Genotype Groups Research Articles

Ecological trade-offs drive phenotypic and genetic differentiation of Arabidopsis thaliana in Europe

Plant diversity is shaped by trade-offs between traits related to competitive ability, propagule dispersal, and stress resistance. However, we still lack a clear understanding of how these trade-offs influence species distribution and population dynamics. In Arabidopsis thaliana, recent genetic analyses revealed a group of cosmopolitan genotypes that successfully recolonized Europe from its center after the last glaciation, excluding older (relict) lineages from the distribution except for their north and south margins. Here, we tested the hypothesis that cosmopolitans expanded due to higher colonization ability, while relicts persisted at the margins due to higher tolerance to competition and/or stress. We compared the phenotypic and genetic differentiation between 71 European genotypes originating from the center, and the south and north margins. We showed that a trade-off between plant fecundity and seed mass shapes the differentiation of A. thaliana in Europe, suggesting that the success of the cosmopolitan groups could be explained by their high dispersal ability. However, at both north and south margins, we found evidence of selection for alleles conferring low dispersal but highly competitive and stress-resistance abilities. This study sheds light on the role of ecological trade-offs as evolutionary drivers of the distribution and dynamics of plant populations.

Phenotypic characterization of two-row barley (Hordeum vulgare L. ssp. vulgare) germplasm conserved in Osman Tosun Genebank of Türkiye by multivariate analysis model

AbstractBarley is a crucial cereal crop with a diverse genetic heritage that includes landraces-traditionally cultivated variants that have adapted to varying agro-climatic conditions over centuries. Preserving barley landraces in genebanks is of utmost importance for safeguarding genetic diversity and aiding future breeding endeavors.This study aims an agro-morphological characterization of a selected collection of two row barley landraces conserved in the Osman Tosun Genebank. A total of 262 barley accessions were assessed in controlled field conditions to analyze various agro-morphological traits. The study unveiled notable disparities in the morphological traits of the genotypes, specifically in flag leaf anthocyanin, flag leaf sheath wax, spike shape, spike density, lemma color, grain color, lodging tendency, days to 50% flowering, plant height, spike length, spikelet quantity, and thousand grain weight, among other critical agronomical characteristics. To scrutinize the morphological disparities, the research utilized principal component analysis and ascertained that nearly 77.22% of the overall variance was accounted for by the first two principal components. The first four principal components accounted for 90.96% of the total variation, thus indicating significant genetic diversity among genotypes. The results of the cluster analysis revealed the presence of diverse genetic resources within the collection, with distinct groups of genotypes exhibiting similar traits being identified. The results of the agro-morphological characterization are a valuable resource for researchers and breeders, aiding them in making informed decisions regarding the management and application of barley landraces in breeding programs.

Impact of the rs822393 Variant on Adiponectin Levels and Metabolic Parameters after Weight Loss Secondary to a High-Fat Hypocaloric Diet with Mediterranean Pattern.

The effects of the rs822393 variant of ADIPOQ gene on metabolic parameters such as insulin resistance and adiponectin levels following weight loss through dietary intervention are still uncertain. The aim of this study was to evaluate the role of rs822393 of ADIPOQ gene on adiponectin levels and metabolic parameters after weight loss with a high-fat hypocaloric diet with Mediterranean pattern during 12 weeks. A population of 283 patients with obesity was allocated to a dietary intervention trial with a high-fat hypocaloric diet during 12 weeks. Adiposity and biochemical parameters were determined. rs822393 was assessed with a dominant model analysis (CC vs. CT + TT). These patients had three different genotypes: CC (59.0%), CT (33.6%), and TT (7.4%). The allelic frequencies for C and T were 0.89 and 0.20, respectively. Basal and post-intervention HDL cholesterol, adiponectin levels, and adiponectin/leptin ratio were lower in T-allele than non-T-allele carriers. After dietary intervention, BMI, weight, fat mass, waist circumference, systolic blood pressure, insulin, HOMA-IR, leptin, total cholesterol, and LDL cholesterol levels improved significantly in both genotype groups. Moreover, HDL cholesterol (CC vs. CT + TT) (delta: 8.9 ± 1.1 mg/dL vs. 1.7 ± 0.8 mg/dL; p = 0.02), serum adiponectin in non-T-allele carriers (43.1 ± 5.9 ng/dL vs. 2.8 ± 3 0.0 ng/dL; p = 0.01), and adiponectin/leptin ratio (1.37 ± 0.1 units vs. 0.17 ± 0.08 units; p = 0.02) improved only in non-T-allele carriers after weight loss. Individuals with obesity and without the T allele of rs822393 experienced improvements in adiponectin levels, adiponectin/leptin ratio, and HDL cholesterol levels after following a high-fat hypocaloric diet with a Mediterranean pattern.

Pharmacogenetics of Efavirenz Exposure in Cervicovaginal Fluid during Pregnancy and Postpartum.

In this study, we investigated the combined influence of pregnancy and genetic polymorphisms on efavirenz pharmacokinetics in cervicovaginal fluid (CVF) of women receiving antiretroviral therapy. Women receiving efavirenz-containing antiretroviral therapy were recruited from two hospitals in Nigeria during 2017-2020. Sparse CVF and plasma samples were obtained during pregnancy to assess the possible association between drug concentration and CYP2B6 polymorphisms (stage I). Participants were stratified into three CYP2B6 516G>T (rs3745274) genotype groups and re-enrolled for intensive pharmacokinetic sampling (stage II). Overall, 159 women (142 pregnant and 12 postpartum) contributed samples in stage I (88 CVF, 81 plasma and 73 paired). CYP2B6 516G>T (rs3745274) remained independently associated with log10 efavirenz CVF concentration during pregnancy after adjusting for plasma concentration, with β (Log10 efavirenz concentration, 95%CI) of 0.204 (0.027, 0.382), P = 0.025). Median (IQR) efavirenz C min in CVF during pregnancy (n = 12) vs. postpartum (n = 12) was 243 ng/mL (168-402) vs. 447 ng/mL (159-974), C max was 1,031 ng/mL (595-1,771) vs. 1,618 ng/mL (675-2,695), and AUC0-24h was 16,465 ng.h/mL (9,356-30,417) vs. 30,715 ng.h/mL (10,980-43,714). CVF-to-plasma AUC ratio was 0.36 during pregnancy and 0.46 postpartum. Upon stratification, efavirenz clearance during pregnancy was 57.9% higher than postpartum in patients with the CYP2B6 516GT genotype; the AUC0-24h and C max were 33.8% and 8.6% lower, respectively. Efavirenz C min in CVF exceeded the protein binding-adjusted IC90 (PBIC90) of 126 ng/mL during pregnancy and postpartum. Efavirenz is well distributed into the CVF; both pregnancy and CYP2B6 polymorphisms affect the extent of exposure.

ECOG-ACRIN EAZ171: Prospective validation trial of germline variants and taxane type in association with taxane-induced peripheral neuropathy (TIPN) in Black women with early-stage breast cancer.

LBA503 Background: Black women experience higher rates of TIPN compared to White women when receiving weekly paclitaxel (WP) for early-stage breast cancer. This disparity impacts health equity, as TIPN leads to more frequent dose reductions and higher recurrence rates in Black women. Conversely, disparities in TIPN by race are not seen in women receiving every three-week docetaxel (3D). Further, retrospective analyses have identified specific genotypes associated with differential risk of grade 2-4 TIPN in women of African ancestry receiving WP . The primary aim of EAZ171 was to prospectively validate germline predictors of TIPN in Black women receiving WP. Secondary objectives included comparing rates of TIPN and dose reductions in Black women receiving WP compared to 3D. Methods: Women with early-stage breast cancer who self-identified as Black and were planned by physician choice to receive (neo)adjuvant WP (80mg/m2 x 12 doses) or 3D (75 mg/m2 x 4-6 doses) were eligible. Genotyping determined germline neuropathy risk, defined as high ( FCAMR homozygous wt or SBF2 mutated) or low (variant allele in FCAMR and SBF2 wt). Grade 2-4 TIPN by physician-reported CTCAE v.5 was compared between high vs. low risk genotypes, and between the WP vs. 3D arms at one year using Fisher exact tests with two-sided alpha of 0.1. Patient-rated TIPN was captured using PRO-CTCAE items, and patient-reported outcomes (PROs) assessed TIPN symptoms and functional interference (FACT/GOG-NTx, EORTC CIPN20). Results: 249 patients were enrolled between 6/27/19-3/31/22, including 121 receiving at least one dose of WP and 118 receiving a dose of 3D. Of those with genotype data, 91/117 (77.8%) in the WP arm and 87/118 (73.7%) in the 3D arm were classified as high risk. Physician-reported grade 2-4 TIPN was not significantly different in the high vs. low risk genotype groups with WP (47% vs. 35% p=0.27) nor with 3D (28% vs. 19% p=0.47). Grade 2-4 TIPN was significantly higher in the WP vs. 3D arm by physician-rated CTCAE (45% vs. 29% p=0.02) and PRO-CTCAE (40% vs. 24% p=0.03). Trends in worsening neuropathy scores were similar over time using the FACT/GOG-NTx and EORTC CIPN20 questionnaires, but were not significantly different between the two arms at 1 year. Patients receiving WP required more dose reductions due to TIPN (28% vs. 9% p<0.001) or due to any cause (39% vs. 25% p=0.02) than patients receiving 3D. Conclusions: In this prospective trial enrolling only Black women with breast cancer, germline variation did not significantly impact risk of TIPN with WP or 3D. However, 3D was more tolerable evidenced by less grade 2-4 TIPN and fewer dose reductions compared to WP. Given the disparate burden of TIPN and its potential impact on cure rates, this trial suggests docetaxel should be considered the preferred taxane for Black women with early-stage breast cancer. Clinical trial information: NCT04001829 .

DUS Characterization of Rajmash (Phaseolus vulgare L.) Genotypes for Morpho-physiological Traits under Rainfed Conditions

Background: The current investigation was carried out in the year 2021-22 at Dryland Agriculture Research Station (DARS), Budgam. The experiment was laid out in randomized complete block design with three replications in field and completely randomized design (CRD) in vitro conditions for evaluating different traits of genotypes. DUS characterization was conducted as per the DUS testing guidelines by Protection of Plant Varieties and Farmers Act, Authority, Descriptors for rajmash (Phaseolus vulgaris L.) GOI, New Delhi [reproduced from Plant Variety Journal of India. Vol.1 (1), 2007]. Methods: The observations were recorded on 18 DUS characters including morphological and quality attributes and physiological characters. For all the features studied, the analysis of variance for morpho-physiological and qualitative attributes found significant differences, providing adequate chance to select the genotypes with desired qualities. DUS traits were examined in accordance with the descriptor, “state” and “code” provided for each character. Result: The observed range of variation were recorded for different traits for different genotypes. Cluster analysis for morphological, maturity, yield and quality characteristics arranged the rajmash genotypes into 11 clusters, as per Mahalanobis D2 analysis using Tocher’s method with cluster III having the maximum number of genotypes (8), followed by cluster I, II, IV and V with 6 genotypes, 2 genotypes were grouped in cluster VII and XI and the remaining clusters with 1 genotype each. Diversity analysis showed grouping of genotypes in 11 clusters, which will help in selection of genetically divergent parents for exploitation in hybridization programme and would constitute an essential gene pool for future breeding programme.

Associations between fasting glucose rate-of-change and the missense variant, rs373863828, in an adult Samoan cohort.

The A allele of rs373863828 in CREB3 regulatory factor is associated with high Body Mass Index, but lower odds of type 2 diabetes. These associations have been replicated elsewhere, but to date all studies have been cross-sectional. Our aims were (1) to describe the development of type 2 diabetes and change in fasting glucose between 2010 and 2018 among a longitudinal cohort of adult Samoans without type 2 diabetes or who were not using diabetes medications at baseline, and (2) to examine associations between fasting glucose rate-of-change (mmol/L per year) and the A allele of rs373863828. We describe and test differences in fasting glucose, the development of type 2 diabetes, body mass index, age, smoking status, physical activity, urbanicity of residence, and household asset scores between 2010 and 2018 among a cohort of n = 401 adult Samoans, selected to have a ~2:2:1 ratio of GG:AG: AA rs373863828 genotypes. Multivariate linear regression was used to test whether fasting glucose rate-of-change was associated with rs373863828 genotype, and other baseline variables. By 2018, fasting glucose and BMI significantly increased among all genotype groups, and a substantial portion of the sample developed type 2 diabetes mellitus. The A allele was associated with a lower fasting glucose rate-of-change (β = -0.05 mmol/L/year per allele, p = 0.058 among women; β = -0.004 mmol/L/year per allele, p = 0.863 among men), after accounting for baseline variables. Mean fasting glucose and mean BMI increased over an eight-year period and a substantial number of individuals developed type 2 diabetes by 2018. However, fasting glucose rate-of-change, and type 2 diabetes development was lower among females with AG and AA genotypes. Further research is needed to understand the effect of the A allele on fasting glucose and type 2 diabetes development. Based on our observations that other risk factors increased over time, we advocate for the continued promotion for diabetes prevention and treatment programming, and the reduction of modifiable risk factors, in this setting.

ECOG-ACRIN EAZ171: Prospective Validation Trial of Germline Predictors of Taxane-Induced Peripheral Neuropathy in Black Women With Early-Stage Breast Cancer.

Black women experience higher rates of taxane-induced peripheral neuropathy (TIPN) compared with White women when receiving adjuvant once weekly paclitaxel for early-stage breast cancer, leading to more dose reductions and higher recurrence rates. EAZ171 aimed to prospectively validate germline predictors of TIPN and compare rates of TIPN and dose reductions in Black women receiving (neo)adjuvant once weekly paclitaxel and once every 3 weeks docetaxel for early-stage breast cancer. Women with early-stage breast cancer who self-identified as Black and had intended to receive (neo)adjuvant once weekly paclitaxel or once every 3 weeks docetaxel were eligible, with planned accrual to 120 patients in each arm. Genotyping was performed to determine germline neuropathy risk. Grade 2-4 TIPN by Common Terminology Criteria for Adverse Events (CTCAE) v5.0 was compared between high- versus low-risk genotypes and between once weekly paclitaxel versus once every 3 weeks docetaxel within 1 year. Patient-rated TIPN and patient-reported outcomes were compared using patient-reported outcome (PRO)-CTCAE and Functional Assessment of Cancer Therapy/Gynecologic Oncology Group-Neurotoxicity. Two hundred and forty of 249 enrolled patients had genotype data, and 91 of 117 (77.8%) receiving once weekly paclitaxel and 87 of 118 (73.7%) receiving once every 3 weeks docetaxel were classified as high-risk. Physician-reported grade 2-4 TIPN was not significantly different in high- versus low-risk genotype groups with once weekly paclitaxel (47% v 35%; P = .27) or with once every 3 weeks docetaxel (28% v 19%; P = .47). Grade 2-4 TIPN was significantly higher in the once weekly paclitaxel versus once every 3 weeks docetaxel arm by both physician-rated CTCAE (45% v 29%; P = .02) and PRO-CTCAE (40% v 24%; P = .03). Patients receiving once weekly paclitaxel required more dose reductions because of TIPN (28% v 9%; P < .001) or any cause (39% v 25%; P = .02). Germline variation did not predict risk of TIPN in Black women receiving (neo)adjuvant once weekly paclitaxel or once every 3 weeks docetaxel. Once weekly paclitaxel was associated with significantly more grade 2-4 TIPN and required more dose reductions than once every 3 weeks docetaxel.

Real-World Impact of an In-House Dihydropyrimidine Dehydrogenase (DPYD) Genotype Test on Fluoropyrimidine Dosing, Toxicities, and Hospitalizations at a Multisite Cancer Center.

Fluoropyrimidine-related toxicity and mortality risk increases significantly in patients carrying certain DPYD genetic variants with standard dosing. We implemented DPYD genotyping at a multisite cancer center and evaluated its impact on dosing, toxicity, and hospitalization. In this prospective observational study, patients receiving (reactive) or planning to receive (pretreatment) fluoropyrimidine-based chemotherapy were genotyped for five DPYD variants as standard practice per provider discretion. The primary end point was the proportion of variant carriers receiving fluoropyrimidine modifications. Secondary end points included mean relative dose intensity, fluoropyrimidine-related grade 3+ toxicities, and hospitalizations. Fisher's exact test compared toxicity and hospitalization rates between pretreatment carriers, reactive carriers, and wild-type patients. Univariable and multivariable logistic regression identified factors associated with toxicity and hospitalization risk. Kaplan-Meier methods estimated time to event of first grade 3+ toxicity and hospitalization. Of the 757 patients who received DPYD genotyping (median age 63, 54% male, 74% White, 19% Black, 88% GI malignancy), 45 (5.9%) were heterozygous carriers. Fluoropyrimidine was modified in 93% of carriers who started treatment. In 442 patients with 3-month follow-up, 64%, 31%, and 30% of reactive carriers, pretreatment carriers, and wild-type patients had grade 3+ toxicity, respectively (P = .085); 64%, 25%, and 13% were hospitalized (P < .001). Reactive carriers had 10-fold higher odds of hospitalization compared with wild-type patients (P = .001), whereas no significant difference was noted between pretreatment carriers and wild-type patients. Time-to-event of toxicity and hospitalization were significantly different between genotype groups (P < .001), with reactive carriers having the earliest onset and highest incidence. DPYD genotyping prompted fluoropyrimidine modifications in most carriers. Pretreatment testing reduced toxicities and hospitalizations compared with reactive testing, thus normalizing the risk to that of wild-type patients, and should be considered standard practice.

GLUT1DS focus on dysarthria

Research purposeGLUT1 deficiency syndrome (GLUT1DS) is a rare genetic disorder caused by a mutation in the SLC2A1 gene that limits the transport of glucose across the blood-brain barrier. Speech disorders and dysarthria are typical findings in patients with GLUT1DS, but have never been deeply phenotyped. The aim of the present study was to characterize speech abilities in a sample of patients with GLUT1DS. Results30 patients with GLUT1DS were recruited. We reported impairments in different speech and oromotor domains: the speech was characterized by dysarthria, inaccurate articulation of consonants, abnormal nasal resonance, errors in intonation and prosody and low intelligibility. We observed difficulties in motor planning and programming. Moreover, we observed a significant difference between the dysarthric level of impairment with genotype groups. ConclusionsThe presence of a speech disorder in patients with GLUT1DS represents a core feature of the syndrome. Our findings suggest that patients with GLUT1DS would benefit from a comprehensive neurocognitive assessment to detect strengths and weaknesses of the speech profile. Understanding the speech and language phenotype in GLUT1DS is critical for planning early intervention to positively influence the global development of patients with GLUT1DS.

Comparison of HPV-positive triage strategies combining extended genotyping with cytology or p16/ki67 dual staining in the Italian NTCC2 study

Each high-risk HPV genotype has different oncogenic potential, and the risk of CIN3+ varies according to genotype. We evaluated the performance of different strategies of HPV-positivity triage combining cytology, p16/ki67 dual staining (DS), and extended genotyping. Samples from 3180 consecutive women from the NTCC2 study (NCT01837693) positive for HPV DNA at primary screening, were retrospectively analyzed by the BD Onclarity HPV Assay, which allows extended genotyping. Genotypes were divided into three groups based on the risk of CIN3+. HPV DNA-positive women were followed up for 24 months or to clearance. Combining the three groups of genotypes with cytology or DS results we identify a group of women who need immediate colposcopy (PPV for CIN3+ from 7.8 to 20.1%), a group that can be referred to 1-year HPV retesting (PPV in those HPV-positive at retesting from 2.2 to 3.8), and a group with a very low 24-month CIN3+ risk, i.e. 0.4%, composed by women cytology or DS negative and positive for HPV 56/59/66 or 35/39/68 or negative with the Onclarity test, who can be referred to 3-year retesting. Among the baseline HPV DNA positive/cytology or DS negative women, the extended genotyping allows to stratify for risk of CIN3+, and to identify a group of women with a risk of CIN3+ so low in the next 24 months that they could be referred to a new screening round after 3 years. Italian Ministry of Health (grant number RF-2009-1536040). Hologic-Genprobe, Roche Diagnostics, and Becton & Dickinson provided financial and non-financial support.

In-vitro induced drought and heat stress on seed germination of diverse African sorghum germplasm

Abstract One of the critical growth and development stages that is vulnerable to drought and heat stress even in hardy staple crops is germination. Sorghum is a critically essential, resilient, and diverse crop that displays genotypic variations in its ability to withstand such harsh conditions, limiting crop stand and ultimately leading to yield losses. Therefore, the goal of this study was to evaluate the performance of 50 high potential genotypes of African sorghum, including landraces, breeding lines and check varieties to simulated drought and heat stress at germination stage. The study used a split plot arrangement for temperature treatments, laid in a completely randomized design with three replications. Final germination percentage, mean germination time, germination index and coefficient variation of germination time (CVt) were determined. Data was subjected to generalized linear model, principal component analysis, hierarchical agglomerative cluster analysis and principal coordinate analysis to determine statistical differences in genotypes and visualize groups of genotypes according to their overall performance in assessed germination parameters. Drought stress and supra-optimal temperatures suppressed and delayed germination. The genotypes were grouped into six distinct clusters based on their performance. Genotypes NPGRC1593, NPGRC1782, NPGRC1476 and IS224426 performed exceptionally well under both stressors and outperformed check varieties in almost all parameters assessed. To improve crop establishment and increase agricultural yields, breeding and crop improvement programs should focus on genotypes that can withstand both stresses.

Genotype-phenotype severity correlation in a multicentric portuguese cohort of ABCA4-associated retinopathy

PurposeTo investigate genotype-phenotype correlations in ABCA4-associated retinopathy and further validate a recently proposed genotype-phenotype correlation model. DesignMulticentric, cross-sectional cohort study. MethodsConsecutive patients with genetically confirmed ABCA4-associated retinopathy from three Portuguese centres were included. Patients were categorized into distinct phenotype groups according to the degree of hypoautofluorescence and retinal background appearance in ultra-widefield fundus autofluorescence (UW-FAF) imaging. Genotype classification was performed using two criteria: one according to the presence of the p.Gly1961Glu variant, a hypomorphic variant, at least one moderate variant, or two biallelic severe/PVS1 variants (genotype classification A, which corresponds to the newly described criteria); and another one based on the number of null variants identified (genotype classification B). Associations between clinical data and phenotype and genotype groups were analysed. ResultsA total of 50 patients were included. Significant correlations between age of onset, best-corrected visual acuity (BCVA), and both phenotype and genotype groups were found, with patients in more severe phenotype and genotype categories exhibiting earlier disease onset and poorer visual function (p < 0.001; p < 0.001; p < 0.001; p < 0.001, p < 0.001; and p = 0.004, respectively). Genotype classification A better predicted phenotype severity on UW-AF imaging, demonstrating milder genotypes in patients with less severe phenotypes and more severe genotypes in those with advanced disease (p < 0.001). A genotype-phenotype correlation matrix was constructed based on the classification of the two disease-causing variants and their corresponding phenotypic staging. ConclusionOur findings support the utility of the newly described genotype classification in evaluating ABCA4-associated retinopathy phenotype severity, with possible implications in future understanding of the disease genetics and assessment of individual prognosis for patients.

Genetic diversity in safflower (Carthamus tinctorius L.) germplasm for vegetative and agronomic characteristics in semi-arid regions

Abstract Safflower, a semiarid crop, contains a healthy oil with high unsaturated fatty acids. Genetically diverse accessions are important for genetic maintenance of safflower and breeding proposes. The objectives of present investigation were to evaluate the morphological variation of 100 safflower accessions across two years (2022 and 2023), to explore similar genotypic groups and to identify the higher contribution of traits with to the observed variability. The highest coefficient of variation (CV) was observed for seeds per secondary capitulum, number of capitula per plant and weight of lateral capitulum in the first year and the highest CV values were observed for number of capitula per plant and capitula per lateral branch in the second year. The factor analysis identified five factors in the first year and six factors in the second as yield components, height, seed yield, capitulum diameter and phonology while number of branches was identified as the extra factor in the second year. Results showed that the variation of morphologic traits was made up of from the most measured traits of safflower. We defined seven distinct clusters, which made it possible to differentiate safflower accessions based on measured traits across two years. Of 45 accessions were grouped in similar clusters across two years, without any or similar genotype by environment interaction. Some high yielding accessions like C-47 and Lesaf-175 can be entered directly in multi-environmental trials for cultivar release proposes. The recognized variation improves as a good resource, indicating an important issue for future projects for safflower germplasm maintenance and breeding.

SSR‐based analysis of structural variation of the Russian population of Puccinia striiformis f. sp. tritici in 2019–2021

AbstractThe importance of monitoring and management of yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), has markedly increased in Russia over recent years because of intensifying negative effects of this destructive disease on wheat production. The Pst virulence survey was conducted in 2019–2021 in the European (North‐West, Volga, North Caucasus) and Asian (Siberia) parts of Russia, and the same 109 isolates have been genotyped here with 20 SSR markers. Fifty‐three multilocus genotypes (MLGs) were detected, seven of which occurred in two or more regions. The most frequent MLG was found in three European Pst collections (except Dagestan) and Siberia. SSR‐based variation within the regional collections was low because many MLGs were closely related. Nevertheless, each collection contained relatively different small genotype groups. No clear geographic structure of the Russian Pst population was observed because the five studied regional collections shared groups of similar genotypes. The most singular SSR genotype was identified in the North‐West collection, but genotypes of four invasive isolates belonging to the PstS2 temperature‐adapted aggressive strain did not considerably differ from others. The observed heterozygosity at all SSR loci exceeded the expected one in all regional Pst collections, which could imply asexual reproduction of the pathogen. Both the SSR and virulence analyses demonstrated similar patterns of relationships between the regional Pst collections, although the magnitude of differences between the collections was larger for virulence pathotypes. However, no significant association was established between the virulence pathotypes and SSR genotypes because multiple pathotypes had the same genotype and vice versa.

Association between uncoupling protein 1-3826 A/G polymorphism and the effects of anaerobic exercises on serum oxidative stress

ObjectivesAerobic exercise promotes uncoupling protein-1 (UCP-1) induced white adipose tissue browning by increasing serum nitric oxide (NO), irisin and interleukin-6 (IL-6). However, oxidative stress (OS) occurring during anaerobic exercise downregulates UCP-1. Moreover, UCP-1-3826 A/G polymorphism (UCP1P) is associated with weight gain due to impaired thermogenesis which may be due to UCP1P induced modification in OS. Therefore, our purpose was to investigate the role of UCP1P on the effects of acute maximal exercise (AME) and chronic anaerobic exercise (CAT) on serum OS, UCP-1, NO, irisin and IL-6 levels. Equipments and methodsSport group (SG, n=43) was formed of anaerobic athletes, while control group (CG, n=43) comprised physically inactive men. Postprandial blood was taken from SG and CG before and after AME to determine serum UCP-1, irisin, IL-6, NO, and oxidative stress index (OSI=total oxidant/antioxidant status [TOS/TAS] ratio). To investigate the effects of CAT on serum parameters, SG and CG's results were compared. UCP1P was determined by restriction fragment length polymorphism analysis. ResultsAME significantly increased all parameters in SG and CG (P<0.05). However, CAT increased only OSI and IL-6 (P<0.05), decreased UCP-1 and TAS and did not affect TOS, NO and irisin. OSI of GG homozygous athletes were significantly higher than other genotype groups (P<0.05). Although significant negative correlations were found between UCP-1 and OS markers in GG and AA genotype groups before AME, significant positive correlations were found between UCP-1 and TAS in AA genotype group after AME. GG homozygous athletes may be more prone to higher OS. Decrease in UCP-1 due to CAT may be affected by GG genotype group's genetic disposition for OS.

Strategy to identify common beans with resistance to white mould for dry‐irrigated areas: Additional evidence

AbstractIn a previous study, common bean (Phaseolus vulgaris L.) genotypes were selected in the field for reactions to white mould (WM), caused by Sclerotinia sclerotiorum. These genotypes, along with the resistant control A195, were then evaluated in both field and greenhouse (straw test) conditions. The results showed that field trials effectively identified high‐yielding WM‐resistant genotypes for dry‐irrigated conditions. Here we challenge the results of this study with new data and methodology by conducting six sprinkler‐irrigated trials from 2015 to 2017 with five genotype groups (G). Three groups comprised genotypes previously studied: G1, seven partially resistant; G4, two intermediately resistant; and G5, three susceptible. G2 consisted of four lines selected for partial resistance in the current study. The resistant control group, G3, comprised the genotypes A195, G122, Cornell605, and Ouro Branco. WM was absent (one trial), or pressure was either low/moderate (two trials) or moderate/high (three trials). The average seed yield ranged from 2207 (G3) to 3178 kg/ha (G1). The contrast G1, G2 versus G3 was nonsignificant for incidence and severity index, indicating that genotypes selected for resistance in the field were as resistant as the resistant control genotypes. Additionally, the groups selected for resistance yielded 43% more and produced 33% less sclerotia weight compared with the control group. Our results reinforce the effectiveness of selecting WM‐resistant genotypes using beans originally bred for purposes other than WM‐resistance, specifically targeting dry‐irrigated areas. Furthermore, our results suggest that the use of genotypes selected for partial resistance reduces inoculum levels in the soil.

The Role of OPRM1 in the Neonatal Autoresuscitation Reflex and Sudden Infant Death Syndrome

Opioid receptors are widely expressed throughout the brain and integral in nociception as well as homeostatic regulation of autonomic processes including respiration through modulation of respiratory rhythmogenesis and chemosensory responses. Perturbations to homeostatic mu opioid receptor (MOR) signaling via opiate overdose results in respiratory depression, aberrant breathing, and often death. With the rise of opioid use over the last two decades, many infants are being diagnosed with Neonatal Abstinence Syndrome (NAS), a congenital cardio-respiratory disorder resulting from prenatal exposure to opioids. Infants born with NAS have a fourfold increased risk for Sudden Infant Death Syndrome (SIDS). SIDS and related Sudden Unexpected Infant Death takes the lives of approximately 3,400 infants annually under the age of one and its etiology remains mostly unknown. Currently SIDS is explained via the triple risk model that proposes that SIDS occurs in a vulnerable infant during a critical developmental period when triggered by an external stressor, converging on the failure of the neonate autoresuscitation reflex in most cases. Recently a study identified an association between a mutation in the OPRM1 gene encoding MORs and SIDS cases. However, how this gene and perturbations in its native function modulates respiratory regulation are poorly understood. We hypothesize that native OPRM1 function is integral to protective neonate respiratory reflexes and that perturbation of native OPRM1 signaling negatively affects the neonatal autoresuscitation reflex. Male and female OPRM1 loss of function mice were assayed for their autoresuscitation reflex on our novel testbed, Looper. Mice were exposed to repeated bouts of anoxia and allowed to autoresuscitate until death occurred. Preliminary data suggest that loss of OPRM1 function results in a higher mortality rate on the autoresuscitation assay with OPRM1 KO mice surviving significantly less anoxic challenges compared to wild type controls. No sex differences were observed between male and female survival for all genotype groups. Results indicate that perturbation of the native function of OPRM1 produces a vulnerability to autoresuscitation dysfunction and mitigated survival. Our data demonstrate the first functional assessment of OPRM1 in neonatal cardiovascular function and autoresuscitation and reveal an important risk factor that may be implicated in perpetuating SIDS and NAS phenotypes. Additional analyses of distinct parameters from respiratory trace data for OPRM1 loss of function mice will aid in a deeper, mechanistic understanding of features implicated in autoresuscitation dysfunction. Future studies aim to characterize specific splice variants of OPRM1, known to produce neomorphic function and model the SIDS associated VUS, to further characterize the implication of OPRM1 and its variants in congenital respiratory diseases. Funding sources NIH/NHLBI R01HLN161142-01 and R01HL130249-07. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Tibia properties in broilers raised on their own commercial diets with different growth rates and sex during a 10-week rearing period.

Genetic selection applied to broilers results in fast growth and an increase in meat yield. However, this situation causes welfare problems in broilers. The aim of this study is to determine the weekly changes in the tibia characteristics in broilers raised on their own commercial diets. In the study, 168 (84 female and 84 male) slow-growing (Hubbard-Isa Red JA) and 168 (84 female and 84 male) fast-growing (Ross-308) day-old broiler chicks were used. Six broilers from each genotype and sex group were weighed weekly and slaughtered to determine the tibia properties during the 10-week fattening period. Fast-growing broilers had higher tibia weight and longer length, diaphysis diameter and medullary canal diameter than those of slow-growing broilers at the same age. In fast-growing genotypes, the cortical index was low only in the 2nd week, and Robusticity and Seedor indices were observed to be better throughout the whole fattening. The ash content of the total tibia in the fast-growing broilers was higher in all of the examined weeks except the 4th week and the 9th week of fattening than that in the slow-growing broilers. Although the amount of ash per unit body weight in the 1st week of fattening was higher in fast-growing broilers, this situation reversed after the 4th week. The level of all minerals examined in total tibia weight is high in fast-growing broilers, and they differed according to the fattening period. When comparing tibia characteristics of two different genotypes fed their own commercial diets, the tibia structure was found to be stronger in fast-growing broilers compared to other genotypes at the same age, but slow-growing broilers were more prominent in terms of body weight. It was observed that the mineral density was higher in male broilers, except in the 1st week.

Gene Methylation Affects Salivary Levels of the Taste Buds' Trophic Factor, Gustin Protein.

The salivary protein, Gustin/carbonic anhydrase VI, has been described as a trophic factor responsible for the growth of taste buds. We found, in a genetically homogeneous population, that the polymorphism rs2274333 (A/G) of the Gustin gene is crucial for the full functionality of the protein and is associated with taste sensitivity. However, other studies have failed to find this evidence. Here, we verified if Gustin gene methylation can affect the salivary levels of the protein, also concerning the polymorphism rs2274333 and PROP bitter responsiveness. The Gustin gene methylation profiling and the quantification of the Gustin salivary levels were determined in sixty-six volunteers genotyped for the polymorphism rs2274333 (A/G) (Ser90Gly in the protein sequence). The fungiform papillae density was also determined. The results confirm our earlier observations by showing that AA genotypes had a greater density of fungiform taste papillae, whereas the GG genotypes showed a lower density. We also found variations in the protein levels in the three genotype groups and an inverse relationship between Gustin gene methylation and the salivary levels of the protein, mostly evident in AA and ST volunteers, i.e., in volunteers who would be carriers of the functional isoform of the protein. These findings could justify the conflicting data in the literature.