Frequency Of Single Nucleotide Polymorphisms Research Articles

Frequency of the rs2015 (T>G) and rs2241703 (G>A) polymorphisms in the miRNA-SIRT2 gene in type 2 diabetes mellitus in Saudi Arabia.

To investigate the prevalence of rs2015 (T>G) and rs2241703 (G>A) polymorphisms in the miRNA-SIRT2 gene in Saudi Arabia and their possible associations with type 2 diabetes mellitus (T2DM). Blood samples were collected from 428 participants from Jazan University Hospital, Jazan, Saudi Arabia between September 2021 and June 2022 and subjected to TaqMan single-nucleotide polymorphisms (SNP) genotyping assay for rs241703 (G>A) and rs2015 (G>T). Genotype frequencies were determined in control (n=217). The A allele of rs2241703 was undetected in our population, and all samples carried the GG genotype. The rs2015 SNP frequency was 29.4% for GG, 45.6% for GT, and 24% for TT. However, logistic regression analysis of the dominant inheritance model showed no association between the T allele and T2DM calculated odds ratio [OR]=0.80, 95% confidence interval=0.53 to 1.20, p=0.301). Although rs2241703 SNP of Sirtuins 2 is not present, rs2015 SNP is highly prevalent in Saudi Arabia, but no direct link was identified with T2DM.

Allelic Frequencies of Single Nucleotide Polymorphisms (SNPs) in the N-acetyltransferase 2 (NAT2) Gene of Filipinos

Objectives. The present study aims to determine the frequency of occurrence of NAT2*4, NAT2*5A, NAT2*6B, NAT2*7A and NAT2*14A alleles by PCR-RFLP among Filipino volunteers. These alleles correspond to substitutions in the following sites: C341T, G590A, G857A and G191A, respectively, of the NAT2 gene. The presence of specific SNP combination was also used to deduce acetylation status and estimate genotype frequency and describe them in comparison with other populations based on literature.
 Methods. Genomic DNA from peripheral blood lymphocytes from 129 healthy Filipino volunteers was used to amplify the NAT2 gene segment. The RFLP analysis was done by restricting the expected PCR product with Kpn1, Taq1, BamH1 and Msp1/Al1, respectively, to detect the 4 alleles: NAT2*4, NAT2*5A, NAT2*6B, NAT2*7A and NAT2*14A.
 Results. The calculated allelic frequencies in Hardy-Weinberg equilibrium of NAT2*5A (C481T), NAT2*6B (G590A), NAT2*7A (G857A) and NAT2*14A (G191A) were 0.058, 0.097, 0.182 and 0.046, respectively. NAT2*4 had an allele frequency of 0.617. Nine genotypes were determined: NAT2*4/*4, NAT2*4/*5A, NAT2*4/*6B, NAT2*4/*7A, NAT2*4/*14A, NAT2*5A/*7A, NAT2*6B/*7A, NAT2*6B/*14A and NAT2*7A/*14A. From these genotypes, acetylator phenotypes were deduced. A trimodal pattern of distribution was established: rapid, intermediate and slow acetylators with the following percentages, 47.3%, 41.1 % and 11.6%. Among the slow acetylator SNPs determined, NAT2*7A was found as the most frequent allele and NAT2*14A was found as the least frequent allele.
 Conclusion. The study showed the mutation profile and observed genotypic similarities and differences of Filipinos with other Asian populations and Americans and other Caucasians based on literature. The results also suggest a trimodal pattern of distribution of acetylators and lesser number of slow acetylators among Filipino populations, a characteristic similar to other Asian populations but significantly different from Americans and other Caucasians. The occurrence of NAT2*7A and NAT2*14A can be further sequenced to verify the observed genotype.

Frequency of rs2228570 single nucleotide polymorphism of Vitamin-D Receptor (VDR) gene among the Kazakh ethnic group

The article presents the results of the study of vitamin D receptor (VDR) gene rs2228570 single nucleotide polymorphism (SNP) genotypes and individual alleles frequency among the Kazakh ethnic group representatives living in the Karaganda region. This SNP was determined by real-time polymerase chain reaction using TaqMan technology. The study relevance is due to the fact that genetic variations in rs2228570 affect the synthesis of the VDR protein and its activity as a transcription factor that regulates the expression of other genes. This mechanism determines the association of individual rs2228570 genotypes or alleles with susceptibility, course, and outcomes of various diseases. The polymorphism frequency may be depending on ethnicity. According to the study results, the most common genotypes of rs2228570 SNP among the Kazakhs were AG (32.8 %) and GG (25.2 %). The rarest are homozygotes TT (1.7 %) and CC (0.8 %). The frequency of all rs2228570 alleles was detected simultaneously in the present study for the first time. G became the predominant allele (51.3 %), less common was A (31.0 %), and the C and T alleles were the rarest (11.8 % and 5.9 %, respectively). The potential value of this SNP further study as a possible factor influencing the body’s susceptibility to various diseases, including COVID-19, is shown.

A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.).

Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.

Potential role of FKBP5 single-nucleotide polymorphisms in functional seizures.

We investigated the associations between FKBP5 single-nucleotide polymorphisms (SNPs) and functional seizures (FS). Seventy patients with FS, 140 with major depressive disorder (MDD), and 140 healthy controls were studied. Their DNAs were analyzed for the rs1360780 in the 3' region and rs9470080 in the 5' region of the FKBP5. Childhood trauma questionnaire and hospital anxiety and depression scale were used. Patients with FS and those with MDD had less GG and more AA genotypes in both rs9470080 and rs1360780 SNPs compared with those in healthy controls. Similar results were observed for allelic frequencies. There were no significant differences between FS and MDD groups in terms of genotype and allelic frequencies for both SNPs. The results of multinomial logistic regression analysis showed that FKBP5 polymorphisms were not associated with the diagnosis. Patients with FS and those with MDD had significantly different genotypes in both rs9470080 and rs1360780 SNPs compared with those in healthy controls. However, it seems that FKBP5 polymorphisms were not associated with FS in the absence of depression. Further genetic investigations of patients with FS may increase our understanding of the neurobiological underpinnings of this condition, but such studies should be large enough and very well designed; they should include a comparison group with depression in addition to a healthy control group.

Genetic polymorphisms of pharmacogenomic VIP variants in the Hui population from Ningxia Province of China.

Pharmacogenomics has been widely used to study the very important pharmacogenetic (VIP) variants among different populations. However, there is little pharmacogenomic information about the Chinese Hui population. Our research aimed to reveal the outstandingly different loci in the Hui population, and provide a theoretical foundation for personalized drug use in the Hui population, so as to facilitate more effective treatment of diseases. This study genotyped 53 VIP variants of 26 genes in 200 independent Hui individuals based on the Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB). Remarkable differences in the genotype and allele frequencies between the Hui and 26 other populations from the 1000 Genomes Project were assessed using the χ2 test. The genotype and allele frequencies of single nucleotide polymorphisms (SNPs) in PTGS2 (rs20417), NAT2 (rs1801280), NAT2 (rs1208), ACE (rs4291), and CYP2D6 (rs1065852) were considerably different in the Hui population compared with those in the other 26 populations. Besides, using the PharmGKB database, we identified several VIP variants that may alter the drug metabolism of ibuprofen, rofecoxib (PTGS2), captopril (ACE), citalopram, and escitalopram (CYP2D6). We also discovered other variants associated with adverse reactions to cisplatin and cyclophosphamide (NAT2). Our study indicated that the loci of PTGS2 (rs20417), NAT2 (rs1801280 and rs1208), ACE (rs4291), and CYP2D6 (rs1065852) in the Hui population were obviously different from those in the other 26 populations, which provides reliable information for predicting drug efficacy. Besides, it supplements the pharmacogenomic knowledge of the Hui population and lays the foundation for the individualized treatment for the Hui population.

Association Analysis of 27 Single Nucleotide Polymorphisms in a Chinese Population with Essential Tremor.

Genetic factors play a major role in essential tremor (ET) pathogenesis. This study aimed to assess variant burden in ET-associated genes in a relatively large Chinese population cohort. We genotyped 27 single nucleotide polymorphisms (SNPs) previously reported to be associated with ET by multiplex PCR amplicon sequencing assay in 488 familial and sporadic ET patients and 514 healthy controls (HCs). Then, we performed allelic and genotypic association test by Pearson chi-square test or Fisher's exact test. A total of 1002 samples were included in our analysis, consisting of 488 ET patients and 514 sex and age-matched HCs. For rs10937625, the C allele was linked to increased risk of ET (P = 0.019, OR = 1.503, 95% CI = 1.172-1.928). The carriers of the C/C homozygote and C/T heterozygote showed a significantly higher risk of ET, compared with the T/T homozygote under the dominant model (P = 0.019, OR = 1.628, 95% CI = 1.221-2.170). There were no statistically significant differences in the frequency of other SNPs between ET patients and healthy controls. Rs10937625 (STK32B) may increase the risk of ET in eastern Chinese population.

Emergence of Ancylostoma caninum parasites with the benzimidazole resistance F167Y polymorphism in the US dog population

BackgroundAnthelmintic resistance to benzimidazole has been detected in the canine hookworm, Ancylostoma caninum. Benzimidazole resistance is believed to have developed originally in greyhounds, but has also been detected in non-greyhound pet dogs. The aim of this study was to validate a probe-based allele-specific real-time PCR tests for the F167Y polymorphism on the β-tubulin isotype-1 gene and to determine the geographic distribution. MethodsAllele-specific real-time PCR tests were established and validated to detect the codon 167 polymorphism in the Ancylostoma caninum β-tubulin isotype-1gene. Additionally, real-time PCR tests were validated for Ancylostoma spp. and Uncinaria stenocephala. Two nucleic acid extraction protocols were validated including mechanical disruption of parasite structures in stool. The frequency of the F167Y single nucleotide polymorphism (SNP) was determined in hookworm confirmed stool samples. Samples with the resistant 167Y genotype were confirmed by β-tubulin gene sequencing and allele frequencies were determined. ResultsThe Ancylostoma spp. and A. caninum F167Y allele-specific real-time PCR tests were highly sensitive and specific when tested against synthetic DNA, spiked samples, and characterized parasites. Using an optimized total nucleic acid extraction protocol, 54 of 511 (10.6%) were found to contain the benzimidazole resistance allele. All 55 samples containing hookworms with the resistance mutation were confirmed by β-tubulin gene sequencing. The majority of resistant hookworms (44 resistant, 183 tested; 24.4%) originated from Florida, five from California (103 tested, 4.9%), three from Idaho (40 tested, 7.5%), two from Nevada (22 tested, 9.1%), and one sample from Hawaii (13 tested, 7.7%). Resistant genotypes were found in 14 different dog breeds including eight in Greyhounds. Allele-frequency determination revealed resistance allele frequencies between 1 and 100% with 58% above 50%. ConclusionsThis data strongly supports recent findings of benzimidazole resistant canine hookworms present throughout the general US pet dog population.

Current sika deer effective population size is near to reaching its historically highest level in the Japanese archipelago by release from hunting rather than climate change and top predator extinction

Deer species were repeatedly overexploited and protected for their meat and fur and they had strong impacts on ecosystems and human society by damaging crops and planted trees, altering vegetation, deer vehicle collision, and increasing ticks that vector zoonosis. To accomplish appropriate population management, the historical demography and its main driver need to be clarified. In this study, we estimated the historical demography of effective population size ( Ne) of sika deer ( Cervus nippon Temminck) in Hokkaido and Hyogo Prefectures of the Japanese archipelago. We estimated Ne of >100 generations from present (2020) by folded single nucleotide polymorphisms (SNP) frequency spectra and, within 100 generations from present, by linkage disequilibrium between SNP. In Hokkaido, Ne drastically increased around 3.0 ky BP and decreased around 100–150 years ago with the assumption of their generation length as 4 or 9 years. The Ne decreased by a 10th before the recent bottleneck. In Hyogo, Ne increased around 80 and 1 ky BP and decreased around 100–250 years ago. Ne decreased by a 100th before the recent bottleneck. After these recent bottlenecks, Ne of both regions recovered and the current Ne has nearly reaches the highest level of the last 100 ky BP. Literature survey and paleoclimate indicates that the decrease and increase of Ne of sika deer in Japanese archipelago may be caused by variations in the hunting activity of humans rather than climate change or the top predator extinction.

Isogenic Cell Lines Derived from Specific Organ Metastases Exhibit Divergent Cytogenomic Aberrations

Aneuploidy, a deviation in chromosome numbers from the normal diploid set, is now recognized as a fundamental characteristic of all cancer types and is found in 70-90% of all solid tumors. The majority of aneuploidies are generated by chromosomal instability (CIN). CIN/aneuploidy is an independent prognostic marker of cancer survival and is a cause of drug resistance. Hence, ongoing research has been directed towards the development of therapeutics aimed at targeting CIN/aneuploidy. However, there are relatively limited reports on the evolution of CIN/aneuploidies within or across metastatic lesions. In this work, we built on our previous studies using a human xenograft model system of metastatic disease in mice that is based on isogenic cell lines derived from the primary tumor and specific metastatic organs (brain, liver, lung, and spine). As such, these studies were aimed at exploring distinctions and commonalities between the karyotypes; biological processes that have been implicated in CIN; single-nucleotide polymorphisms (SNPs); losses, gains, and amplifications of chromosomal regions; and gene mutation variants across these cell lines. Substantial amounts of inter- and intra-heterogeneity were found across karyotypes, along with distinctions between SNP frequencies across each chromosome of each metastatic cell line relative the primary tumor cell line. There were disconnects between chromosomal gains or amplifications and protein levels of the genes in those regions. However, commonalities across all cell lines provide opportunities to select biological processes as druggable targets that could have efficacy against the primary tumor, as well as metastases.

Genome-wide comparisons reveal broad variations in intraspecific SNP frequencies among species in Agaricomycetes, Basidiomycota

Background:Genome sequence analyses can provide crucial information for understanding population history, speciation, and taxonomy. In Class Agaricomycetes where most mushroom-forming fungi belong, most species so far have been defined based on morphological, ecological, and/or molecular features. At present, there is little information on how species defined based on such features reflect their genome sequence diversity. In this study, we investigated genome-wide single nucleotide polymorphism (SNP) frequencies between strains within species to understand the patterns of variation.Methods:A total of 112 species in 72 genera of Agaricomycetes contained the nuclear and/or mitochondrial genome sequences from at least two strains each in public databases. Together, we obtained 398 and 106 available nuclear and mitochondrial genomes respectively from these taxa. Pairwise strain comparisons of the nuclear and mitochondrial genomes within individual species were conducted to obtain their SNP frequencies.Results:The SNP frequencies between nuclear genomes within individual species ranged 0–7.69% while for the mitochondrial genome, the pairwise strain SNP frequencies ranged 0–4.41%. The Spearman’s non-parametric rank correlation test showed a weak but statistically significant positive correlation between the paired nuclear and mitochondrial genome SNP frequencies. Overall, we observed a significantly higher SNP frequency in the nuclear genome than in the mitochondrial genomes between strains within most species. Interestingly, across the broad Basidiomycetes, the ratios of mitochondrial genome SNPs and nuclear genome SNPs between pairs of strains within each species were almost all lower than 1, with a mean of 0.24.Conclusions:Our analyses revealed broad variations among species in their intraspecific SNP frequencies in both the nuclear and mitochondrial genomes. However, there was broad consensus among the examined species in their mitochondrial to nuclear genome SNP ratios, suggesting that such a ratio could potentially serve as an indicator for genome sequence-based species identification.

Serum Androgen Metabolites Correlate with Clinical Variables in African and European American Men with Localized, Therapy Naïve Prostate Cancer.

Dihydrotestosterone (DHT) and testosterone (T), which mediate androgen receptor nuclear translocation and target gene transcription, are crucial androgens and essential molecular triggers required for the proliferation and survival of prostate cancer cells. Therefore, androgen metabolism is commonly targeted in the treatment of prostate cancer. Using a high-pressure liquid chromatographic assay with tandem mass spectral detection, we determined the serum levels of metabolites produced during DHT/T biosynthesis in African American (AA) and European American (EA) men with localized, therapy naïve prostate cancer. Serum progesterone and related metabolites were significantly lower in AA men than in EA men, and these differences were associated with rapid disease progression. Multivariate analysis revealed significant differences between a subset of intermediate androgen metabolites between AA and EA men and between men with <=3 + 4 and >=4 + 3 Gleason score disease. AA men have a significantly higher frequency of single nucleotide polymorphisms in CYP11B1 and CYP11B2, enzymes that regulate corticosterone-aldosterone conversion. Finally, higher levels of T and pregnenolone were associated with a lower risk of progression-free survival only in AA men. This work provides new insight into androgen metabolism and racial disparities in prostate cancer by presenting evidence of dysregulated androgen biosynthesis in therapy naïve disease that correlates with clinical variables.

Association of single nucleotide polymorphisms in heat stress protein 70 (HSP70) and 90 (HSP90) with the susceptibility of Pakistani sheep breeds to hemoparasitic infections

The present study was designed to report the genotypic and allelic frequency of single nucleotide polymorphism (SNP) at 222 G > A in HSP70 and at ex6-7390T22G in the HSP90 gene of 204 sheep (Baluchi = 11, Kajli = 29, Latti = 06 and Mundri = 158) enrolled from District Rajanpur in Punjab and to report the susceptibility of these sheep to the blood-borne parasitic infection. The tetra-primer amplification refractory mutation system–polymerase chain reaction (T-ARMS–PCR) approach revealed a significant variation (p < 0.001) in the genotype frequency of four enrolled sheep breeds at SNP 222 G > A in the HSP70 gene while the allelic frequency remained unaffected (p = 0.08). In all sheep breeds, GG (wild) genotype was most common. T-ARMS–PCR analysis revealed a similar trend for ex6-7390T22G in the HSP90 gene and it was observed that sheep had significantly higher wild-type (GG) (p < 0.05) at the studied SNPs. Studied epidemiological factors (sex and sampling sites) were not found associated with both SNPs. Chi-square test revealed that no specific genotype and allelic frequency at 222 G > A in HSP70 and at ex6-7390T22G in the HSP90 gene of the enrolled sheep breed was associated with the susceptibility to blood-borne parasitic infection (p > 0.05). In conclusion, we are reporting that Pakistan is blessed to have majority of sheep, from all breeds, having wild genotype at analyzed SNPs in heat stress genes. We highly recommend the genotypic screening of sheep before their selection as breeders to reduce the possibility of having sheep with polymorphic genotypes at 222 G > A in HSP70 and at 7390T22G in HSP90 genes that will improve the profitability and sustainability of animal production systems in Pakistan.

Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations

Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.

Comparison of Risk Allele Frequencies of Psoriasis-Associated Single-Nucleotide Polymorphisms in Different Population Groups.

The prevalence of psoriasis differs by population, and it appears to be more common among Europeans than in East Asians. Recent genome-wide association studies (GWAS) have identified alleles that increase the risk of psoriasis, and these alleles may present different frequencies in different geographic regions. We aimed to gain insights into the causes of differences in disease frequencies according to populations and the factors affecting prevalence and pattern differences. We collected a total of 147 psoriasis-associated single-nucleotide polymorphisms (SNPs) from the GWAS catalog and compared the allele frequency differences in 27 populations using public population frequency in the 1000 Genomes Project phase 3 (n=2,504) and the Korean Reference Genome Database (n=1,722). Additionally, we calculated the composited genetic risk scores across the population groups. There were distinct patterns of allele frequencies in different population groups. In many cases, East Asians exhibited allele frequencies opposite to that of Europeans. The genetic risk score was higher in Europeans (average: 0.487) and Americans (average: 0.492) than in East Asians (average: 0.471). The prevalence of psoriasis correlated with the average genetic risk score of the population. We observed a difference in the allele frequencies of psoriasis-associated SNPs between the studied populations. This result suggests that the difference in the prevalence of psoriasis between population groups can be interpreted to some extent by the genotype.

Abstract C059: SELENOF is a novel tumor suppressor and a new target to overcome breast cancer racial disparity

Abstract African American women die of breast cancer at a much higher rate than Caucasian women. While the reasons behind this racial disparity are multifactorial, recent findings point to biological components that remain to be fully elucidated. We have recently identified SELENOF as a new tumor suppressor in breast cancer. Consequently, its reduction or loss may drive disease progression and poor outcome. Conversely, we have shown that restoring SELENOF expression elicited anti-tumor activity. Therefore, therapeutic strategies to mitigate the loss of SELENOF may be exploited to improve outcome for patients affected by the loss of SELENOF. Based on two different Chicago-based cohorts, we reported that the breast tumors from African Americans exhibited a 5-10-fold higher frequency of SELENOF single nucleotide polymorphisms (SNPs) compared to Caucasians; these genetic variations result in attenuated translation of SELENOF and thus reduced SELENOF levels. This is supported by preliminary data showing that SELENOF expression is significantly lower in breast tumors from African American patients compared to Caucasians, and lower SELENOF expression predicts shorter survival in these patients. Our goal is to elucidate the role of SELENOF in breast cancer and determine its impact on breast tumorigenesis. We hypothesize that either enhancing SELENOF levels or mimicking its downstream signaling can be exploited to mitigate the loss of SELENOF and elicit anti-tumor activity. Targeting tumor suppressors remains challenging. We identified the eukaryotic initiation factor 4a3 (eIF4a3) as a putative translational repressor of SELENOF, and our preliminary data shows that pharmacologic inhibition of eIF4a3 results in increased SELENOF protein levels. We also found that SELENOF overexpression induces cell death by engaging the inositol-requiring enzyme 1 (IRE1) to determine cell fate. The therapeutic strategies under investigation are likely to result in novel and more effective personalized medicine, and may help close the breast cancer racial disparity gap. Citation Format: Roudy C. Ekyalongo, Alexandra Zigrossi, Brenna Flowers, Alan M. Diamond, Irida Kastrati. SELENOF is a novel tumor suppressor and a new target to overcome breast cancer racial disparity [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C059.

FTO genotypes (rs9939609 T>A) are Associated with Increased Added Sugar Intake in Healthy Young Adults

Introduction: Single-nucleotide polymorphism (SNP) rs9939609 in the FTO gene has been associated with dietary intake and appetite traits, mainly in participants with obesity; however, it remains widely unexplored in normal weight participants. Thus, the aims of this study were (1) to compare the changes in subjective appetite sensations, ghrelin, and insulin concentrations according to the SNP rs9939609 T>A in FTO and (2) to compare dietary intake between rs9939609 genotype groups in normal weight young participants. Methods: We conducted a quasi-experimental study involving 88 normal weight participants to analyze subjective perception of appetite, hormonal response for hunger and satiety, and dietary intake according to the rs9939609 SNP. Participants received a standardized single breakfast. Visual analogue scales (VAS) were utilized for assessing the subjective perception of appetite at fasting and immediately after breakfast and at 30, 60, 90, and 120 min postprandially. Glucose, lipid profile, ghrelin, and insulin were measured at fasting and at 120 min after breakfast. Dietary intake was assessed with a 3-day food record. The SNP was determined by allelic discrimination with TaqMan probes. To compare dietetic, biochemical, and the subjective appetite sensations, Student t test, ANCOVA test, and the repeated measures ANOVA were used. The linear regression model and the linear mixed model were used for the association analysis. Pearson correlation was used to test the correlation between two quantitative variables. Results: A total of 88 people participated, 81.8% were female, with a mean body mass index of 21.8 ± 2.0 kg/m² and a mean age of 20.6 ± 2.0. Genotype frequencies of the rs9939609 SNP were 52% for the TT allele and 48% for the TA/AA. The subjective perception of appetite named hunger, fullness, satiety, desire to eat, and prospective food consumption were similar between genotypes of the rs9939609. Participants with the TA/AA genotype showed a higher intake of added sugar (p = 0.039) than TT participants. No differences were found in ghrelin, insulin, glucose, or lipid parameters between genotypes. Conclusion: Carriers of the A allele from FTO gene SNP rs9939609 may have an increased preference for foods, specifically for added sugars.

The effect of chlorantraniliprole on the transcriptomic profile of Spodoptera frugiperda: a typical case analysis for the response of a newly invaded pest to an old insecticide.

Chlorantraniliprole is a diamide insecticide widely used in China over the last 15 years. The fall armyworm (FAW), Spodoptera frugiperda, newly invaded China in 2019. The response of FAW to chlorantraniliprole deserves more attention, in the context of many destructive lepidopteran species are resistant to diamide insecticides and the patent on core chemical of chlorantraniliprole in China expired in August 2022. This study investigated the response profile in larvae under chlorantraniliprole-induced (LC50) stress using methods of bioassay, RNA-Seq and qPCR. We observed growth inhibition and lethal effects in FAW larvae, but at a relatively high LC50 value compared to other several pests. Additionally, under chlorantraniliprole-induced stress, 3309 unigenes were found to be differentially expressed genes. The impacted genes included 137 encoding for detoxification enzymes, 29 encoding for cuticle proteins, and 20 key enzymes involved in the chitin metabolism, which all associated with metabolic resistance. Finally, we obtained the single nucleotide polymorphisms (SNPs) of two RyR genes, which are the target proteins for chlorantraniliprole. We also investigated the causes of the high LC50 value in our FAW, which possibly related to the stabilized 4743M on SNP frequency of RyR. These findings documented the genetic background of RyR of FAW and indicated that application of chlorantraniliprole has a high risk of controlling FAW in China. In brief, our results provide a better understanding of the mechanisms of chlorantraniliprole toxicity and detoxification in FAW, and will aid in monitoring the development of resistant strains for a newly pest to an old insecticide.

Additive and Dominance Effects of MC4R and PIT1 Polymorphisms on Production and Carcass Traits in Duroc Pigs

This study aimed to estimate the allelic and genotypic frequencies of single nucleotide polymorphisms (SNPs) of MC4R (melanocortin-4-receptor gene) and PIT1 (pituitary specific transcription factor-1) genes, and their additive dominance genetic effects on production and carcass traits in Duroc pigs. A total of 2170 tail tissue samples (1728 gilts and 442 male pigs) were collected from Dabaco Nucleus Breeding Pig Company, Bac Ninh province, Vietnam from January 2017 to June 2020. Polymorphisms in the MC4R and PIT1 genes were detected using the PCR-RFLP method. For MC4R, the frequencies of alleles A and G were 0.430 and 0.570, respectively. For PIT1, the frequencies of alleles A and B were 0.460 and 0.540, respectively. The genotype frequency distribution of the MC4R gene was in Hardy-Weinberg equilibrium (P = 0.375), but the genotype frequency distribution of PIT1 (P &lt;0.001) was not. The MC4R and PIT1 polymorphisms were significantly associated with final body weight and average daily gain (P &lt;0.001). Significant additive effects were also found (P &lt;0.05) for the two traits. The selection of individuals with the MC4R genotype AA and PIT1 genotype AA could improve final body weight and average daily gain in Duroc pigs.

Investigation of anticoagulant rodenticide resistance induced by Vkorc1 mutations in rodents in Lebanon

Anticoagulant rodenticides (AR) remain the most effective chemical substances used to control rodents in order to limit their agricultural and public health damage in both rural and urban environments. The emergence of genetically based resistance to AR worldwide has threatened effective rodent control. This study gives a first overview of the distribution and frequency of single nucleotide polymorphism in the vitamin K epoxide reductase subcomponent 1 (Vkorc1) gene in rodents in Lebanon. In the Mus genus, we detected two missense mutations Leu128Ser and Tyr139Cys, that confer resistance to anticoagulant rodenticides in house mice and a new missense mutation Ala72Val in the Mus macedonicus species, not previously described. In the Rattus genus, we found one missense mutation Leu90Ile in the roof rat and one missense mutation Ser149Ile in the Norway rat. This is the first study to demonstrate potential resistance to AR in Lebanese rodents and therefore it provides data to pest control practitioners to choose the most suitable AR to control rodents in order to keep their efficacy.