove height (0.9161), clove diameter (0.6412). Days to maturity and leaf length were negatively correlated with bulb yield at genotypic and phenotypic level. Consequences of path analyses indicated that bulb polar diameter (1.2478), clove height (1.0911), clove weight (0.9621), plant height (0.9057) and plant vigor (0.9762) had the highest positive direct effect on bulb yield at genotype level in first season and number of clove per bulb (0.9971), leaf width (0.9126), neck thickness (0.9912) in the 20221 season. On the other hand, most of the indirect effects of yield components on bulb yield were significant and positive. Because of the significant direct effects and positive correlations of those traits on bulb yield at phenotypic and genotypic levels, may be observed as important traits for garlic genotypes selection programs.

Transcriptome response in a marine copepod under multigenerational exposure to ocean warming and Ni at an environmentally realistic concentration.

Due to anthropogenic activities, coastal areas have been challenged with multi-stresses such as ocean warming and nickel (Ni) pollution. Currently, studies have concerned the combined effects of Ni and warming in marine organisms at the phenotypic level; however, the underlying molecular mechanisms are poorly known. In this study, a marine copepod Tigriopus japonicus was maintained under warming (+ 4℃) and an environmentally realistic level of Ni (20 μg/L) alone or combined for three generations (F0-F2). Transcriptome analysis was performed for the F2 individuals. We found that the gene transcripts of copepods were predominantly down-regulated after Ni and warming exposure. Based on the results of GO and KEGG analysis, chitin metabolism, detoxification, antioxidant, apoptosis, and energy metabolism were screened in this study. Among the above functions, the combined exposure enriched more differential expression genes and had a larger fold change compared to Ni exposure alone, suggesting that warming increased the negative effect of Ni on marine copepods from a molecular perspective. Specifically, the combined exposure exacerbated the down-regulation of defense, apoptosis, xenobiotic efflux, GSH system, and energy metabolism, as well as the up-regulation of detoxification and peroxidase system. Overall, this study indicates that both ocean warming and Ni pollution adversely affect the marine copepod T. japonicus from multigenerational transcriptome analysis, especially warming increased Ni toxicity to marine copepods, and our results also provide references to the mechanism concerning the effects of Ni and warming on marine copepods.

Genetic associations of colostrum yield with antibodies concentration and gross composition for selective breeding in Italian Holsteins.

The quality of bovine colostrum, primarily determined by IgG concentration, is essential for the transfer of passive immunity and the development of the gastrointestinal tract in neonates. High IgG concentration in bovine colostrum (BC) is pivotal for the calf at first meal; however, while neonates often refuse to voluntarily drink the recommended amount of BC in the first hours of life, the dam frequently fails to produce a sufficient volume of colostrum at first milking. This study seeks to estimate the h2 of colostrum yield (CY) and its genetic correlations with total Ig, IgG, protein, and fat concentrations for the first time in the Italian Holstein population. Colostral Ig concentration and gross composition were assessed on individual samples collected using ad hoc near-infrared prediction models. The infrared-predicted traits along with the measured CY were used as phenotypes (n = 2,938) for the estimation of genetic parameters through linear animal models. Parity, photoperiod at calving, and classes of CY of the dam significantly impacted on the colostral composition, with parity having the most substantial influence. Colostrum of older cows, in fact, had greater total Ig, IgG, and protein concentrations than colostrum of younger cows. Colostral quality and CY were higher when calvings occurred in months with decreasing photoperiod. Also, CY was maximum in second-parity cows. Heritability estimates of IgG and total Ig concentrations were 0.225 ± 0.05 and 0.211 ± 0.05, approximately twice the h2 estimate for CY (0.101 ± 0.03). The correlation between CY and IgG concentration was positive (0.219 ± 0.032) at the phenotypic level and negative at the genetic level (-0.147 ± 0.190). Spearman rank correlations between EBV of the colostrum traits and official EBV/indexes for which there is selection ongoing in Italian Holstein breed were generally weak or moderate, and not always significant. Specifically, the CY was unfavorably associated with the PFT (production, functionality, and type; -0.300) and the IES index (economic health; -0.335), and IgG concentration was favorably linked to the official index for udder health/mastitis resistance (0.154) and fertility (0.166), mirroring those calculated for total Ig. Selection toward an intermediate optimum for CY at calving can be potentially pursued in the Italian Holstein breed through a balanced index without incurring additional costs for the IgG concentration.

Evaluation of the toxicity of perfluorooctanoic acid toward human colorectal cancer cells using multi-dimensional approaches

While human exposure to perfluorooctanoic acid (PFOA) can lead to ulcerative colitis, the molecular mechanisms responsible for PFOA-induced intestinal toxicity are unclear. Herein, we examined the toxicity of PFOA toward human colorectal cancer cells (HCT116) from three dimensions: the cytotoxic phenotype, cell respiration, and transcription levels of metabolism-related genes. Formazan was used to assess how PFOA exposure affects HCT116-cell relative viability, after which the mitochondrial respiratory activities of these cells were determined by analyzing extracellular flux. The quantitative real-time polymerase chain reaction (qPCR) method was used to detect metabolism-related gene expression levels. The cytotoxicity assay revealed that the HCT116 showed significantly inhibited relative activities compared to those of the control when exposed to 300 μmol/L PFOA for 48 h (p<0.01), with most cells retained at the G0/G1 stage. In contrast, the mitochondrial respiratory activities of the HCT116 were promoted by concentrations of PFOA as low as 50 μmol/L. Two genes related to cellular metabolism (dipeptidase 1 (DPEP1) and sphingosine kinase 1 (SPHK1)) were found to be related to the PFOA-promoted formation of ulcerative colitis using our self-developed Metabolic Gene and Pathway Query software and Comparative Toxicogenomics Database (CTD). The qPCR studies revealed that DPEP1 and SPHK1 expression levels were enhanced by 8-10 times in HCT116 exposed to 300 μmol/L PFOA relative to the control, whereas this trend was not observed for HCT116 exposed to 50 μmol/L PFOA. Collectively, these results suggest that the respiratory activity of cellular mitochondria may serve as an index for determining the interference effects associated with PFOA and that metabolic pathways mediated by DPEP1 and SPHK1 may be involved in the development of PFOA-induced ulcerative colitis. Future studies should investigate the relationships between changes in metabolism-related genes (DPEP1 and SPHK1) and the mitochondrial respiratory activities of intestinal cells, and verify the roles played by the DPEP1 and SPHK1 genes in PFOA-induced intestinal inflammation using in-vivo models.

SLAMF7 defines subsets of human effector CD8 T cells

Long-term control of viral replication relies on the efficient differentiation of memory T cells into effector T cells during secondary immune responses. Recent findings have identified T cell precursors for both memory and exhausted T cells, suggesting the existence of progenitor-like effector T cells. These cells can persist without antigenic challenge but expand and acquire effector functions upon recall immune responses. In this study, we demonstrate that the combination of SLAMF7 with either CD27 or TCF-1 effectively identifies progenitor-like effector CD8 T cells, while SLAMF7 with GPR56 or TOX defines effector CD8 T cells. These markers allow for the clear segregation of these distinct cell subsets. SLAMF7+ CD8T cells are dynamically modulated during viral infections, including HIV, HCV, CMV, and SARS-CoV-2, as well as during aging. We further characterize the SLAMF7 signature at both phenotypic and transcriptional levels. Notably, during aging, the SLAMF7 pathway becomes dysregulated, resulting in persistent phosphorylation of STAT1. Additionally, SLAMF7 ligation in the presence of IL-15 induces TCF-1 expression, which promotes the homeostatic proliferation of progenitor-like effector CD8 T cells.

Variability analysis in genotypes of black pepper (Piper nigrum L.) for yield and yield related traits

Black pepper (Piper nigrum L.) is the world’s major spice crop. India faces tough competition from other black pepper-producing countries in both production volume and productivity. There is a pressing need to enhance production per unit area by developing improved varieties with superior quality attributes. Ten genotypes of black pepper developed by different centers of the All India Co-ordinated Research Project on Spices were evaluated. The relationships between dry berry yield and yield-related traits in black pepper were analyzed. Data were collected on five quantitative traits, namely spike length (cm), number of berries per spike, fresh berry yield per plant (kg), dry berry yield per plant (kg) and dry recovery (%) during 2022-23. Analysis of variance revealed highly significant differences for all characters. Highest genotypic coefficient of variation and phenotypic coefficient of variation were observed for the number of berries per spike, spike length and dry berry yield per plant. Lowest values of genotypic coefficient of variation and phenotypic co-efficient of variation were noted for dry recovery. Genotypes exhibited high heritability and genetic improvement over the mean for the number of berries per spike and spike length. This suggests that additive gene effects influence the expression of these traits. Yield of dry berries per plant showed a very strong correlation with fresh berry yield, dry recovery and the number of berries per spike, both at the phenotypic and genotypic levels. In the path analysis, yield of fresh berries, dry recovery percentage and the number of berries per spike exhibited strong positive direct and indirect effects on the yield of dry berries. Genotype PRS 161 exhibited superior performance in terms of morphological traits, yield and yield-related characteristics, followed by SV 11 among the various genotypes analyzed. High yielding genotypes identified in this study can be considered for developing new varieties and can also be utilized in future breeding programs.

Phenotypic and Genetic Diversity Analysis of 18 Ornamental Strawberries

The red-flowered strawberry is a novel ornamental plant. This study aimed to assess the genetic diversity among ornamental strawberry germplasm resources. In this investigation, 17 red-flowered strawberry germplasms and 1 white-flowered strawberry germplasm were analyzed for genetic diversity and genetic relationships using a combination of phenotypic data, inter-simple sequence repeats (ISSR), and conserved DNA-derived polymorphism (CDDP) molecular markers. The results indicated that the 18 strawberry germplasms exhibited significant variability and genetic diversity at both phenotypic and molecular levels. The clustering results revealed notable differences between phenotypic clustering and molecular marker clustering, while the ISSR and CDDP markers grouped into broadly similar clusters. We further consolidated the ISSR and CDDP marker data to conduct the cluster analysis and population structure analysis of the 18 strawberry germplasms. The cluster analysis classified these germplasms into four clusters at a genetic similarity coefficient of 0.77. The population structure analysis categorized the germplasms into three groups, with 88.89% exhibiting a Q value ≥ 0.6, and 11.11% demonstrating a Q value &lt; 0.6. This finding suggests that the genetic background of the 18 strawberry germplasms is relatively homogeneous. Notably, ‘Summer Breeze-Rose’ and ‘Summer Breeze-Cherry’ possess relatively complex genetic backgrounds (Q &lt; 0.6). Furthermore, the floral, foliar, and plant traits of both germplasms display significant ornamental value and can serve as vital resources for the development and utilization of ornamental strawberries, as well as for the selection and breeding of new varieties.

Phenotypic and Genomic Signatures of Latitudinal Local Adaptation Along With Prevailing Ocean Current in a Coastal Goby.

In the marine realm, unidirectional ocean currents often lead to high migration rates of marine organisms and, therefore, inhibit the formation of their latitudinal genetic structure. In contrast, cryptic latitudinal structures associated with local adaptation may frequently exist in widespread species generally exposed to a strong environmental heterogeneity. However, our understanding of the evolvability of locally adapted populations in open marine environments still needs to be completed. The coastal area along the Sea of Japan, where the Tsushima Warm Current flows from south to north in the Japanese Archipelago, provides a good model system for exploring this question. This study explored evidence for latitudinal local adaptation along with the prevailing ocean current in the ice goby Leucopsarion petersii at the phenotypic and genomic levels. Common garden experiments clearly showed genetically based clinal variation in growth rate, strongly suggesting local adaptation through conutergradient selection of this fitness-related trait. Analyses based on reduced-representation sequencing revealed a slight signal of genetic differentiation between the southern and northern populations, although continuous historical gene flow between them was supported by demographic modelling. Also, whole-genome resequencing showed their independent demographic history during the last glacial period. Thus, these results suggest that gene flow along with the prevailing ocean current is somewhat limited, and the populations are not completely panmictic. Furthermore, the selection scan based on low-coverage genome-wide sequencing detected putative genomic signatures of latitudinal adaptation of growth-related genes. Thus, our integrative study provided a novel example of marine local adaptation under a large ocean current.

Prognostic factors affecting ALS progression through disease tollgates.

Understanding factors affecting the timing of critical clinical events in ALS progression. We captured ALS progression based on the timing of critical events (tollgates), by augmenting 6366 patients' data from the PRO-ACT database with tollgate-passed information using classification. Time trajectories of passing ALS tollgates after the first visit were derived using Kaplan-Meier analyses. The significant prognostic factors were found using log-rank tests. Decision-tree-based classifications identified significant ALS phenotypes characterized by the list of body segments involved at the first visit. Standard (e.g., gender and onset type) and tollgate-related (phenotype and initial tollgate level) prognostic factors affect the timing of ALS tollgates. For instance, by the third year after the first visit, 80-100% of bulbar-onset patients vs. 43-48% of limb-onset patients, and 65-73% of females vs. 42-49% of males lost the ability to talk and started using a feeding tube. Compared to the standard factors, tollgate-related factors had a stronger effect on ALS progression. The initial impairment level significantly impacted subsequent ALS progression in a segment while affected segment combinations further characterized progression speed. For instance, patients with normal speech (Tollgate Level 0) at the first visit had less than a 10% likelihood of losing speech within a year, while for patients with Tollgate Level 1 (affected speech), this likelihood varied between 23 and 53% based on additional segment (leg) involvement. Tollgate- and phenotype-related factors have a strong effect on the timing of ALS tollgates. All factors should be jointly considered to better characterize patient groups with different progression aggressiveness.

Genetic Variability and Character Association among Common Bean (Phaseolus vulgaris L.) Genotypes at Areka, Southern Ethiopia

Evaluating genetic variability among genotypes is vital for identifying superior genotypes because selecting parents who create segregating populations is critical in breeding programs. The current study was done at Areka Agricultural Research Center during the 2020/21 major cropping season, with the goal of estimating genetic diversity and character connection among 25 common bean genotypes. The experiment consisted of two replications of a 5 x 5 simple lattice design. Data were obtained on 12 quantitative parameters, and the analysis of variance revealed extremely significant variations between genotypes for all characters. It demonstrated that genotypes vary significantly. GCV and PCV were highest in plant height, number of pods per plant, biological yield, number of seeds per plant, and seed yield, while lowest in days to flowering and days to maturity. Plant height, number of pods per plant, number of seeds per plant, biological yield, and seed yield all showed significant broad-sense heritability (H2) and high predicted genetic advance as a percentage of mean GAM. This suggested the presence of additive gene activity in the inheritance of these traits. The number of major branches per plant, biological yield, days of 50% flowering, hundred seed weight, and harvest index all show a highly substantial and positive link with seed yield at both genotypic and phenotypic levels. The biological yield and harvest index both have a strong positive direct effect on seed output. As indicated, these traits could be utilized for selection to increase seed output. Based on the D2 value, 25 common bean genotypes were divided into four clusters. Clusters I and IV had the greatest inter-cluster distance (766.78), whereas clusters I and II had the smallest (53.78). Breeding programs could use genotypes from distant clusters to increase variety. Thus, the enormous genetic variation among common bean genotypes must be evaluated for use in common bean breeding efforts.

Every Cog and Wheel: Identifying Biocomplexity at the Genomic and Phenotypic Level in a Population Complex of Chinook Salmon

Genetic diversity is the fundamental building block of biodiversity and the necessary ingredient for adaptation. Specifically, the intra-specific diversity (biocomplexity) comprised of phenotypic and genetic variation partitioned within and among populations can determine the ability of a species to respond to changing environmental conditions. Here, we explore the biocomplexity of California’s Central Valley Chinook salmon (Oncorhynchus tshawytscha) population complex at the genomic level by quantifying population genomic diversity among and within migration life-history phenotypes. Notably, despite apparent gene flow among populations with the same migration (life history) phenotypes inhabiting different tributaries, each group is characterized by a distinct component of unique genomic diversity. While enumerating biodiversity contained within individual hierarchical levels is informative, it is important to consider inter- and intra-specific diversity simultaneously as there may be emergent properties at higher levels due to presence of diversity at lower ones. Our results emphasize the importance of formulating conservation goals focused to maintain biocomplexity at both the phenotypic and genotypic level. Doing so will preserve the species’ adaptive potential and increase the probability of persistence of the population complex despite changing environmental pressures.

Triplet therapy for metastatic castration-sensitive prostate cancer: Rationale and clinical evidence.

Prostate cancer (PC) growth is hormone-dependent and it frequently develops distant metastases as disease progresses. Patients with metastatic castration-sensitive prostate cancer (mCSPC) initially respond to androgen deprivation therapy (ADT) but eventually become refractory and develop metastatic castration-resistant prostate cancer (mCRPC). Castration-resistance is associated with high lethality and metastases confer poor prognosis, therefore unmet needs in treatment for mCSPC remain high. So far, improvements in survival in mCSPC have been achieved by doublet combination therapy such as docetaxel or an androgen-receptor signaling inhibitor (ARSI) in addition to ADT. Further, recent phase 3 trials have shown that triplet therapy-a combination of ARSI, docetaxel, and ADT improves prognosis compared with docetaxel plus ADT in mCSPC. PC tumors manifest intra- and inter-tumoral heterogeneity at both the genetic and phenotypic level. As heterogeneity increases during sequential treatment and disease progression, it is reasonable to initiate combination therapy using drugs with different mechanisms of action early in the course of disease, such as mCSPC. Previous research about tumor heterogeneity and drug resistant mechanism support this rationale, as well as preclinical studies and real-world data provide the scientific evidence of benefit by combining ARSI and docetaxel. Here, we review the rationale and clinical evidence for triplet therapy in patients with mCSPC.

Correlation between Phenotype and Coagulation Factor Activity Level in Rare Bleeding Disorders: A Systematic Review.

Rare bleeding disorders (RBDs) represent 3 to 5% of congenital bleeding disorders and are primarily inherited in an autosomal recessive manner, with increased prevalence in consanguineous populations. Clinically, RBDs can be accompanied by mild to severe bleeding episodes, often assessed using bleeding assessment tools (BATs) such as the International Society on Thrombosis and Hemostasis (ISTH)-BAT. However, the correlation between bleeding severity and coagulation factor activity levels remains inconsistent. This systematic review investigates this relationship to enhance understanding and improve management strategies for patients with RBD. This review adhered to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and was registered with the International Prospective Register for Systematic Reviews (PROSPERO) (CRD42024504537). Using the PICO (Population, Intervention, Comparator, and Outcomes) framework, the study focused on RBD patients to explore the correlation between coagulation factor activity levels and bleeding severity. A comprehensive search was conducted across PubMed, Scopus, and Web of Science until April 1, 2024, with data extracted on bleeding severity, phenotype, and coagulation factor activity levels. The analysis highlights complex and often inconsistent relationships between coagulation factor levels and the severity of bleeding. In cases of fibrinogen deficiency, three out of four studies (n = 73 of 111 cases, 66%) demonstrated a moderate to strong correlation between fibrinogen levels and bleeding severity. In prothrombin deficiency, one of two studies (n = 16 of 29 cases, 55%) found a strong correlation between FII levels and bleeding severity. Four of six studies (n = 106 of 139 cases, 76%) in FV deficiency found a weak or no correlation between factor activity and bleeding severity. In combined FV and FVIII deficiency, two of three studies (n = 26 of 60 cases, 43%) found a significant correlation between factor activity and bleeding severity. In FVII deficiency, four (of nine) studies with a study population of 325 patients (65%) found a weak correlation between factor activity and severity of bleeding. Almost all studies (five of six studies, n = 114 of 118 patients, 97%) in FX deficiency revealed a strong correlation between FX levels and bleeding severity. In FXI deficiency, most studies (five of seven studies, n = 254 patients, 93%) found a weak or no correlation between factor activity and bleeding severity or symptoms. For FXIII deficiency, there was a moderate to strong correlation between FXIII activity and bleeding severity in all three studies (n = 61 patients). In conclusion, despite current controversies, this review highlights a moderate or strong correlation between factor activity and bleeding severity in fibrinogen, FX, and FXIII deficiencies, but no correlation or weak correlation for FV, FVII, and FXI deficiencies. Further prospective studies with standardized BATs on a large number of patients are needed to better understand these relationships and optimize patient management.

Character Association and Path Analysis in Bitter Gourd (Momordica charantia L.) for Yield and Its Attributes

The field experiment was carried out in Department of Vegetable Science, College of Horticulture at Banda University of Agriculture and Technology during kharif to evaluate the 15 bitter gourd genotypes with three replications in randomized block design were to correlation and path coefficient for yield and its component traits. At phenotypic level fruit yield per plot displayed positive and highly significant correlation with internodal length, number of fruits per plant, average fruit weight, fruit length, vine length and number of primary branches per plant. At genotypic level fruit yield per plot exhibited positive and significant correlation with number of primary branches per plant, intermodal length, number of fruits per plant, vine length, average fruit weight and fruit length. Path analysis at phenotypic level have highest positive direct effect on yield per plot was exerted by average fruit weight followed by number of fruits per plant, days to first male flower anthesis, node number to first pistillate flower, fruit length, intermodal length and node number to first stamin ate flower. At genotypic level, highest positive direct effect on yield per plot was exerted by average fruit weight followed by number of fruits per plant, internodal length, node number to first pistillate flower, TSS and days to first female flower anthesis.

Nicotinamide mononucleotide suppresses cellular senescence and increases aquaporin 5 expression in the submandibular gland of aged male mice to ameliorate aging-related dry mouth.

Dry mouth results from decreased saliva secretion due to aging or drug side effects. Decreased saliva secretion causes dryness in the oral cavity that makes swallowing difficult and increases the risk of aspiration pneumonia. There are few fundamental treatments for dry mouth. Here we investigated whether treatment of old mice with nicotinamide mononucleotide (NMN) improved factors associated with dry mouth. Young (16-week-old) and old (113-week-old) male mice were treated subcutaneously with saline or NMN (300mg/kg) once every two days for four weeks and saliva secretion was measured. The amount of nicotinamide adenine dinucleotide (NAD+) in salivary gland tissues was measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gene expression in the intestinal tract and salivary glands was measured by real-time PCR. The population of cells with acetylation in the submandibular gland was quantified by immunohistological staining. SA-β-gal activity in the submandibular gland was measured to assess cell senescence. Statistical analysis was performed by one-way analysis of variance with Tukey post hoc analysis. The submandibular glands from old mice treated with NMN exhibited increased saliva secretion and NAD+ levels, which both decrease with aging. In addition, the submandibular glands from NMN-treated old mice had decreased acetylation, numbers of senescent cells, and levels of senescence-associated secretory phenotype (SASP) factors, which all increase with aging, as well as increased aquaporin5 (AQP5) mRNA expression. NMN administration may improve dry mouth by regulating cellular senescence in the submandibular gland and increasing expression of AQP5, a water channel involved in saliva secretion, to inhibit age-related decreases in saliva secretion. It is necessary to elucidate further mechanism and confirm its effectiveness in humans.

Deciphering new insights into copy number variations as drivers of genomic diversity and adaptation in farm animal species.

The basis of all improvement in (re)production performance of animals and plants lies in the genetic variation. The underlying genetic variation can be further explored through investigations using molecular markers including single nucleotide polymorphism (SNP) and microsatellite, and more recently structural variants like copy number variations (CNVs). Unlike SNPs, CNVs affect a larger proportion of the genome, making them more impactful vis-à-vis variation at the phenotype level. They significantly contribute to genetic variation and provide raw material for natural and artificial selection for improved performance. CNVs are characterized as unbalanced structural variations that arise from four major mechanisms viz., non-homologous end joining (NHEJ), non-allelic homologous recombination (NAHR), fork stalling and template switching (FoSTeS), and retrotransposition. Various detection methods have been developed to identify CNVs, including molecular techniques and massively parallel sequencing. Next-generation sequencing (NGS)/high-throughput sequencing offers higher resolution and sensitivity, but challenges remain in delineating CNVs in regions with repetitive sequences or high GC content. High-throughput sequencing technologies utilize different methods based on read-pair, split-read, read depth, and assembly approaches (or their combination) to detect CNVs. Read-pair based methods work by mapping discordant reads, while the read-depth approach works on detecting the correlation between read depth and copy number of genetic segments or a gene. Split-read methods involve mapping segments of reads to different locations on the genome, while assembly methods involve comparing contigs to a reference or de novo sequencing. Similar to other marker-trait association studies, CNV-association studies are not uncommon in humans and farm animals. Soon, extensive studies will be needed to deduce the unique evolutionary trajectories and underlying molecular mechanisms for targeted genetic improvements in different farm animal species. The present review delineates the importance of CNVs in genetic studies, their generation along with programs and principles to efficiently identify them, and finally throw light on the existing literature on studies in farm animal species vis-à-vis CNVs.

PsyRiskMR: a comprehensive resource for identifying psychiatric disorders risk factors through Mendelian randomization

BackgroundPsychiatric disorders pose an enormous economic and emotional burden on individuals, their families and society. Given that the current analysis of the pathogenesis of psychiatric disorders remains challenging and time-consuming, elucidating the modifiable risk factors becomes crucial for the diagnosis and management of psychiatric disorders. However, inferring the causal risk factors in these disorders from disparate data sources is challenging due to constraints in data collection and analytical capabilities. MethodsBy leveraging the largest available genome-wide association studies (GWAS) summary statistics for ten psychiatric disorders and compiling an extensive set of risk factor datasets, including 71 psychiatric disorders-specific phenotypes, 3,935 brain imaging traits, and over 30 brain tissue/cell-specific xQTL datasets (covering 6 types of QTLs), we performed comprehensive Mendelian randomization (MR) analyses to explore the potential causal links between various exposures and psychiatric outcomes using genetic variants as instrumental variables. ResultsAfter Bonferroni correction for multiple testing, we identified multiple potential risk factors for psychiatric disorders (including phenotypic level and molecular level traits), and provided robust MR evidence supporting these associations utilizing rigorous sensitivity analyses and colocalization analyses. Furthermore. we have established the PsyRiskMR database (http://bioinfo.ahu.edu.cn/PsyRiskMR/), which serves as an interactive platform for showcasing and querying risk factors for psychiatric disorders. ConclusionsOur study offered a user-friendly PsyRiskMR database for the research community to browse, search, and download all MR results, potentially revealing new insights into the biological etiology of psychiatric disorders.

Integrating transcriptome and physiological analysis reveals the stress responses of rose petals to surface water in the iron-mining area

Mining activities in the iron area mining have caused serious pollution of surface water in the area, which in turn affects the normal growth and development of plants. As a restorative plant with heavy metal adsorption function, the stress response mechanism of rose to surface water in the iron-mining area remains unelucidated. In this study, we investigated the effects of surface water treatment on the phenotypic, physiological and molecular levels of the plant using rose as a material. The results showed that surface water in the Bayan Obo iron mining area caused darkening and soft rotting of rose petals, increased degree of petal damage, decreased the content of MDA (Malondialdehyde), increased the ratio of GSH/GSSG (glutathione/oxidized glutathione) and NADPH/NADP+(nicotinamide adenine dinucleotide phosphate/oxidized nicotinamide adenine dinucleotide phosphate), suggesting that the rose produces more GSH to prevent oxidative stress. Transcriptome analysis further revealed a large number of differentially expressed genes (DEGs) involved in the TCA (the tricarboxylic acid) cycle and the phenylpropanoid biosynthesis pathways under surface water stress, and these DEGs can promote the production of NADPH, which in turn positively regulates the content of GSH. Multiple peroxidase-related genes (RhPRXs) also exhibited a significant stress response in this process. In summary, our research results reflect that roses under surface water stress in the iron-mining area exhibit certain defense mechanisms at both physiological and transcriptional levels, and also provide a reference for cultivating effective rose resources for repairing pollution in mining areas and evaluating excessive iron pollution as a biological indicator.