Potential Loci Research Articles

Unraveling the genetic architecture of stripe rust resistance in ICARDA spring wheat

Stripe rust, also known as yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most destructive fungal diseases affecting global wheat productivity. Identifying genetic loci associated with Pst resistance is crucial for developing durable Pst-resistant wheat varieties. This study aimed to discover genetic markers linked to Pst-resistance in wheat using a 15 K single-nucleotide polymorphism (SNP) array. Field screenings were conducted over two years (2018 and 2019) on a panel of 245 wheat breeding lines developed by the International Center for Agricultural Research in the Dry Areas (ICARDA) at the Kulumsa Agricultural Research Center in Ethiopia. Importantly, 36 breeding lines exhibited consistent immunity or resistance across both growing seasons. Genome-wide association studies (GWAS) identified 34 marker-trait associations (MTAs) across 10 loci that surpassed the significance threshold. Half of these SNP markers were located on chromosome 7B, while the remaining were distributed across chromosomes 1B, 2B, 4B, 5 A, and 6B. Many identified quantitative trait loci (QTLs) were in close proximity to known Pst resistance genes/QTLs, suggesting they correspond to the same genetic regions. Additionally, three QTLs—EWYY5A.2, EWYY6B.1, and EWYY7B.3—were notably distant from any of previously identified Pst resistance genes, emerging as potential novel loci from this study. These QTLs represent promising candidates for marker-assisted selection, facilitating the development of wheat cultivars with enhanced resistance to Pst. Additionally, this study recommends incorporating the 36 consistently resistant lines into national and international wheat breeding programs to enhance Pst disease management efforts.

Effect of UGT1A6 and UGT2B7 polymorphisms on the valproic acid serum concentration and drug-induced liver injury.

Aim: Valproic acid (VPA) is a classic broad-spectrum antiepileptic drug, with significant pharmacokinetic variability. Genetic polymorphisms contribute to this variability, influencing both VPA trough serum concentration (VPA concentration) and VPA-induced liver injury. Our study aims to investigate the association between polymorphisms of uridine diphosphate glucuronyl transferase (UGT) 1A6, UGT2B7 and VPA concentration and screen for potential genetic loci affecting VPA-induced liver injury.Methods: This study included epilepsy patients treated with VPA. PCR-RFLP method was used to determine the genotypes of UGT1A6 and UGT2B7. Chemiluminescent microparticle immunoassay was used to measure VPA concentration. Multiple linear regression and logistic regression were employed to analyze factors influencing VPA concentration and VPA-induced liver injury, respectively.Results: The correlation between UGT polymorphism and VPA concentration was analyzed in 133 samples. For VPA-induced liver injury, 105 patients were analyzed, with 29 in the liver injury group and 76 in the control group. Our finding showed patients with the UGT1A6-T19G variant had significantly lower VPA concentrations compared with wild-type patients and UGT1A6-T19G, A541G, A552C and UGT2B7-C802T, G211T, A268G polymorphisms showed no impact on VPA-induced liver injury.Conclusion: This study demonstrated UGT1A6-T19G polymorphisms affected the VPA concentration, providing a theoretical basis for the individualized clinical use of VPA.

Genomic insights into the diversity of mango cultivars in Saudi Arabia: Fluorescent SSR marker analysis

ObjectivesThis study presents a comprehensive genetic analysis of twelve mango cultivars from Saudi Arabia, investigating their genetic diversity, population structure, and potential loci under selection. MethodsUtilizing ten SSR loci, we conducted a thorough assessment of allele variation, revealing diverse patterns across loci and defined genetic diversity among cultivars. ResultsNotably, certain loci exhibited extensive allele diversity, with Loci M02 and M06 displaying five and seven alleles, respectively, while others showed more limited profiles, such as Locus M01 with only two alleles. Surprisingly, clustering patterns based on genetic relatedness did not consistently align with anticipated geographic groupings, suggesting additional factors influencing genetic structure beyond geography. Further analysis of allele sharing provided insights into the genetic relatedness among cultivars, highlighting both close genetic affinities and significant divergence. Subsequent Allele Sharing Matrix analysis unveiled sub-clustering within clusters, revealing finer-scale genetic structures within the population. Assessment of genetic differentiation using Analysis of Molecular Variance demonstrated significant variations among clusters and individuals, with variations among clusters ranging from 3% to 53%. Additionally, testing for loci under selection identified potential markers, such as locus M11, with observed heterozygosity greater than expected (1.024) and a relatively low observed FST value of 0.2695. ConclusionsOverall, our findings contribute to the characterization of mango genetic resources in Saudi Arabia, providing crucial information for breeding programs, germplasm conservation efforts, and agricultural practices. By leveraging advanced genomic technologies and interdisciplinary collaborations, future research can delve deeper into the genetic basis of adaptive traits and agronomic characteristics, paving the way for innovative strategies to enhance mango production and sustainability in Saudi Arabia.

Drosophila as a Model for Human Disease: Insights into Rare and Ultra-Rare Diseases.

Rare and ultra-rare diseases constitute a significant medical challenge due to their low prevalence and the limited understanding of their origin and underlying mechanisms. These disorders often exhibit phenotypic diversity and molecular complexity that represent a challenge to biomedical research. There are more than 6000 different rare diseases that affect nearly 300 million people worldwide. However, the prevalence of each rare disease is low, and in consequence, the biomedical resources dedicated to each rare disease are limited and insufficient to effectively achieve progress in the research. The use of animal models to investigate the mechanisms underlying pathogenesis has become an invaluable tool. Among the animal models commonly used in research, Drosophila melanogaster has emerged as an efficient and reliable experimental model for investigating a wide range of genetic disorders, and to develop therapeutic strategies for rare and ultra-rare diseases. It offers several advantages as a research model including short life cycle, ease of laboratory maintenance, rapid life cycle, and fully sequenced genome that make it highly suitable for studying genetic disorders. Additionally, there is a high degree of genetic conservation from Drosophila melanogaster to humans, which allows the extrapolation of findings at the molecular and cellular levels. Here, I examine the role of Drosophila melanogaster as a model for studying rare and ultra-rare diseases and highlight its significant contributions and potential to biomedical research. High-throughput next-generation sequencing (NGS) technologies, such as whole-exome sequencing and whole-genome sequencing (WGS), are providing massive amounts of information on the genomic modifications present in rare diseases and common complex traits. The sequencing of exomes or genomes of individuals affected by rare diseases has enabled human geneticists to identify rare variants and identify potential loci associated with novel gene-disease relationships. Despite these advances, the average rare disease patient still experiences significant delay until receiving a diagnosis. Furthermore, the vast majority (95%) of patients with rare conditions lack effective treatment or a cure. This scenario is enhanced by frequent misdiagnoses leading to inadequate support. In consequence, there is an urgent need to develop model organisms to explore the molecular mechanisms underlying these diseases and to establish the genetic origin of these maladies. The aim of this review is to discuss the advantages and limitations of Drosophila melanogaster, hereafter referred as Drosophila, as an experimental model for biomedical research, and the applications to study human disease. The main question to address is whether Drosophila is a valid research model to study human disease, and in particular, rare and ultra-rare diseases.

Screening the Best Risk Model and Susceptibility SNPs for Chronic Obstructive Pulmonary Disease (COPD) Based on Machine Learning Algorithms.

Chronic obstructive pulmonary disease (COPD) is a common and progressive disease that is influenced by both genetic and environmental factors, and genetic factors are important determinants of COPD. This study focuses on screening the best predictive models for assessing COPD-associated SNPs and then using the best models to predict potential risk factors for COPD. Healthy subjects (n=290) and COPD patients (n=233) were included in this study, the Agena MassARRAY platform was applied to genotype the subjects for SNPs. The selected sample loci were first screened by logistic regression analysis, based on which the key SNPs were further screened by LASSO regression, RFE algorithm and Random Forest algorithm, and the ROC curves were plotted to assess the discriminative performance of the models to screen the best prediction model. Finally, the best prediction model was used for the prediction of risk factors for COPD. One-way logistic regression analysis screened 44 candidate SNPs from 146 SNPs, on the basis of which 44 SNPs were screened or feature ranked using LASSO model, RFE-Caret, RFE-Lda, RFE-lr, RFE-nb, RFE-rf, RFE-treebag algorithms and random forest model, respectively, and obtained ROC curve values of 0.809, 0.769, 0.798, 0.743, 0.686, 0.766, 0.743, 0.719, respectively, so we selected the lasso model as the best model, and then constructed a column-line graph model for the 25 SNPs screened in it, and found that rs12479210 might be the potential risk factors for COPD. The LASSO model is the best predictive model for COPD and rs12479210 may be a potential risk locus for COPD.

Is God a Woman? Female Faces of God in Contemporary Cinema

Film, as a medium, serves not only as a significant source of entertainment but also as a powerful instrument in shaping attitudes, beliefs, behaviours, social norms, and identities. Since its inception, cinematic art has been closely intertwined with religious themes, with many film narratives drawing implicitly or explicitly from biblical texts and religious traditions. Consequently, theologians and ecclesiastical authorities were quick to identify film as a potential locus theologicus. Given film’s ability to spark debates on deeply ingrained views and beliefs, feminist theology, which critically reflects on gender power relations within religious communities and theological texts, finds it intriguing to explore how cinematic narratives can challenge the millennia-old depiction of God as a man. This article aims to examine how the art of cinema contributes to theological reflections on the female metaphors of God, particularly through female Christ-figures and God-figures, which occasionally appear in films such as Chocolat, All That Jazz, Always, Dogma, and The Shack. These characters defy traditional religious language, which often employs masculine imagery and metaphors for God, portraying female God as an independent chocolatier, a single mother, an elegant hairdresser, a beautiful young seductress, a curvaceous African American bread maker, and a witty, clownish girl. In these cinematic depictions, female God is compassionate, empathetic, kind, witty, forgiving, and profoundly in love with her human creations. At the same time, all of these female characters are powerful, assertive, strong, and self-confident.

Investigating the shared genetic links between hypothyroidism and psychiatric disorders: a large-scale genomewide cross-trait analysis

BackgroundAssociations between thyroid diseases and psychiatric disorders have been mainly described before. However, the genetic mechanism behind hypothyroidism and psychiatric disorders remains unexplained. MethodsWe examined the genetic architecture of hypothyroidism and 8 psychiatric disorders. Firstly, the global and local genetic relationship between the paired traits was explored. Secondly, cross-trait analysis was performed to investigate the genomic loci and genes between psychiatric disorders and hypothyroidism. Thirdly, the significant expression of these genes and the causal relationships were investigated. Lastly, enrichment analysis was conducted on these genes to explore their biological mechanisms. ResultsWe observed significant positive genetic correlations between psychiatric disorders and hypothyroidism. The cross-trait meta-analysis identified 62 shared genetic loci between hypothyroidism and psychiatric disorders. The colocalization analysis additionally revealed 15 potential pleiotropic loci with a posterior probabilities.H4 (PP·H4) value >0.7. We also found 2308 genes shared between both traits, which were highly enriched in biological pathways such as immune cell differentiation and autoimmune diseases, as well as in tissue structures like the frontal cortex and cerebral cortex. Especially, many pleiotropic genes were significantly expressed for multiple pairwise traits, such as BCL11B, RERE, and SUOX. Lastly, the Latent causal variable model (LCV) analysis did not find any causal components in the genetic structure between them. LimitationsThe limitations of this study include that the conclusions were drawn from a European population. ConclusionsThese findings not only deepens our understanding of their biological mechanisms but also has significant implications for the intervention and treatment of these diseases.

Multi-step gene set analysis identified HTR3 family genes involving childhood acute lymphoblastic leukemia susceptibility.

In our previous conventional genome-wide association study (GWAS), WWOX was a susceptibility gene associated with acute lymphoblastic leukemia (ALL) development. Nowadays, advancements in genetic association analyses promote an in-depth exploration of ALL genomics. We conducted a two-step enrichment analysis at both gene and pathway levels based on ALL GWAS data including 269 cases and 1039 controls of Chinese descent. The following functional prediction and experiments were used to evaluate the genetic biology of candidate variants and genes. The serotonin-activated cation-selective channel complex gene-set was a potential biological pathway involved in ALL occurrence. Of which, individuals carrying the T allele of rs33940208 exhibited a prominent reduced risk of ALL [odds ratio (OR) = 0.71, 95% confidence interval (CI) = 0.53 to 0.96, P = 2.81 × 10-2], whereas those with the A allele of rs6779545 demonstrated an increased risk (OR = 1.23, 95% CI = 1.01 to 1.51, P = 4.11 × 10-2). Notably, the two variants displayed a better prediction capability when combined, that the risk of developing childhood ALL increased by 131% in subjects with 2-4 risk alleles compared to those with 0-1 risk alleles (Ptrend = 2.05 × 10-3). In addition, the T allele of rs33940208 could reduce HTR3A mRNA level, while the A allele of rs6779545 increased HTR3D mRNA expression. In this study, we identified HTR3A rs33940208 and HTR3D rs6779545 as potential susceptibility loci for ALL in Chinese children. Future validation and functional research will elucidate the underlying molecular processes, refining preventive strategies for this disease.

Evaluation of the Frequency of (rs2227981 and rs2282055) Single Nucleotide Polymorphisms in Programmed Cell Death 1 and Its Ligand Genes of Iraqi Patients With Multiple Sclerosis

Abstract Multiple sclerosis (MS) is a central nervous system disease that causes demyelination and persistent inflammation and most of them among young adults. The current study aimed to assess gene polymorphism of PDCD1 and PDLCD1 genes and the frequency of two SNPs (rs2227981 and rs2282055). MS patients (n=100) were divided into two groups; newly diagnosed (42), and patients with ongoing treatments (58). These groups were compared to healthy subjects (n=55); the mean age ±SD was (30±8.46 years), (37±8.06years), and (31±8.73 years) for MS newly patients, patients with ongoing treatments, and healthy subjects, respectively. Studies for gene polymorphism of PDCD1 and PDLCD1 Genes and the Frequency of Two SNPs (rs2227981 and rs2282055) were measured by Real-time PCR by used HRM. The results of this study found that the genotypic frequencies of MS patient were 31% (n=31) normal AA and 48 % (n=48) heterozygous AG. Mutant homozygous was found in GG 21 % (n=21). In controls, the results demonstrate 69% (n=38) wild type AA, 27.27% (n=15) heterozygous AG and mutant homozygous GG 3.6% (n=2). The odds ratio for the GG genotype was 12.8 (0.2-5.9) with p=0.001 indicating that the homomutant genotype In PD1 gene polymorphism rs2227981 GG was a higher risk of MS than the wild-type PD1 gene polymorphism rs2227981 AA, The PD1 gene polymorphism rs2227981 AG genotype has the second risk of MS after PD1 gene polymorphism rs2227981GG with 3.92 fold high risk than the wild type AA (OR =3.92 (1.8-8.2) p=0.0003). The present study concludes that the population-based case-control study, which focused on the three PD-1 SNPs PD-1.3, PD-1.5, and PD-1.9, found that polymorphism variation might actually be a disease-modifying factor as opposed to an MS risk factor. There were substantially more PD-L1 gene SNP loci in MS patients compared to controls, and there were significantly more PD-L1 gene SNP loci in MS patients compared to controls. The pathogenesis of MS might be connected to PD-1 and PD-L1 SNPs. PD-L1 gene SNP locus rs2282055 and PD-1 gene SNP locus rs2227981 might be potential MS candidate polymorphism loci.

The shared genetic etiology of antisocial behavior and psychiatric disorders: Insights from pleiotropy and causality analysis

BackgroundAntisocial behavior (ASB) infringes on the rights of others and significantly disrupts social order. Studies have shown that ASB is phenotypically associated with various psychiatric disorders. However, these studies often neglected the importance of genetic foundations. MethodsThis study utilized genome-wide association studies and pleiotropy analysis to explore the genetic correlation between ASB and psychiatric disorders. Linkage disequilibrium score regression (LDSC) and high-definition likelihood (HDL) methods were employed to assess genetic correlations, and the PLACO method was used for pleiotropy analysis. Functional annotation and biological pathway analysis of identified pleiotropic genes were performed using enrichment analysis. Furthermore, Mendelian randomization (MR) analysis was conducted to validate these causal relationships. ResultsLDSC and HDL analysis showed that significant positive genetic correlations were between ASB and attention deficit hyperactivity disorder (ADHD), schizophrenia (SCZ), major depressive disorder (MDD), and post-traumatic stress disorder (PTSD). Multiple potential pleiotropic genetic loci were identified, particularly the FOXP2 and MDFIC genes located at the 7q31.1 locus. Enrichment analysis showed that these pleiotropic genes are highly expressed in several brain regions (such as the hypothalamus, cerebellar hemisphere, cortex, and amygdala) and immune-related cells. MR analysis further confirmed the causal effects ADHD, SCZ, and MDD on ASB risk. ConclusionThis study reveals significant genetic correlations and potential causal mechanisms between ASB and various psychiatric disorders. The MR analysis confirmed the causal effects of psychiatric disorders on ASB. These findings deepen our understanding of the genetic architecture of psychiatric disorders and ASB.

Clinical characteristics and genetic analysis of a case of a patient with familial hereditary breast cancer: a case report

BackgroundBreast cancer has emerged as the foremost cause of female mortality worldwide, with triple negative breast cancer accounting for approximately 10–15% of all breast cancer cases. The triple negative breast cancer family has obvious familial heritability, but no potential pathogenic variation was found in BRCA1/2.Case presentationThe patient was a 56-year-old woman of Han ethnicity. The clinical characteristics of this patient with breast cancer were summarized, peripheral blood of one normal female and two patients with breast cancer in this family was collected, DNA was extracted, and the potential pathogenic variation was analyzed by whole exome sequencing. The normal female and two patients with breast cancer in this family shared a maternal grandmother. The proband’s right breast mass was punctured, and the biopsy showed invasive carcinoma of the right breast, grade II–III, with necrosis. No mutation was found in BRCA1/2 gene test; immunohistochemical of surgical specimens showed triple negative breast cancer. Three mutation types and 17 gene mutation sites were detected through bioinformatics prediction analysis on the basis of co-segregation of genotype and phenotype within the family and whole exome sequencing results. Combined with the Cancer Genome Atlas database comprehensive analysis, the MT1E c.G107A (p.C36Y) mutation may be a potential pathogenic site.ConclusionsThrough whole exome sequencing, we identified a total of 17 potential pathogenic mutation loci, none of which have been reported thus far. Therefore, our work expanded the gene mutation spectrum of familial hereditary triple negative breast cancer, which can provide more basis for family genetic counseling.

Genome wide association study to identify the potential genetic loci responsible for Budd Chiari Syndrome in Indian population: Study from a tertiary care centre

Genome wide association study to identify the potential genetic loci responsible for Budd Chiari Syndrome in Indian population: Study from a tertiary care centre

Extreme genetic signatures of local adaptation in a notorious rice pest, Chilo suppressalis

ABSTRACT Climatic variation stands as a significant driving force behind genetic differentiation and the evolution of adaptive traits. Chilo (C.) suppressalis, commonly known as the rice stem borer, is a highly destructive pest that crucially harms rice production. The lack of natural population genomics data has hindered a more thorough understanding of its climate adaptation, particularly the genetic basis underlying adaptive traits. To overcome this obstacle, our study employed completely resequenced genomes of 384 individuals to explore the population structure, demographic history, and gene flow of C. suppressalis in China. This study observed that its gene flow occurred asymmetrically, moving from central populations to peripheral populations. Using genome-wide selection scans and genotype-environment association studies, we identified potential loci that may be associated with climatic adaptation. The most robust signal was found to be associated with cold tolerance, linked to a homeobox gene, goosecoid (GSC), whose expression level was significantly different in low and high latitudes. Moreover, downregulating the expression of this gene by RNAi enhances its cold tolerance phenotypes. Our findings have uncovered and delved into the genetic foundation of the ability of C. suppressalis to adapt to its environment. This is essential in ensuring the continued effectiveness and sustainability of novel control techniques.

Exploring the Association of Biochemical Characterization and Genetic Determinants of TNF-α, CXCR2, and CCR5 Delta 32 Mutation with Predisposition to Polycystic Ovary Syndrome.

In this case control study, we used amplification-refractory mutation system (ARMS)-PCR to detect and determine the presence of the polymorphic variants TNF-α, CCR5-delta32, and CXCR2 in the study subjects. These gene polymorphs may serve as critical candidate gene variants in PCOS pathogenesis and therapeutics. The case-control study's findings revealed that the majority of the biochemical and endocrine serum biomarkers examined in the investigation-including lipids (LDL, HDL, and cholesterol), T2DM markers (fasting glucose, free insulin, and HOMA-IR), and hormones (FSH, LH, testosterone, and progesterone)-exhibited statistically significant changes in PCOS patients. The distributions of TNF-α (rs1800629), CCR5-delta32, and CXCR2 (rs2230054) genotypes analyzed within PCOS patients and healthy controls in the considered population were significant (p < 0.05). The heterozygosity of CXCR2-CA, TNF-α GA, and CCR5(WT+Δ32*) genotypes was significantly associated with PCOS susceptibility, with high OR and p < 0.05 in the codominant model. Similarly, the A allele of the TNF-α and CXCR2 genes, along with the CCR5Δ32*(mutant) allele, was significantly associated with PCOS susceptibility, with high OR and p < 0.05. Likewise, the CXCR2 (CA+AA) vs CC genotype was associated with increased susceptibility to PCOS, with OR 2.25, p < 0.032. Our study concludes that TNF-α rs1800629G>A, CXCR2-rs2230054C>T, and CCR5-Delta32 rs333 are potential loci for developing PCOS in the Tabuk population. These findings might eventually be useful in identifying and classifying those who are at risk for PCOS. To validate these results, it is advised that further longitudinal studies be conducted in diverse ethnic populations and with larger sample sizes.

Association of RAN and RANBP2 Gene Polymorphisms With Glioma Susceptibility in Chinese Children.

Glioma is the most prevalent pediatric central nervous system malignancy. RAN, member RAS oncogene family (RAN), is a key signaling molecule that regulates the polymerization of microtubules during mitosis. RAN binding protein 2 (RANBP2) is involved in DNA replication, mitosis, metabolism, and tumorigenesis. The effects of RAN and RANBP2 gene polymorphisms on glioma susceptibility in Chinese children are currently unknown. This study aimed to evaluate the association between RAN and RANBP2 gene polymorphisms and glioma susceptibility in Chinese children. We recruited 191 patients with glioma and 248 children without cancer for this case-control study. Polymerase chain reaction-based TaqMan was applied to gene sequencing and typing. Logistic regression model-calculated odds ratio and 95% confidence interval were used to verify whether the gene polymorphisms (RAN rs56109543 C>T, rs7132224 A>G, rs14035 C>T, and RANBP2 rs2462788 C>T) influence glioma susceptibility. Based on age, gender, tumor subtype, and clinical stage, stratified analyses of risk and protective genotypes were conducted. p values for mutant genotype analyses were all >0.05, indicating no significant correlation between these gene polymorphisms and glioma risk. RAN and RANBP2 gene polymorphisms were not found to be statistically significantly associated with glioma susceptibility in Chinese children. Other potential functional gene polymorphism loci of RAN and RANBP2 will need to be evaluated in the search for novel glioma biomarkers.

Potential Association of The Pathogenic Kruppel-like Factor 14 (KLF14) and Adiponectin (ADIPOQ) SNVs with Susceptibility to T2DM.

To evaluate the associations of the pathogenic variants in Kruppel-like Factor 14 (KLF 14) and Adiponectin (ADIPOQ) with susceptibility to type 2 diabetes mellitus (T2DM). Type 2 diabetes mellitus (T2DM) is a pandemic metabolic disease characterized by increased blood sugar and caused by resistance to insulin in peripheral tissues and damage to pancreatic beta cells. Kruppel-like Factor 14 (KLF-14) is proposed to be a regulator of metabolic diseases, such as diabetes mellitus (DM) and obesity. Adiponectin (ADIPOQ) is an adipocytokine produced by the adipocytes and other tissues and was reported to be involved in T2DM. To study the possible association of the KLF-14 rs972283 and ADIPOQ-rs266729 with the risk of T2DM in the Saudi population. We have evaluated the association of KLF-14 rs972283 C>T and ADIPOQ-rs266729 C>G SNV with the risk to T2D in the Saudi population using the Amplification Refractory Mutation System PCR (ARMS-PCR), and blood biochemistry analysis. For the KLF-14 rs972283 C>T SNV we included 115 cases and 116 healthy controls, and ADIPOQ-rs266729 C>G SNV, 103 cases and 104 healthy controls were included. Results indicated that the KLF-14 rs972283 GA genotype and A allele were associated with T2D risk with OR=2.14, p-value= 0.014 and OR=1.99, p-value=0.0003, respectively. Results also ADIPOQ-rs266729 CG genotype and C allele were associated with an elevated T2D risk with an OR=2.53, p=0.003 and OR=1.66, p-value =0.012, respectively. We conclude that SNVs in KLF-14 and ADIPOQ are potential loci for T2D risk. Future large-scale studies to verify these findings are recommended. These results need further verifications in protein functional and large-scale case control studies before being introduced for genetic testing.

Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis

The Quercus L. species is widely recognized as a significant group in the broad-leaved evergreen forests of tropical and subtropical East Asia. These plants hold immense economic value for their use as firewood, furniture, and street trees. However, the identification of Quercus species is considered challenging, and the relationships between these species remain unclear. In this study, we sequenced and assembled the chloroplast (cp.) genomes of four Quercus section Cyclobalanopsis species (Quercus disciformis, Quercus dinghuensis, Quercus blackei, and Quercus hui). Additionally, we retrieved six published cp. genome sequences of Cyclobalanopsis species (Quercus fleuryi, Quercus pachyloma, Quercus ningangensis, Quercus litseoides, Quercus gilva, and Quercus myrsinifolia). Our aim was to perform comparative genomics and phylogenetic analyses of the cp. whole genome sequences of ten Quercus section Cyclobalanopsis species. The results revealed that: (1) Quercus species exhibit a typical tetrad structure, with the cp. genome lengths of the newly sequenced species (Q. disciformis, Q. dinghuensis, Q. blakei, and Q. hui) being 160,805 bp, 160,801 bp, 160,787 bp, and 160,806 bp, respectively; (2) 469 SSRs were detected, among which A/T base repeats were the most common; (3) no rearrangements or inversions were detected within the chloroplast genomes. Genes with high nucleotide polymorphism, such as rps14-psaB, ndhJ-ndhK, rbcL-accD, and rps19-rpl2_2, provided potential reference loci for molecular identification within the Cyclobalanopsis section; (4) phylogenetic analysis showed that the four sections of Cyclobalanopsis were grouped into sister taxa, with Q. hui being the first to diverge from the evolutionary branch and Q. disciformis being the most closely related to Q. blackei. The results of this study form the basis for future studies on taxonomy and phylogenetics.

Multi-ethnic genome-wide association study to identify a novel locus for susceptibility to immune-related adverse events from immune checkpoint inhibitors.

3090 Background: Immune-related adverse events (IrAEs) arising from immune checkpoint inhibitors (ICIs) can be unpredictable. As genomic variation underlies both disease susceptibility and drug responses, genomic markers may predict for the development of IrAEs. We perform a pioneering pharmacogenomic study across a multi-ethnic Asian patient population to uncover genomic biomarkers associated with IrAEs from ICIs. Methods: From March 2018 – July 2023, cancer patients treated with ICIs from the National University Cancer Institute Singapore and Tan Tock Seng Hospital were recruited. IrAEs were characterized and graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events (CTCAE) version 5. DNA was extracted and genotyped by Infinium Global Screening Array (700K markers). Statistical analyses were performed by SVS/HelixTree, PLINK and R. Genetic association was performed by logistic regression (additive model), accounting for all possible confounding factors. Bonferroni corrected P &lt; 1.28E-07 (0.05/390,925 SNPs passed QC) was considered statistically significant. Results: Genome-wide association study (GWAS) was conducted amongst 507 patients of Asian Ancestry (Chinese, Malay, Indian and Others). Median age was 63. Majority were male (66.5%), Chinese (76.7%), ECOG PS 0-1 (40.1%) and had stage IV cancer at diagnosis (67.2%). Non-small cell lung cancer (37.1%), renal cell carcinoma (12.2%) and hepatocellular carcinoma (7.7%) were the three most common cancers. Top four ICIs used were pembrolizumab, nivolumab, durvalumab and atezolizumab, respectively (47.1%, 23.9%, 12.5%, 11.3%). 0.8% of patients received dual ICIs concurrently. Median duration of treatment was 142 days and median follow-up was 147 days. IrAEs were seen in 43.7% of patients. Skin (24.1%), endocrine (8.1%) and hepatotoxicity (6.1%) were the most common IrAEs. 4.9% of patients had grade ≥3 toxicity, of which skin (3.6%), hepatotoxicity (3.0%) and pulmonary toxicity (1.8%) were the most common. Multi-ethnic GWAS analysis identified one potential novel genetic locus associated with CTCAE grade ≥3 IrAEs. chr3:163402331 rs146525069; P = 7.29E-08, OR (95%CI) = 17.08 (5.40- 54.04); minor allele = A, 10.91% in Cases vs 0.71% in Controls. Conclusions: This pharmacogenomics GWAS uncovered a novel locus for susceptibility to serious immune-related adverse events from immune checkpoint inhibitors. Further pharmacogenomic discovery/replication and functional validation studies are currently on-ongoing. Our study provides a potential biological mechanism for IrAEs and a step towards more effective clinical translation of pharmacogenetic testing to personalize ICI use.

Polymorphisms of ITGA9 Gene and Their Correlation with Milk Quality Traits in Yak (Bos grunniens).

A single-nucleotide polymorphism (SNP) is a genome-level trait that arises from a variation in a single nucleotide, leading to diversity in DNA sequences. SNP screening is commonly used to provide candidate genes for yak breeding efforts. Integrin Subunit Alpha 9 (ITGA9) is an integrin protein. It plays an important role in cell adhesion, signalling, and other processes. The aim of this study was to discuss the association between genetic polymorphisms in the ITGA9 gene and milk quality traits and to identify potential molecular marker loci for yak breeding quality. We genotyped 162 yaks using an Illumina Yak cGPS 7K liquid chip and identified the presence of polymorphisms at nine SNP loci in the ITGA9 gene of yaks. The results showed that the mutant genotypes in the loci g.285,808T>A, g.306,600T>C, and g.315,413C>T were positively correlated with the contents of casein, protein, total solids (TS), and solid nonfat (SNF) in yak milk. In other loci, heterozygous genotypes had a positive correlation with nutrient content in yak milk. Then, two ITGA9 haplotype blocks were constructed based on linkage disequilibrium, which facilitated a more accurate screening of ITGA9 as a candidate gene for yak milk quality improvement. In conclusion, we identified SNPs and haplotype blocks related to yak milk quality traits and provided genetic resources for marker-assisted selection in yak breeding.

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron.

Research on the mechanism of marine polysaccharide utilization by Bacteroides thetaiotaomicron has drawn substantial attention in recent years. Derived from marine algae, the marine algae polysaccharides could serve as prebiotics to facilitate intestinal microecological balance and alleviate colonic diseases. Bacteroides thetaiotaomicron, considered the most efficient degrader of polysaccharides, relates to its capacity to degrade an extensive spectrum of complex polysaccharides. Polysaccharide utilization loci (PULs), a specialized organization of a collection of genes-encoded enzymes engaged in the breakdown and utilization of polysaccharides, make it possible for Bacteroides thetaiotaomicron to metabolize various polysaccharides. However, there is still a paucity of comprehensive studies on the procedure of polysaccharide degradation by Bacteroides thetaiotaomicron. In the current study, the degradation of four kinds of marine algae polysaccharides, including sodium alginate, fucoidan, laminarin, and Pyropia haitanensis polysaccharides, and the underlying mechanism by Bacteroides thetaiotaomicron G4 were investigated. Pure culture of Bacteroides thetaiotaomicron G4 in a substrate supplemented with these polysaccharides were performed. The change of OD600, total carbohydrate contents, and molecular weight during this fermentation were determined. Genomic sequencing and bioinformatic analysis were further performed to elucidate the mechanisms involved. Specifically, Gene Ontology (GO) annotation, Clusters of Orthologous Groups (COG) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were utilized to identify potential target genes and pathways. Underlying target genes and pathways were recognized by employing bioinformatic analysis. Several PULs were found that are anticipated to participate in the breakdown of these four polysaccharides. These findings may help to understand the interactions between these marine seaweed polysaccharides and gut microorganisms. The elucidation of polysaccharide degradation mechanisms by Bacteroides thetaiotaomicron provides valuable insights into the utilization of marine polysaccharides as prebiotics and their potential impact on gut health. Further studies are warranted to explore the specific roles of individual PULs and their contributions to polysaccharide metabolism in the gut microbiota.