Specific SNP Research Articles

Developing drought and heat-resistant grapevine cultivars through marker-assisted breeding

Climate change poses significant challenges to viticulture, particularly through increased drought and heat stress. This study integrates physiological, biochemical, genomic, and field performance assessments to identify traits and genetic markers associated with stress tolerance in five grapevine cultivars: Cabernet Sauvignon, Chardonnay, Syrah, Merlot, and Riesling. Genomic analysis revealed specific SNP markers on chromosomes 4 and 8, linked to water-use efficiency (WUE) and proline accumulation, crucial for osmotic balance under drought conditions. Physiological assessments showed that Cabernet Sauvignon and Merlot maintained high relative water content and low stomatal conductance, reducing water loss. Biochemical analysis indicated that Chardonnay and Syrah had elevated heat shock protein (HSP) expression and low malondialdehyde (MDA) levels, supporting cellular stability under heat. Field trials further validated these traits, with Cabernet Sauvignon and Chardonnay demonstrating yield stability and high sugar content despite stress. This research underscores the potential of marker-assisted breeding to develop climate-resilient grapevine cultivars, offering practical insights for sustainable viticulture in the face of global climate shifts.

Parental Reconstruction from a Half-Sib Population of Stoneless Jujube Ziziphus jujuba Mill. Based on Individual Specific SNP Markers Using Multiplex PCR.

The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in their genome by multiplex PCR, which is utilized for genotyping of 332 half-sib plants of Ziziphus jujuba.This cost-effective method makes as much as possible to utilize the same amount of each pair of various targeted loci primers. After PCR amplification of targeted genome parts, the mixed products can be directly used in a next-generation sequencing platform. We concomitantly amplified 10 unique SNP loci at 10 different chromosomes of male JingZao 39 plants in 332 half-sib plants and sequenced them on the Illumina Novaseq 6000 platform. Analysis of SNP genotyping accuracy of 332 half-sib plants showed that all 10 unique SNPs in all 332 plants were correctly amplified in this multiplex PCR method. Furthermore, based on Mendelian inheritance, we identified 124 full-sib plants that have 10 unique SNPs in their genomes. These results were further confirmed by whole genome resequencing of 82 randomly selected half-sib plants, and the identity-by-descent values of all full-sib plants were between 0.4399 to 0.5652. This study displayed a cost-effective multiplex PCR method and proper identification of pollen parent through specific SNPs in half-sib progenies and firstly obtained a full-sib population between 'Wuhezao' and 'JingZao 39', segregating for stone and stoneless fruit.

Association between dopamine genes, adiposity, food addiction, and eating behavior in Chilean adult.

A frequent consumption of high sugar/fat foods can affect dopamine signaling in the brain and cause sustained stimulation of the reward system. It has been hypothesized that a hypodopaminergic trait results in an individual overeating in order to increase brain DA. Genetic variants in this route have been connected with addiction and eating behaviors. Most studies focus on a specific SNP, and few studies have used multilocus genetic scores, which quantify genetic risk on a continuum. To assess the relationship between multilocus genetic scores based on multiple gene variants in the dopaminergic pathway and measurements of anthropometry, eating behavior, food reinforcement, and food addiction (FA) in Chilean adults. We recruited 221 Chilean adults for a cross-sectional study. A standard anthropometric measurement procedure was followed and eating behavior was examined using the Three Factor Eating questionnaire (TFEQ), Food Reinforcement Value Questionnaire (FRVQ), Yale Food Addiction Scale (YFAS) and 24-h diet recall. Multilocus genetic scores were calculated using TaqMan assays (rs1800497-rs1799732-rs6277-rs4680). No differences were found in the entire sample for anthropometric measurements, by MLGS. We found that participants with a score ≥ 2.0 in the MLGS showed higher food choices on the RVFQ and lower energy intake in protein, lipids, SAFA, MUFA, PUFA, dietary cholesterol, omega-3 and Omega-6 fatty acids in the 24-h recall (p < 0.05). Stratified by nutritional condition, the group with obesity had inferior scores on cognitive restriction, greater scores on uncontrolled eating, emotional eating, and responding to palatable food in the RVFQ. Also, in subjects with obesity, there was more food addiction in the group scoring "MLGS ≥2.0 or low dopamine signaling" (53%), compared to the group scored "MLGS <2.0 or high dopamine signaling" (23%) (p-value; 0.05). Emotional Eating scores correlated positively with MLGS in subjects with obesity. In adults with obesity, the MLGS of the dopamine pathway, reflecting hypodopaminergic signaling, was associated with greater scores on food addiction and altered eating behavior traits.

Influence of Single Nucleotide Polymorphisms on CRS Outcomes: A Preliminary Observational Study.

To conduct a preliminary investigation into the relationship between specific SNP variants, type II inflammation, and the effectiveness of dupilumab therapy and surgery in patients with CRS. In this prospective study, 48 subjects were enrolled, comprising 32 CRS patients and 16 healthy controls. The CRS patients were subjected to either dupilumab therapy or endoscopic surgery according to EPOS guidelines. SNP variants were identified using the TaqMan SNP genotyping technique. The identified SNP profiles were compared between the control group and CRS patients, and their potential influence on treatment outcomes was evaluated. Treatment responses were assessed based on symptom scores, such as SS-I, SNOT-22, disease progression using the NPS findings, and SNP profiles at a 6-month follow-up. The primary measures included the Nasal Polyp Score, Smell Identification Test (SIT) score, and SNOT-22 outcomes. Dupilumab therapy and surgery significantly decreased NPS, with the last showing superior results. However, dupilumab therapy resulted in a significantly improved SIT score. Significant differences were observed in SNP profiles, particularly with rs1800629 (TNFA), rs2856838 (IL1a), rs17561 (IL1a), and rs1805011 (IL4R). In particular, the expression of rs2856838 and rs1805011 variants in the dupilumab group was associated with significantly better SIT and SNOT-22 outcomes than non-expressors. Also, the surgery group patients expressing the rs2856838 variant reported significant improvements in SNOT-22 scores. These preliminary findings suggest that SNP genotypes may guide personalized treatment strategies for CRS. Further larger prospective studies are required to confirm these initial observations. 2 Laryngoscope, 2024.

Mitochondrial DNA D-loop SNPs unveil molecular signatures of milk production variation in Murrah buffalo.

The Murrah buffalo, pivotal in Asian agriculture, faces challenges in maximizing milk production despite significant breeding efforts. Recognizing its economic importance, this studyinvestigates mtDNA D-loop variations in Murrah buffalo as potential indicators of milk production variability, addressing challenges in maximizing yield despite significant breeding efforts. Analyzing mtDNA D-loop sequences from 50 buffaloes, we categorized them into Low (Group 1), Medium (Group 2), and High ECM (Group 3) groups based on milk yields, fat and protein percentage of a 30-day period data. Somatic cell mtDNA D-loop analysis revealed distinct genetic variations, with significant differences among ECM groups. Group 2 showed higher SNP prevalence, group 3 had more insertions/deletions, and Group 1 exhibited the highest transition frequency. Notably, a consistent "C" deletion at the 714th position occurred in Groups 1 and 3, prevalent in 68% of Group 2. A G-A variation at the 93rd position was specific to the medium ECM group. Negative Tajima D values indicated unique variations in each group, with Group 1 having the highest number, and a specific SNP linked to Group 2 was identified. These SNPs in the D-loop region could impact mtDNA replication, influencing mitochondrial content among animals. Our results provide valuable insights into the role of mtDNA D-loop polymorphisms in milk production traits in Murrah buffalo. Our research highlights the potential for valuable markers of cellular energy efficiency in Murrah buffalo. Exploring diverse cytoplasmic backgrounds opens avenues for mtDNA-based selection strategies, enhancing milk production and optimizing genetic traits for the dairy industry.

Calcium deposition in chicken eggshells: role of host genetics and gut microbiota

Eggshell is predominantly composed of calcium carbonate, making up about 95% of its composition. Eggshell quality is closely related to the amount of calcium deposition in the shell, which requires chickens to maintain a robust state of calcium metabolism. In this study, we introduced a novel parameter, Total Eggshell Weight (TESW), which measures the total weight of eggshells produced by chickens over a period of 10 consecutive d, providing valuable information on the intensity of calcium metabolism in chickens. Genome-wide association study (GWAS) was conducted to explore the genetic determinants of eggshell calcification in a population of 570 Rhode Island Red laying hens at 90 wk of age. This study revealed a significant association between a specific SNP (rs14249431) and TESW. Additionally, using random forest modeling and 2-tailed testing, we identified 3 genera, Lactobacillus in the jejunum, Lactobacillus, and Fournierella in the cecum, that exhibited a significant association with TESW. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of claudin-1 and occludin genes in individuals with low TESW and high abundance of jejunal Lactobacillus confirmed that the inhibitory effect of jejunal Lactobacillus on calcium uptake was achieved through the up-regulation of tight junctions in intestinal epithelial cells. Notably, both host and microbial factors influence TESW, displaying a mutually influential relationship between them. The microbiome-wide Genome-Wide Association Study (mb-GWAS) identified significant associations between these 3 genera and specific genomic variants, such as rs316115020 and rs316420452 on chromosome 5, rs313198529 on chromosome 11, linked to Lactobacillus in the cecum. Moreover, rs312552529 on chromosome 1 exhibited potential association with Fournierella in the cecum. This study highlights the influence of host genetics and gut microbiota on calcium deposition in eggshells during the late laying phase, providing a foundational reference for studying calcium metabolism in hens.

First molecular characterization of Burkholderia mallei strains isolated from horses in Mongolia

Glanders, a highly contagious and often fatal disease affecting equids, is caused by Burkholderia mallei. Although sporadic cases of equine glanders have recently been documented in Mongolia, genome sequencing and molecular studies of the bacteria within this region are lacking. This study provided the first molecular characterization of B. mallei isolated from four native Mongolian horses from two different provinces in 2019 and 2022 by applying whole-genome sequencing with two SNP types (previously developed genotyping with 15 SNP markers that provide global coverage of the B. mallei population and the core genome coding SNP typing developed in this study). The Mongolian isolates were located within the L3B1 cluster, which was previously associated with the V-120 strain from Russia. Within the L3B1 cluster shared by neighboring countries, they were in a unique subbranch. In this study, specific SNP markers unique to the Mongolian strains were identified to track these strains using a high-resolution melting analysis (HRMA). This study revealed the unique phylogenetic background of Mongolian strains isolated from the eastern part of Mongolia. HRMA specific to the Mongolian subbranch may contribute to the molecular epidemiological monitoring of glanders in Mongolia and surrounding countries.

The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa.

Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and the extent of the non-additive genetic variance associated with its autotetraploid genome. To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as tetraploid and diploid dosages, plus allele ratios) and SNP marker subsetting (all available SNPs, only genic regions, and only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used genotyping by sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and the onset of flowering, which were assessed in 143 genotyped plants from a genetically broad European reference population and their phenotyped half-sib progenies. On average, the allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), while using all the SNPs offered an advantage compared with any specific SNP subsetting (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting achieved better performances. We also released Legpipe2, an SNP calling pipeline tailored for reduced representation (GBS, RAD) in medium-sized genotyping experiments.

Site-specific PCR identification of animal species and formula particles of Scorpio

Scorpio, a commonly used animal medicine in China, is derived from Buthus martensii as recorded in the Chinese Pharmacopoeia. China harbors rich species of Scorpionida and adulterants exist in the raw medicinal material and deep-processed products of Scorpio. The microscopic characteristics of the deep-processed products may be incomplete or lost during processing, which makes the identification difficult. In this study, the maximum likelihood(ML) tree was constructed based on the morphology and cytochrome C oxidase subunit I(COⅠ) to identify the species of Scorpio products. The results showed that the main adulterant of Scorpio was Lychas mucronatus. According to the specific SNP sites in the COⅠ sequence of B. martensii, the stable primers were designed for the identification of the medicinal material and formula granules of Scorpio. The polymerase chain reaction(PCR) at the annealing temperature of 61 ℃ and 30 cycles produced bright specific bands at about 150 bp for both B. martensii and its formula particles and no band for adulterants. The adaptability of the method was investigated, which showed that the bands at about 150 bp were produced for Scorpio medicinal material, lyophilized powder, and formula granules, and commercially available formula granules. The results showed that the established method could be used to identify the adulterants of Scorpio and its formula granules, which could help to improve the quality control system and ensure the safe clinical application of Scorpio formula granules.

The RAAS system SNPs polymorphism is associated with essential hypertension risk in rural areas in northern China.

Objectives: Epidemiological evidence has shown that genetics and environment are associated with the risk of hypertension. However, the specific SNP effects of a cluster of crucial genes in the RAAS system on the risk of hypertension are unclear. Methods: A case-control study was performed on the baseline participants of Environment and Chronic Disease in Rural Areas of Heilongjiang China (ECDRAHC) study. According to the inclusion and exclusion criteria, 757 subjects (428 hypertensive patients) were enrolled. A total of 32 SNP sites and related haplotypes, involved in AGT (angiotensinogen), ACE (angiotensin-converting enzyme), AGTR1, CYP11B2 (aldosterone-synthase), LDLR (low-density lipoprotein receptor), LRP5 (low-density lipoprotein receptor associated protein 5), LRP6 (low-density lipoprotein receptor associated protein 6), PPARG (peroxisome proliferator-activated receptor gamma) and ACE2 (angiotensin-converting enzyme 2) genes which exert important roles in renin-angiotensin-aldosterone system (RAAS) system were analyzed. Furthermore, a polygenic scoring model was established to assess individual risk of developing hypertension based on the comprehensive SNPs effects in genes related the RAAS system. Results: After controlling the impact of confounding factors, multivariate logistic regression analysis revealed that the distribution of AGT/rs5046, LRP6/rs12823243 and ACE2/rs2285666 was associated with susceptibility to essential hypertension. In genetic score model, the score > -0.225 had a higher risk, the OR (95%CI) was 1.229 (1.110, 1.362). Conclusions: To the best of our knowledge, this is the first time a hypertension risk scoring model on RAAS associated gene cluster has been constructed, which will provide a novel approach for prevention and control of essential hypertension.

Marker-Trait Associations of Agronomic Traits in Barley (Hordeum vulgare L.) under Semi-Arid Conditions

Heading date, plant height, and spike-related phenotypes are key traits that affect the yield potential and adaptation of barley to Mediterranean environments. These traits are controlled by a complex network of genes as well as environmental effects. Marker-trait associations (MTAs) were performed using a set of 361 barley genotypes, evaluated phenotypically for three years under semi-arid conditions. In total, 24 MTAs were detected using the recently developed GWAS method (BLINK) at –log p ≥ 5. These included one MTA with awn length (Awl) on chromosome 2H; twelve MTAs with heading date (HD) distributed over all chromosomes except 4H; three MTAs with grains per spike (GPS) on chromosomes 1H, 2H, and 6H; six MTAs were detected for plant height (PH) on 2H (2), 3H, 4H, 6H, and 7H; and two MTAs with spike length (SL) on 3H and 7H. The results showed novel and known associations between specific SNP markers and heading date, plant height, and spike-related traits, suggesting that these markers can be used in breeding programs to improve these traits in barley. This study provides valuable information for breeders and geneticists working to develop new barley varieties that are better adapted to semi-arid climates and have improved yield and quality characteristics.

Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm.

Comprehensive cis-regulatory landscapes are essential for accurate enhancer prediction and disease variant mapping. Although cis-regulatory element (CRE) resources exist for most tissues and organs, many rare - yet functionally important - cell types remain overlooked. Despite representing only a small fraction of the heart's cellular biomass, the cardiac conduction system (CCS) unfailingly coordinates every life-sustaining heartbeat. To globally profile the mouse CCS cis-regulatory landscape, we genetically tagged CCS component-specific nuclei for comprehensive assay for transposase-accessible chromatin-sequencing (ATAC-Seq) analysis. Thus, we established a global CCS-enriched CRE database, referred to as CCS-ATAC, as a key resource for studying CCS-wide and component-specific regulatory functions. Using transcription factor (TF) motifs to construct CCS component-specific gene regulatory networks (GRNs), we identified and independently confirmed several specific TF sub-networks. Highlighting the functional importance of CCS-ATAC, we also validated numerous CCS-enriched enhancer elements and suggested gene targets based on CCS single-cell RNA-Seq data. Furthermore, we leveraged CCS-ATAC to improve annotation of existing human variants related to cardiac rhythm and nominated a potential enhancer-target pair that was dysregulated by a specific SNP. Collectively, our results established a CCS-regulatory compendium, identified novel CCS enhancer elements, and illuminated potential functional associations between human genomic variants and CCS component-specific CREs.

SNP Genotyping with Amplifluor-Like Method.

For SNP genotyping, amplification of fluorescence (Amplifluor) is a popular and actively developing method in the plant sciences. The "Amplifluor-like" is a "home-made" modification of the original commercial Amplifluor method. Amplifluor-like genotyping requires two essential components: (1) two allele-specific forward primers targeting the SNP site with one common reverse primer; and (2) a universal part with two non-allele-specific molecular probes containing one of the two used fluorophores and a quencher. Allele discrimination is based on the fluorescence score, where the dominance of one dye over the other confirms the presence of each specific SNP allele. The Amplifluor-like method is similar to commercial KASP and original Amplifluor methods but is much cheaper because all components can be ordered as regular and modified oligos. The easily adaptable Amplifluor-like method can be modified by any researcher to make it suitable for available instruments, reagents and conditions in low-budget laboratories for SNP genotyping of any plant species with identified genetic polymorphism.

Polymorphic differences within HLA-C alleles contribute to alternatively spliced transcripts lacking exon 5.

The HLA genes are amongst the most polymorphic in the human genome. Alternative splicing could add an extra layer of complexity, but has not been studied extensively. Here, we applied an RNA based approach to study the influence of allele polymorphism on alternative splicing of HLA‐C in peripheral blood. RNA was isolated from these peripheral cells, converted into cDNA and amplified specifically for 12 common HLA‐C allele groups. Through subsequent sequencing of HLA‐C, we observed alternative splicing variants of HLA‐C*04 and *16 that resulted in exon 5 skipping and were co‐expressed with the mature transcript. Investigation of intron 4 sequences of HLA‐C*04 and *16 compared with other HLA‐C alleles demonstrated no effect on predicted splice sites and branch point. To further investigate if the unique polymorphic positions in exon 5 of HLA‐C*04 or *16 may facilitate alternative splicing by acting on splicing regulatory elements (SRE), in‐silico splicing analysis was performed. While the HLA‐C*04 specific SNP in exon 5 had no effect on predicted exonic SRE, the HLA‐C*16 specific exon 5 SNP did alter exonic SRE. Our findings provide experimental and theoretical support for the concept that polymorphisms within the HLA‐C alleles influence the alternative splicing of HLA‐C.

High prevalence of blaTEM-135 and genetic epidemiology of blaTEM-135-carrying Neisseria gonorrhoeae isolates in Shandong, China, 2017-19.

Only one additional specific SNP in blaTEM-135 in penicillinase-producing Neisseria gonorrhoeae (PPNG) isolates is required for TEM-135 to evolve into an ESBL that is capable of degrading all extended-spectrum cephalosporins (ESCs). Identification of the blaTEM-135 gene was achieved by performing a mismatch amplification mutation assay PCR. PPNG isolates were then genotyped using MLST and N. gonorrhoeae multiantigen sequence typing (NG-MAST) techniques. Finally, phylogenetic analyses based on MLST and NG-MAST were performed on all of the PPNG isolates, and genogroups were classified according to the phylogenetic relatedness on the basis of each MLST and NG-MAST gene typing and the blaTEM allele varieties. Among the 197 PPNG isolates, one (0.5%) isolate possessed the blaTEM-220 allele, 90 (45.7%) possessed the blaTEM-135 allele, and 106 (53.8%) possessed the blaTEM-1 allele. Among the blaTEM-135-carrying PPNG isolates, MLST ST8109 (n = 30) and NG-MAST ST12199 (n = 5), ST12754 (n = 5) and ST15073 (n = 5) were the most prevalent in the Shandong province of China. The phylogenetic analyses revealed that MLST ST8109, ST8140 and ST14417, mainly carrying the blaTEM-135 allele, belonged to the same genogroup, G1, while NG-MAST ST12199 and ST15073, mainly carrying the blaTEM-135 allele, belonged to the same genogroup, Ga. This study has shown that the molecular epidemiology of PPNG isolates carrying the blaTEM-135 allele in Shandong has a dynamically changing status. Therefore, it is very pressing to continuously monitor the prevalence and mutation of the blaTEM-135 allele and the genetic epidemiology of PPNG isolates carrying the blaTEM-135 allele in this district.

The Influence of Caffeine Consumption and the Polymorphisms of DRD2 and ADORA2A Genes on Fine Motor Task Performance

Caffeine is the most commonly used psychoactive drug and has been associated with increased attention, focus and motor activity through adenosine receptor (ADORA2A) antagonism. ADORA2A and DRD2 are co‐localized in the central nervous system and blocking the adenosine receptor has been show to act as a dopamine receptor (DRD2) agonist which influence focus and motor tasks. Finally, single nucleotide polymorphisms of ADORA2A varies in response to caffeine which may influence the dopamine response.PURPOSEThe purpose of this study was to determine the influence of caffeine as well as the effects of the adenosine (ADORA2A) and dopamine (DRD2) polymorphisms during unilateral and bilateral motor tasks.METHODSThirty‐four subjects (age: 18‐23) were recruited and gave informed consent to participate in the study. An oral bolus of caffeine (CAF), 5mg•kg‐1, or placebo (PLA), maltodextrin, was given in a double‐blind, randomized, and counterbalanced design 60 min prior to testing. The Purdue Pegboard Test (PPT) was used to assess the unilateral movements by placing pegs with the right hand and left hand; this was coded for dominant and non‐dominant. Bilateral movements were also assessed with PPT by placing pegs with both hands and during a peg/washer/collar assembly task. Buccal cells were obtained using a 0.9% NaCl mouth rinse, spun down, and lysed via proteinase k. DNA was extracted using QiAmp Mini spin columns with amplification and allelic discrimination for ADORA2A (rs5751876) and DRD2 (rs1800497) obtained via One‐Step qPCR. All samples were run in duplicate with negative and positive controls. Data was analyzed using a 2 (condition) x 2 (SNP) with repeated measures for each subset of the PPT and a 2 (condition) x 2 (ADORA2A) x 2 (DRD2) with repeated measures to for each subset to find the interaction of ADORA2A and DRD2, p&lt;0.05)RESULTSFor the ADORA2A SNP, the main effect of caffeine demonstrated a significant increase in performance for each unilateral task from placebo to caffeine trials, dominant hand (16.4+1.6 to 17.4, p&lt;0.01), non‐dominant hand, (15.8+1.8 to 16.0, p&lt;0.05) and combined (45.5+4.3 to 46.2, p&lt;0.05). No difference was found for the bilateral movements. ADORA2A interaction effects demonstrated that TT genotype scored better under the caffeine condition, 15.8+1.9 to 16.2+ 0.8 for placebo and caffeine respectively. For DRD2, there were no significant differences in the main effects or interaction effects. The 3‐way ANOVA, condition x ADORA2A x DRD2, demonstrated no significant differences for the main effects or interaction effects.DISCUSSIONA bolus of caffeine improved performance for the test subset scores that involved unilateral movements but had no influence on scores for bilateral movements. The reduction in performance could be due to slower reaction times or neural coupling to coordinate movements between the limbs during bilateral movements. The increased performance in the non‐dominant hand for the TT genotype may be due to the increased sensitivity of this specific SNP to caffeine. While not significant, variations in responses to caffeine were observed when assessing task performance by grouped ADORA2A/DRD2 polymorphisms and the possible combinations. One grouping, TC/CC:AG/AA, demonstrated negative response to caffeine, whereas two other groupings (TT:GG, TC/CC:GG) demonstrated positive responses to caffeine. Further research and an increased sample size will help demonstrate the specific SNP interactions.

The Effects of Plasma Homocysteine Level on the Risk of Three Major Psychiatric Disorders: A Mendelian Randomization Study.

BackgroundHigher homocysteine (Hcy) level has been suggested to be associated with major psychiatric disorders (MPDs), such as schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD). We investigated the causal relationships between plasma Hcy level and MPDs risks using the Mendelian randomization (MR) method.MethodsWe selected 18 loci associated with plasma Hcy level from a large-scale genome-wide association study (GWAS) as genetic instruments. Genetic associations with SCZ, MDD, BD and BD subtypes (BD-I and BD-II) were extracted from several GWAS datasets from the Psychiatric Genomics Consortium. We used the Generalized Summary-data-based Mendelian Randomization (GSMR) method to estimate the associations of genetically predicted plasma Hcy levels with MPDs risks. We also performed inverse variance-weighted (IVW) analysis to verify the GSMR results and used MR-Egger regression and leave-one-out analysis to test the assumptions for a valid MR analysis.ResultsGenetically predicted plasma Hcy levels were associated with risks of SCZ (odds ratio [OR] = 1.12, PGSMR = 1.73 × 10−3) and BD-I (OR = 1.14, PIVW = 5.23 × 10−3) after Bonferroni correction. These associations were statistically significant when using IVW analysis (SCZ: OR = 1.11, PIVW = 2.74 × 10−3; BD-I: OR = 1.13, PIVW = 9.44 × 10−3). Furthermore, no significant horizontal pleiotropy was found by sensitivity analysis, and leave-one-out analyses showed no specific SNP affected the overall estimate. However, genetically determined plasma Hcy levels were not causally associated with MDD, BD, or BD-II risks.ConclusionOur results suggest that elevated plasma Hcy levels may increase the risk of SCZ or BD-I. Further randomized clinical trials are warranted to validate the MR findings in our study.

Characterization of Listeria monocytogenes isolated from wildlife in central New York.

Background Listeria monocytogenes (Lm) present in farming soil and food‐processing facilities threatens food safety, but little is known about the carriage of Lm by wildlife.ObjectivesWe estimated the prevalence of faecal Lm shedding among wildlife admitted to a veterinary medical teaching hospital in central New York and characterized a subset of the Lm isolates.MethodsWildlife samples were collected between May 2018 and December 2019. We characterized the Lm isolates by assessing the growth at three temperatures approximating the body temperatures of reptiles (25°C), mammals (37°C), and birds (42°C) and identifying genotypic characteristics related to transmission and virulence.ResultsThe apparent prevalence of faecal Lm shedding was 5.6% [18/324; 95% confidence interval (CI), 3.3%–8.6%]. Among 13 isolates that represented two lineages and 11 clonal complexes, three and five isolates were grouped into the same SNP clusters with human clinical isolates and environmental isolates, respectively. However, specific SNP difference data showed that Lm from wildlife was generally not closely related (>22 SNP differences) to Lm from human clinical sources and the food‐processing environment. While the stress response locus SSI‐2 was absent, SSI‐1 was found in four isolates. Virulence genes prfA, plcA, hly, mpl, actA, plcB, inlA, inlB, inlC, inlE, inlH, inlJ, and inlK were present, without any premature stop codons, in all isolates. Virulence loci Listeria pathogenicity island 3 (LIPI‐3) and LIPI‐4, which have been linked to hypervirulence, and inlG were found in four, three, and seven isolates, respectively.ConclusionsWildlife represents a potential reservoir for genetically diverse and putatively hypervirulent Lm strains. No statistically significant association between growth parameters and hosts was observed. However, compared to lineage I isolates, lineage II isolates showed significantly (p < 0.05) faster growth at 25°C and significantly slower growth at 42°C, suggesting that wildlife Lm isolates that belong to lineages I and II differ in their ability to grow at 25°C and 42°C.

Genome-wide association study reveals growth-related SNPs and candidate genes in mandarin fish (Siniperca chuatsi)

Mandarin fish (Siniperca chuatsi) is a popular inland farmed fish species with high an economic value. Molecular selective breeding programs are urgently required to improve the growth traits of mandarin fish for farming industry. In this study, using 160 mandarin fish individuals, specific locus-amplified fragment sequencing and SNP genotyping, we performed a genome-wide association study (GWAS) to identify genomic regions and candidate genes that are potentially associated with various growth traits of mandarin fish, such as body weight (BW), body thickness (BT), body height (BH) total length (TL), slaughter weight (SW), and body length (BL). Through genotyping, 5205 high-quality SNPs were found located on 24 chromosomes. A total of 11 significant and 37 suggestive SNPs related to growth traits were obtained, among which five SNPs significantly related to BW were located in the linkage group (LG) 8, 17, 21, and 23, two SNPs significantly related to TL were located in LG 7 and 17, two SNPs significantly related to BH were located on LG 17 and 23, two SNPs significantly related to BT were located on LG 14 and 19, respectively. Furthermore, LG17_937,734 and LG23_23,856,613 were growth-related traits overlap. Within 300 kb upstream and downstream of these significant SNPs, 65 candidate genes were identified within the associated QTLs, many of which were related to bone differentiation, growth and development, cell division and neurogenesis. In particular, asns, tg, mkk6, htra1, rnf213, ttn, tgfbr2, and nck2, were shown to be closely associated with growth, fat, muscle and bone formation. To our knowledge, this is the first GWAS focusing on growth traits of mandarin fish. Our findings establish a foundation for molecular marker-assisted selecting, genomic selecting, and functional analyzing the growth traits of mandarin fish.

Single Nucleotide Polymorphisms in Papillary Thyroid Carcinoma: Clinical Significance and Detection by High-Resolution Melting.

Single nucleotide polymorphisms (SNPs) can have a variety of implications for the progression and development of papillary thyroid carcinomas (PTCs). Identification of SNPs, either as germline variants or mutations occurring in tumor tissue, can thus have useful implications for patient management. There are many potential methods that can be used to identify a specific SNP or other genetic variant, and among these is high-resolution melting (HRM). HRM can be used to detect the presence of a genetic variant in a single sealed tube, involving undertaking a polymerase chain reaction (PCR) in the presence of a saturating intercalating dye. Once PCR is complete, the amplicons produced can be melted through incremental raising of the temperature and the genotype of individual samples determined by changes in the change in fluorescence as the fluorescent dye is released by the melting DNA. In this chapter, we detail a method for the genotyping of DNA samples using HRM.