Haploview: analysis and visualization of LD and haplotype maps

Drug survival of omalizumab in atopic asthma: Impact of clinical and genetic variables

It is estimated that 40-50% of severe asthma has an atopic basis, representing a clinical challenge and a significant economic burden for healthcare systems. The most effective treatment has emerged with the use of biologic therapies such as omalizumab; however, the rate of therapy switching due to loss of efficacy is high, which has a negative impact on the healthcare system. The aim was to evaluate the influence of genetic polymorphisms as predictors of omalizumab survival. We conducted a retrospective observational cohort study of 110 patients with uncontrolled severe allergic asthma treated with omalizumab in a tertiary hospital. We analyzed FCER1A (rs2251746, rs2427837), FCER1B (rs1441586, rs573790, rs1054485, rs569108), C3 (rs2230199), FCGR2A (rs1801274), FCGR2B (rs3219018, rs1050501), FCGR3A (rs10127939, rs396991), IL1RL1 (rs1420101, rs17026974, rs1921622) and GATA2 (rs4857855) by real-time PCR using Taqman probes. Drug survival was defined as the time from initiation to discontinuation of omalizumab. Cox regression analysis adjusted for the presence of respiratory disease, GERD, SAHS and years with asthma showed that the SNPs FCER1B rs573790 - CT (p < .001; HR = 3.38; CI95% = 1.66-6.87), FCGR3A rs10127939-AC (p = .018; HR = 3.85; CI95% = 1.25-11.81) and FCGR3A rs396991-CC (p = .020; HR = 2.23; CI95% = 1.14-4.38) were the independent variables associated with worse survival in patients diagnosed with asthma. A trend toward statistical significance was also found between and FCGR3A rs10127939-CC (p = .080; HR = 0.13; CI95% = 0.01-1.28) and longer drug survival. The results of this study demonstrate the potential influence of the polymorphisms studied on omalizumab survival and the clinical benefit that could be achieved by defining predictive biomarkers of drug survival.

Exploring the genetic influence on hair cortisol concentration: Genetic association of rs11621961 on SERPINA6/1 locus in the 2004 Pelotas Birth Cohort (Brazil)

Genetics plays a critical role in regulating cortisol, as demonstrated by the association of the SERPINA6/1 locus with plasma cortisol concentrations in a genome-wide association meta-analysis (GWAMA). These genes are integral to glucocorticoid transport and regulation, highlighting a direct genetic influence on cortisol availability. This study examines the genetic contribution to hair cortisol concentration (HCC) in adolescents from the 2004 Pelotas (Brazil) Birth Cohort at age 15, employing three distinct approaches: 1) polygenic score (PGS), 2) gene-based analysis, and 3) candidate variations analysis. A total of 1667 individuals were included. The cortisol-PGS was derived from the most recent morning plasma cortisol GWAMA study, and gene-based analyses were performed using MAGMA. For the analysis of candidate variants in the SERPINA6/1 locus, we selected SNPs with P-values ≤ 5 × 10-8 from the cortisol GWAMA and conducted in silico analyses to assess potential regulatory functions. Nineteen SNPs were tested. Our results revealed a significant association between rs11621961 and HCC after multiple testing correction. This intergenic SNP, located 1.1 kb from the 3'-untranslated region (UTR) of SERPINA6, showed that the T allele was associated with higher HCC (β=0.05, FDR-P = 0.038). Functional in silico analyses suggested that rs11621961 might influence gene expression and chromatin structure by altering motifs and acting as an expression quantitative trait locus (eQTL) in lymphoblastoid cell lines. However, neither the cortisol-PGS nor gene-based analyses showed an association with HCC. This study offers important contributions to the understanding of the genetic determinants of HCC, advancing the knowledge of the relationship between genetics and cortisol regulation in adolescents.

Dopamine D3 receptor gene is associated with obsessive-compulsive disorder and antidepressant response

BACKGROUND

Obsessive-compulsive disorder (OCD) is a common neuropsychiatric disorder with a strong genetic component. Previous studies have suggested a role for the dopamine receptor genes in OCD with the dopamine D3 receptor (DRD3) gene being relatively overlooked. There is neurobiological evidence that D3 may be involved in the striatal-cortical circuits that affect compulsive behaviour and anxiety. Thus, we investigated genetic variants of DRD3 in association with OCD and serotonin reuptake inhibitor (SRI) response.

METHODS

We examined nine polymorphisms across DRD3 in 318 individuals with OCD (comprised of 129 small nuclear families, and 196 independent singleton cases) compared to 196 healthy controls matched for age, gender, and ethnicity using the family-based association test (FBAT) and case-control analysis respectively. Quantitative analyses were performed with age at onset (AAO) and Yale-Brown Obsessive-Compulsive Scale (Y-BOCS) severity scores.

RESULTS

Nominally significant biased transmission of alleles in polymorphic sites rs2399504, rs7611535, rs1394016, Ser9Gly, rs167770, and rs2087017 was observed with FBAT. The rs2399504, rs7611535, rs1394016, Ser9Gly, and rs167770 polymorphisms were associated with AAO but not with Y-BOCS scores using FBAT. Five polymorphisms (rs2399504, rs7611535, rs1394016, Ser9Gly, and rs167770) showed a trend in case-control analyses for allele/genotype distributions. Haplotype analyses of the polymorphisms using Haploview revealed several combinations of markers associated with OCD. Nominally positive association between rs167770 and rs11721264 and sertraline response remained significant after correction for multiple testing.

CONCLUSION

This is the first report to our knowledge of involvement of DRD3 in OCD, which requires further research.

The association of genetic variants VDR Taq I rs731236 and AMLEX rs946252 with dental caries susceptibility and severity in Egyptian children

Dental caries is a worldwide ailment and universally affects about 500 million children. We investigated the clinical signature of vitamin D receptor (VDR) Taq I rs731236 and Amelogenin gene on X chromosome (AMLEX) rs946252 variants with dental caries susceptibility and severity in Egyptian children. This study enrolled 200 dental caries children aged 6-12 years, subdivided into 100 moderate and 100 severe dental caries subgroups, and 100 caries-free control children age-matched. The gDNA extraction was executed from buccal swabs and the genotyping was accomplished by TaqMan® allelic discrimination assay. Our study depicted a substantial association between mutant (G) allele of VDR Taq I rs731236 variant and dental caries susceptibility under allelic (OR = 1.68, 95 %CI = 1.16-2.4, P = 0.005), codominant (GG versus AA, OR = 2.66, 95 %CI = 1.22-5.59, P = 0.01), dominant (OR = 1.8, 95 %CI = 1.11-2.98, P = 0.02) and recessive (OR = 2.1, 95 %CI = 1-4.3, P = 0.047) models. Additionally, a substantial association between mutant (G) allele of VDR Taq I rs731236 and dental caries severity under allelic (OR = 1.68, 95 %CI = 1.13-2.5, P = 0.01), codominant (GG versus AA, OR = 2.6, 95 %CI = 1.15-5.9, P = 0.03), and dominant (OR = 1.9, 95 %CI = 1.09-3.5, P = 0.04) models. Contrariwise, our findings revealed a substantial reduction in dental caries susceptibility associated with mutant (T) allele of AMLEX rs946252 variant under codominant (CT versus CC, OR = 0.53, 95 %CI = 0.32-0.89, P = 0.02), dominant (OR = 0.51, 95 %CI = 0.31-0.85, P = 0.01) and allelic (OR = 0.64, 95 %CI = 0.44-0.9, P = 0.01) models. In conclusion, our discoveries suggested that the existence of the VDR Taq I rs731236 variant may predispose the dental caries susceptibility and severity, whereas the presence of AMLEX rs946252 variant may protect against dental caries.

A genome-wide association study of taste liking in the Danish population

BACKGROUND

Taste liking, a complex trait, plays an important role in food choice and eating behavior, thereby influencing the risk of diet-related diseases.

OBJECTIVE

This study aimed to identify novel loci that could explain differences in liking of basic tastes, fat and oral sensations, represented by several food items.

METHODS

Liking scores were derived using a newly developed taste liking questionnaire (TasteLQ), validated in the Danish population. We conducted a genome-wide association study (GWAS) of liking of six modalities (sweet, salty, sour, bitter-astringency, umami, and pungency) and nine factors representing modality subgroups among 6,437 Danish adults. As a secondary analysis, GWASs of 44 single food items from TasteLQ were also undertaken.

RESULTS

We identified one genome-wide significant variant, rs170518 (MAF=0.16), on chromosome 5, associated with liking of an umami factor characterized by glutamate-rich food items (P=3.7x10-8, beta=0.14 standard deviation (SD) (Standard error (SE)=0.03). When analyzing individual food items, four SNPs within one locus, annotated to the bitter taste receptor gene, TAS2R38, were associated with liking of bitter-tasting rocket salad. Finally, our data confirmed some of the previously associated genomic variants with taste perception, food liking, and intake.

CONCLUSIONS

While our findings provide insight into loci involved in taste liking, they remain preliminary and warrant additional validation due to lack of replication in an independent population and limited number of genome-wide significant associations.

Genome-wide association analysis identifies seven loci conferring resistance to multiple wheat foliar diseases, including brown and yellow rust resistance originating from Aegilops ventricosa

We assembled a European bread wheat (Triticum aestivum L.) association mapping panel (n = 480) genotyped using a 90,000 feature single nucleotide polymorphism array, with the aim of identifying genetic loci controlling resistance to four fungal diseases: yellow (stripe) rust (YR), brown (leaf) rust (BR), Septoria tritici blotch (ST) and powdery mildew (PM). Simulations showed our panel to have good power to detect genetic loci, with > 50% probability of identifying loci controlling as little as 5% of the variance when heritability was 0.6 or more. Using disease infection data collected across 31 trials undertaken in five European countries, genome-wide association studies (GWAS) identified 34 replicated genetic loci (20 for YR, 12 for BR, two for PM, 0 for ST), with seven loci associated with resistance to two or more diseases. Construction and analysis of eight bi-parental populations enabled two selected genetic loci, yellow rust resistance locus YR_2A010 (chromosome 2A) and YR_6A610 (6A), to be independently cross-validated, along with the development of genetic markers to track resistance alleles at these loci. Notably, the chromosome 2A yellow and brown rust resistance locus corresponds to the 2NvS introgression from the wild wheat species, Aegilops ventricosa. We found evidence of strong selection for 2NvS over recent breeding history, being present in 48% of the most recent cultivars in our panel. Collectively, we define the genetic architectures controlling resistance to major fungal diseases of wheat under European field environments, and provide resources to exploit these for the development of new wheat cultivars with improved disease resistance.

Population genomics of migratory and resident Spodoptera frugiperda reveals key genes and loci driving migration traits

BACKGROUND

The fall armyworm (Spodoptera frugiperda, FAW) is one of the most devastating invasive pests in the world, owing to its extraordinary migration performance. Research has clarified the migratory pathways and external environmental factors affecting FAW migration. However, the internal genes and loci regulating migration or reside in FAW remain largely unknown.

RESULTS

In this study, we used a tethered flight mill system to distinguish migratory and resident individuals, which exhibit significant differences in flight-related traits such as flight distance, duration, and maximum speed. Selective sweep analysis of 51 resequencing FAW (23 migratory and 28 resident individuals) identified 652 candidate genes, and genome-wide association analysis (GWAS) identified 79 functional annotated genes associated with the most significant trait, flight distance. These candidate genes were mainly concentrated in amino acid metabolism, signal transduction, and environmental adaptation. The neuroendocrine convertase 2 gene was crossed between the two analyses, with 65 selective mutation loci in the intron region. Casein kinase I, which reported regulating circadian rhythm by phosphorylating the period, was simultaneously involved in several enriched signaling pathways, and had 11 selective loci in the regulatory region. These selective mutation loci may affect the expression of target genes and regulate the migration behavior of FAW.

CONCLUSION

Key loci and genes may determine the migration behavior of FAW by regulating the circadian rhythm and other signaling pathways. These findings provide a new perspective for elucidating the internal driving mechanism of migratory insects, and provide a new possibility for developing eco-friendly control strategies for migratory pests. © 2025 Society of Chemical Industry.

Whole exome sequencing revealed new variants and haplotypes associated with monogenic obesity

OBJECTIVES

This study aims to identify new variants and haplotypes associated with monogenic obesity by analyzing known obesity genes in whole exome sequencing (WES) data.

METHODS

The monogenic obesity-associated genes were identified by using the National Institutes of Health (NIH) Genetic Testing Registry (GTR) monogenic obesity panels. WES was performed on (n = 49) extremely obese (children under 5 with weight-for-height greater than 3 standard deviations (SD) above the World Health Organization (WHO) Child Growth Standards median) and (n = 50) control nonobese (25 > body mass index (BMI) < 30) subjects without a history of childhood obesity, and also Iranome WES data of healthy subjects (n = 800).

RESULTS

Seventy-four genes were included in WES analyses. After Bonferroni correction, the T allele of rs2275155 on SDCCAG8 was significantly associated with the increased risk of obesity for allelic and co-dominant models (p˂0.05). Also, a significant association was observed for the T allele of rs116167439 on CEP19 and the T allele of rs201676524 a rare variant on ADCY3; for allelic, dominant, overdominant, and co-dominant models (p˂0.05). In the haplotype association study, TC (on CEP19), CATA (on SDCCAG8), CAA, CTA, CAAA, and TTGA (on ADCY3) haplotypes showed significant associations with monogenic obesity (p < 0.05).

CONCLUSIONS

This study suggested that the T allele of two common variants rs2275155 and rs116167439, also rare variant rs201676524 are associated with an increased risk of monogenic obesity. The significant haplotype associations indicate these variants may be in linkage with causative rare variants and should be considered in future studies.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40200-024-01507-2.

Genome-Wide Association Study on Muscle Stiffness Identified Novel Locus for Predisposition to Muscle Strain Injury

PURPOSE

We aimed to screen the entire genome for genetic variants associated with passive muscle stiffness, which has been suggested as a risk factor for muscle strain injury.

METHODS

This genome-wide association study (GWAS) on passive muscle stiffness included 350 physically active young Japanese individuals. Three hamstring constituents were measured using ultrasound shear wave elastography. Skeletal muscle transcriptomes were compared across the genotypes of GWAS-identified variants in 48 healthy Japanese individuals. Association between GWAS-identified variants and history of muscle strain injury was examined in 1428 Japanese athletes.

RESULTS

Two loci on chromosome 11 demonstrated a genome-wide significant association with passive muscle stiffness of the biceps femoris long head (rs12807854 T/C: P = 5.19 × 10 -10 , rs78405694 T/C: P = 2.09 × 10 -8 ; linear regression analysis adjusted for sex, age, and stretching exercise habits). Skeletal muscle RNA sequencing revealed significantly elevated expression of extracellular matrix-related genes in muscles carrying stiffness-increasing alleles of these variants. Among athletes, rs12807854 T/C was significantly associated with a history of muscle strain injury ( P = 0.0254; logistic regression analysis adjusted for age, sex, competitive level, and main sport). Carriers of the C allele, associated with increased muscle stiffness, exhibited a heightened risk of muscle strain injury (odds ratio = 1.62; 95% confidence interval = 1.06-2.47 per C allele increase). By contrast, rs78405694 did not show a significant association with muscle strain injury in this population.

CONCLUSIONS

A novel locus associated with passive muscle stiffness and muscle strain injury was identified. Elucidating the detailed mechanisms linking the identified locus to passive muscle stiffness may lead to the development of new strategies to prevent muscle strain injuries.

Preliminary insight into the potential role of Leptin Receptor Polymorphisms in Type 2 Diabetes Risk: case-control study and bioinformatics analysis

Background

Type 2 diabetes mellitus (T2DM) develops primarily from obesity as leptin (LEP) functions as an essential adipokine that controls metabolic regulation, energy balance activities, and glucose maintenance. The T2DM and obesity susceptibility traits are believed to be affected by genetic variations in the leptin receptor gene (LEPR), disrupting LEP signaling mechanisms. This case-control study investigates the association of these variants with T2DM risk in a Southeastern Iranian population.

Methods

A case-control study was conducted involving 450 T2DM patients and 450 matched healthy controls from Zahedan. Genomic DNA for this study was isolated from peripheral blood samples, and genotyping for the specified LEPR rs1137100, rs1137101, and rs1805094 polymorphisms was conducted using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Computational analysis created a gene-gene interaction network, highlighting LEPR as a central hub gene and detailing its interactions with related genes.

Results

Genetic models, such as codominant heterozygous (p-value = 0.009), dominant (p-value = 0.006), recessive (p-value = 0.008), and allelic (p-value = 0.011), all showed that the rs1137100 (A/G) polymorphism lowered the risk of T2DM. Several genetic models linked polymorphisms at the rs1137101 (G/A) and rs1805094 (G/C) loci to a higher risk of T2DM: The genetic models that were looked at were polymorphism rs1137101 (G/A) in codominant Homozygous (p-value = 0.031) and recessive (p-value = 0.028), as well as polymorphism rs1805094 (G/C) in codominant heterozygous (p-value = 0.009), dominant (p-value = 0.001), excess (p-value = 0.008), and allelic (p-value = 0.001). The research demonstrated a profound linkage disequilibrium (LD) among studied variants, especially in the LEPR haplotypes and across various blocks, with differing levels of association strength. The gene-gene interaction network for the LEPR gene highlights its strong associations with several key regulatory genes: LEP, PTPN11, STAT3, POMC, JAK2, IL6, and SOCS3.

Conclusion

We found a significant correlation between LEPR gene polymorphisms and the risk of T2DM, highlighting the prominent role of genetic factors in developing such a metabolic disorder. By elucidating the association between LEPR variations and susceptibility to T2DM, our findings enhance the understanding of molecular mechanisms involved in endocrine dysregulation and highlight the importance of including genetic profiling in clinical practice.

TLR8 and TLR9 gene polymorphisms and the risk of high-grade serous ovarian cancer

High-grade serous ovarian carcinoma (HGSOC) is the most prevalent and lethal histotype of epithelial ovarian cancer (EOC). Single nucleotide polymorphisms (SNPs) in Toll-like receptor (TLR) genes may serve as important markers of susceptibility to numerous cancers. We explored the frequency of TLR8 and TLR9 polymorphisms in 325 women and determined their role in susceptibility to EOC and viral infection. The group of patients with EOC included 93 HGSOC and 32 non-HGSOC cases. TLR8 rs3764879, TLR8 rs3764880, TLR9 rs352139, and rs352140 SNPs were genotyped using the allelic discrimination method. The homozygous recessive genotypes for TLR8 rs3764879 and TLR9 rs352139 SNPs were more common in patients with EOC, compared to healthy women, and increased the risk of ovarian cancer (p = 0.0001 and p < 0.05, respectively). The TLR8 rs3764879 SNP reached statistical significance after Bonferroni's correction for multiple tests. The homozygous recessive genotype for TLR8 rs3764879 (-129C>G) was associated with a five-fold increased risk of HGSOC (p = 0.0001). A mutation in at least one allele of the TLR8 rs3764879 was also associated with a higher level of TLR8 expression in tumor tissues (p = 0.0008). The present study demonstrated a strong association between the TLR8 -129C>G SNP and an increased risk of the HGSOC subtype.

Identifying the potential mediators of pathological complete response to neoadjuvant chemotherapy among TACR1 gene polymorphisms: a study on breast cancer patients

PURPOSE

Recent studies have shown that the truncated isoform of the neurokinin-1 receptor (NK-1R) and its ligand, substance P (SP), are overexpressed in tumor cells playing a crucial role in chemoresistance, leading to proliferation, angiogenesis, and metastasis. Hence, this study aims to assess if the polymorphisms of the NK-1R-encoding gene influence the truncated NK-1R level, chemoresistance, and pathological complete response (pCR) achievement in breast cancer patients.

METHODS

The real-time PCR-HRMA was performed to genotype TACR1 eighteen tag SNPs in 153 neoadjuvant chemotherapy-receiving breast cancer patients. Univariate analysis was performed to assess the association of baseline and tumor characteristics with pCR achievement. The association of each variant and pCR achievement was assessed by executing logistic regression while adjusting for covariates and correcting for multiple tests using permutation.

RESULTS

The probability of pCR to neoadjuvant chemotherapy is higher for patients with tumor grade-III as well as stage-I. Assuming the additive, dominant, or recessive models, rs17010664, rs6715729, and rs3771869 were significantly associated with pCR achievement.

CONCLUSION

Positioned close to the truncation-occurring region, belonging to an exon-splicing enhancer motif, the rs17010664 C allele seems to play a crucial role in enhancing the TACR1 last exon splicing leading to increased truncated NK-1R production, chemoresistance, and decreased pCR achievement. Accordingly, The SP/truncated NK-1R axis blockade by NK-1R antagonists seems to be a therapeutic approach to overcoming chemoresistance and achieving pCR in the rs17010664 risk-allele-bearing patients. Hence, conducting further studies to determine the required dose of NK-1R antagonists, repurposed as an antitumor agent, is favored.

Genome-wide association study reveals significant loci and candidate genes for fruit branch length in upland cotton

The length of fruit branches significantly influences plant architecture in upland cotton (Gossypium hirsutum L.), which is crucial for optimizing fiber yield and quality. In this study, a comprehensive genome-wide association study was conducted based on whole-genome resequencing data that identified 249 significant SNPs associated with fruit branch length (FBL), forming 79 distinct quantitative trait loci (QTL) regions. Notably, stable QTL regions qFBL-A10-4 and qFBL-D03-17 were identified, harboring key candidate genes such as Ghir_A10G014390 and Ghir_D03G011390. Superior haplotypes of these genes significantly enhance FBL, fiber yield, and quality, offering valuable targets for cotton breeding programs focused on optimizing plant architecture and productivity.

Coinheritance of polymorphic alleles of PIEZO1, G6PD and HBB enhances protection against malaria

Malaria has exerted potent selective pressure on the human genome over millennia and has been a significant force in shaping human evolution. We have determined in 424 individuals living in malaria-hyperendemic areas in Ghana and in the Democratic Republic of Congo, the genotypes at the loci PIEZO1, G6PD, HBB, and PKLR. By qPCR we have also estimated P. falciparum parasitemia in all these subjects. We found that 41% of individuals tested had one protective variant, 20.5% two variants, 6.4% three variants, and 0.7% four variants. We have confirmed that Pz_E756del, G6pd A-, and HbS are associated with lower parasite density. The highest allele frequency was that of Pz_E756del, approaching 0.2, and we found that it is in linkage disequilibrium with Pz_E750Q. While overall malaria prevalence did not differ significantly among the groups, non-pregnant individuals with multiple protective alleles had lower rates of high-density parasitaemia, suggesting an additive effect of these variants against severe malaria infection, while pregnancy showed different allele protection profile. The high frequency of individuals carrying two or more protective polymorphisms might have implications for malaria transmission and parasite reservoir maintenance. Thus, the significance of additive or possibly synergistic effects of multiple protective genes co-existing in the same person deserves further investigation.

An Exploratory Pharmacogenetic Pilot Study of Two Reverse Transcriptase Inhibitors, Tenofovir Alafenamide Fumarate and Tenofovir Disoproxil Fumarate

BACKGROUND AND OBJECTIVES

The nucleoside reverse transcriptase inhibitors tenofovir alafenamide fumarate and tenofovir disoproxil fumarate are frequently employed in treating human immunodeficiency virus. Further, each form of tenofovir requires laboratory monitoring to determine efficacy and tolerability among patients. This study sought to investigate the relationship, if any, of single nucleotide polymorphisms (SNPs) and selected clinical parameters.

METHODS

The study population, predominantly Caucasian males with a median age of 53.0 years [interquartile range 46.0-59.0], was assayed for genetic variations using an iPLEX ADME PGx Pro v1.0 Panel.

RESULTS

Although several SNP relationships were found with both forms of tenofovir, many of the reported SNPs were displayed only in the comprehensive regimen grouping, making it difficult to distinguish between the two prodrug forms.

CONCLUSIONS

Being an exploratory study, the findings of this substudy serve as potential avenues for further research.

The MNS blood group system in Tunisian blood donors: common and rare alleles

BACKGROUND

The MNS blood group system is highly complex and characterized by the presence of major polymorphic antigens, namely MNS1/MNS2 and MNS3/MNS4. This study aims to examine the genetic basis of the common MNS antigens in Tunisian blood donors and discussed their importance in transfusion immunology.

METHODS AND RESULTS

A group of 229 Tunisian blood donors were genotyped for the major alleles GYPA*01, GYPA*02, GYPB*03 and GYPB*04 using the SSP-PCR method. A specific GYPA region was sequenced in some subjects to examine if there is a rare allele. The statistical analysis was done using the HaploView Software. The molecular analysis showed that 4 blood donors are probably carrier of a rare GYPA allele. Furthermore, it appeared that the GYPA*01 and GYPB*04 alleles; and the GYPA*01-GYPB*04 haplotype are predominant in this series. As for the phenotype, the study showed that the MNS:1,2,-3,4 type is the most frequent in recruited blood donors.

CONCLUSIONS

Overall, the study showed a balanced distribution of the targeted alleles. Furthermore, the observed frequencies appeared to be in harmony with that reported in other populations. Considering the importance of these findings, we think that this work will be an important contribution to the field of public health and epidemiology.

CD28 and CTLA4 polymorphisms associated with ankylosing spondylitis: a study in the context of HLA-B27

BACKGROUND

The human leukocyte antigen (HLA)-B27 gene is highly associated with ankylosing spondylitis (AS). However, not everyone who carries the HLA-B27 antigen develops AS, indicating that factors beyond the HLA-B27 gene contribute to the disease's onset. AS is an autoimmune disease in which co-stimulatory systems have been widely explored. Therefore, we aimed to analyze the association between single-nucleotide polymorphisms (SNPs) in co-stimulatory/inhibitory molecules and AS to identify other key factors involved in developing the disease.

RESULTS

This study recruited 32 patients with AS and 32 controls. DNA was extracted from whole blood, and PCR amplification was performed to target the promoter regions of the CTLA4, CD28, and PDCD1 genes. Chi-square and Fisher's exact tests were used under various genetic models to assess differences in genotype and allele distribution between cases and controls. The results showed that rs201801072 of the CD28 gene (TT + CT vs. CC, p = 0.001) and rs11571319 of the CTLA4 gene were associated with AS (GG vs. AG + AA, p = 0.001). Logistic regression analysis showed that rs201801072 (CD28) and rs11571319 (CTLA4) were independently associated with AS. A significant positive interaction was observed between these SNPs and HLA-B27 positivity, further increasing the risk of AS (T-allele: OR = 6.15; G-allele: OR = 13.30, both p < 0.001). HLA-B27 carriers exhibited an extremely high risk of AS (OR = 65.0, p = 1.19E-06).

CONCLUSIONS

The elevated frequencies of specific alleles in AS patients compared to controls highlight the potential involvement of these SNPs as key factors in the pathogenesis of AS, offering new insights into the genetic mechanisms underlying the disease.

Genetic dissection of hundred-kernel weight through combined genome-wide association study and linkage analysis in tropical maize

BACKGROUND

Hundred-kernel weight (HKW) is a crucial determinant of maize yield. Understanding the genetic mechanisms underlying HKW is vital for maize breeding programs aimed at enhancing productivity. This study aimed to explore the genetic basis of HKW in maize using a multi-parent population (MPP), developed by crossing the common male parent Ye107 with five female parents representing a range of kernel sizes and weights. The MPP was evaluated under two distinct environmental conditions (19DH and 19BS).

RESULTS

Genotyping-by-sequencing (GBS) identified 591,483 high-quality single nucleotide polymorphisms (SNPs), which were used for a genome-wide association study (GWAS) and linkage analysis. The GWAS revealed 21 SNPs significantly associated with HKW, with Zm00001d028188, a gene involved in cell wall synthesis, emerging as a key candidate located on chromosome 1. This gene, encodes Galacturonosyltransferase 1 (GAUT1) and overlapped with two identified quantitative trait loci (QTLs): qHKW1-2 and qHKW1-3, which were further validated through linkage analysis.

CONCLUSIONS

This study identified critical genetic loci and candidate genes, such as Zm00001d028188, involved in regulating HKW in maize. The findings provide valuable genomic resources for maize breeding, potentially contributing to the development of high-yielding maize varieties through an enhanced understanding of the genetic control of HKW.

Association of APOC1 with cortical atrophy during conversion to Alzheimer's disease

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder, with its progression influenced by aberrant gene expression and alterations in the brain network topology. Although APOE has been extensively studied in relation to AD, the role of APOC1 remains relatively underexplored. This study investigated the impact of APOC1 on changes in cortical thickness (CTh) during conversion to AD in a longitudinal setting. Using a normative modeling approach, we examined changes in CTh in patients with mild cognitive impairment (MCI). The spatial patterns of CTh changes were then correlated with APOC1 mRNA expression levels. We estimated the time to conversion to AD and compared progression rates between the low and high APOC1 expression groups. Finally, mediation analysis was performed to assess the indirect effects of APOC1 expression on memory function via CTh changes. In patients with MCI and AD, reduced CTh was observed in the limbic and default mode regions, with a notable impact on the entorhinal cortex, parahippocampus, and fusiform gyrus when comparing baseline and follow-up measurements. The degree of change in CTh was significantly associated with APOC1 expression, with the paralimbic regions identified as particularly vulnerable. Furthermore, the high APOC1 expression group demonstrated more rapid conversion to AD than that observed in the low expression group. Mediation analysis indicated a trend suggesting that APOC1 expression indirectly affected memory and cognitive function through its influence on CTh. These results highlight the potential of APOC1 as an additional focus of AD research, offering insights into the genetic influences on AD pathology.

Divergent adaptation to highland and tropical environments in Bolivian Creole cattle

Bolivian Creole cattle populations evolved under low levels of breeding management and, during more than 500 years of natural selection, became adapted to various environments such as the contrasting highland and subtropical environments. Recently, highland Creole cattle were crossbred with Holstein to improve dairy production. The aim of this research was to evaluate the divergent adaptation through selection footprints of Bolivian Creole cattle from Andean highland and tropical lowlands, and to evaluate the effect of Holstein introgression in highland Creole. For this purpose, 130 Creole cattle (75 highland, 55 lowland) and 88 Holstein were genotyped using a microarray. The database was used to determine population structure and admixture and detect selection sweeps using FST, Rsb, XP-EHH, and ROH. Ancestry inference suggested that selection peaks were not due to Holstein introgression. The NCBI database was used to retrieve genes from the common regions and then perform gene ontology analysis. The most prominent selection peaks were on BTA20 and BTA23 and included the PRLR (slick phenotype) and Class I and IIa BoLA genes. Other windows contained candidate genes for hypoxia (ANXA2, NDUFA4L2), angiogenesis and haematological parameters (ANXA2, CPLANE1, NRP1, NRP2), immune response (IL7R, IL6ST, IL31RA, C6, C7, STAT6, NKG2A, IRAK4, KLR, CLEC), oxidative stress (GSTA, HSD17B6) and morphological traits (PLAG1, CHCHD7, CAP2, ARL15). GO analysis revealed enrichment terms and pathways related to immune response, glutathione and retinol metabolism and reported QTLs for coat characteristics, immune response and tick resistance. The results suggest the complex mechanism in the adaptation of Bolivian Creole cattle to the contrasting highland and subtropical environments.

Integration of GWAS and transcriptome and haplotype analyses to identify QTNs and candidate genes controlling oil content in soybean seeds

The oil content (OC) of soybean is a critical trait with important applications in the development of both food and industrial products. Consequently, enhancing OC has consistently remained a significant objective in soybean breeding programs. In this research, a four-way recombinant inbred line (FW-RIL) population containing 144 lines developed from the cross (Kenfeng14 × Kenfeng15) × (Kenfeng19 × Heinong48) was planted in ten environments to investigate the phenotypic data for OC in seeds. On the basis of the genotype data for 109,676 nonredundant single-nucleotide polymorphism (SNP) markers obtained in previous studies, important quantitative trait nucleotides (QTNs) controlling OC in soybean were identified via five multilocus genome-wide association study (GWAS) methods. A total of 54 significant QTNs were detected by the five methods, including 21 QTNs identified by multiple methods and 2 QTNs detected in two environments. By combining pathway analysis, transcriptome sequencing and gene annotation information, two candidate genes, Glyma.18G027100 and Glyma.03G021800, which are likely related to oil synthesis and metabolism in soybean seeds, were identified, and they were then verified via haplotype analysis. Additionally, 12 of the 23 important QTNs were found for the first time in this study. These results not only contribute to the understanding of the genetic control of OC in soybean seeds but are also helpful in marker-assisted selection (MAS) for breeding high-oil varieties of soybean.

Genome diversity and signatures of natural selection in mainland Southeast Asia

Mainland Southeast Asia (MSEA) has rich ethnic and cultural diversity with a population of nearly 300 million1,2. However, people from MSEA are underrepresented in the current human genomic databases. Here we present the SEA3K genome dataset (phase I), generated by deep short-read whole-genome sequencing of 3,023 individuals from 30 MSEA populations, and long-read whole-genome sequencing of 37 representative individuals. We identified 79.59 million small variants and 96,384 structural variants, among which 22.83 million small variants and 24,622 structural variants are unique to this dataset. We observed a high genetic heterogeneity across MSEA populations, reflected by the varied combinations of genetic components. We identified 44 genomic regions with strong signatures of Darwinian positive selection, covering 89 genes involved in varied physiological systems such as physical traits and immune response. Furthermore, we observed varied patterns of archaic Denisovan introgression in MSEA populations, supporting the proposal of at least two distinct instances of Denisovan admixture into modern humans in Asia3. We also detected genomic regions that suggest adaptive archaic introgressions in MSEA populations. The large number of novel genomic variants in MSEA populations highlight the necessity of studying regional populations that can help answer key questions related to prehistory, genetic adaptation and complex diseases.

CYP1A2 genotype-dependent effects of smoking on mirtazapine serum concentrations

INTRODUCTION

Psychopharmacotherapy with mirtazapine is commonplace. Lower serum concentrations of mirtazapine were reported in smokers due to CYP1A2 induction. However, no previous study that investigated CYP1A2 genetics and mirtazapine treatment considered CYP1A2-inducing parameters.

AIM

We aimed to investigate the association of CYP1A2 variants, mirtazapine serum concentration, and treatment outcome, considering the smoking status of the patients.

METHODS

Two depression cohorts were investigated for the association between serum concentration and treatment response of mirtazapine and CYP1A2-163C>A (rs762551) and -3860G>A (rs2069514) genotype groups, also considering smoking status, sex, and age of the patients. In total, 124 patients (82 non-smokers and 42 smokers) were eligible for the analyses.

RESULTS

Dose-corrected serum concentration (CD) of mirtazapine was associated with smoking status, sex, and age, with lower CD in smokers, females, and older patients. Considering non-smokers and genotype-grouped smokers, CD of mirtazapine in CYP1A2 normal metabolizer smokers (N = 6) did not differ from CD of non-smokers. By contrast, smokers carrying the CYP1A2*1A/*1F and *1F/*1F genotype groups showed 34.4% and 33.4% lower mirtazapine CD compared to non-smokers.

DISCUSSION

As yet, for clinical practice, it may be more relevant to focus on smoking status than on the CYP1A2 gene variants. Considering the relevant impact of smoking on the mirtazapine CD, physicians should monitor an increase in side effects due to the expected increase in mirtazapine serum concentrations. In these cases, measurement of mirtazapine CD and/or subsequent dosage reduction is recommended. The clinical relevance of CYP1A2 genotyping prior to treatment with drugs metabolized by CYP1A2 needs further investigation.

Genetic parameters and haplotype-based genome-wide association study of indicator traits for gastrointestinal parasite resistance in Santa Ines sheep

Genetic parameters are of great importance in animal breeding since they determine the strategies necessary to increase the genetic progress in economic traits, for example indicator traits for resistance to endoparasites in sheep. Furthermore, genetic markers have been used to identify genomic regions associated with economically important traits, which can help increase the genetic response through genomic selection. Therefore, this study aimed to estimate genetic parameters and perform a haplotype-based genome wide association study (GWAS) to identify genomic regions associated with indicator traits for endoparasite resistance in Santa Ines sheep. Haplotype GWAS was performed using linkage disequilibrium blocks (haploblocks) defined by the Haploview software. Records from 1725 animals for Famacha© (FAM, N = 5560), packed cell volume (PCV, N = 5135), total plasma protein (TPP, N = 4356), and fecal egg count (FEC, N = 4248) were used for analysis. The pedigree file contained information from 4821 animals; of these, 638 animals were genotyped using the Ovine SNP50 Genotyping BeadChip. Heritability estimates were moderate for FAM (0.26), PCV (0.26), TPP (0.16), and log-transformed FEC (0.19). Genomic regions that explained more than 0.3 % of the total additive genetic variance of the traits were defined as significant. These regions overlapped with quantitative traits loci associated with eosinophil number, fecal egg count, hematocrit, and immunoglobulin levels. In the top regions for the traits evaluated we found genes individually involved in inflammatory response, immunity, macrophage function in host-pathogen interactions, and other biological functions. All indicator traits for resistance to gastrointestinal parasites evaluated in this study exhibited sufficient genetic variability to respond to selection and can be used to improve the health and consequently the production of Santa Ines sheep.

Genetic variability in ADAM17/TACE is associated with sporadic Alzheimer's disease risk, neuropsychiatric symptoms and cognitive performance on the Rey Auditory Verbal Learning and Clock Drawing Tests

Recent studies have highlighted the significant role of ADAM17/TACE (encoded by ADAM17/TACE) in the pathogenesis of Alzheimer's disease (AD). Yet, the relationship between ADAM17/TACE gene polymorphisms and AD was less studied. This study aims to analyse the relationship of ADAM17/TACE gene polymorphism with the risk, age of onset, neuropsychiatric manifestations, cognitive impairment, and medial temporal lobe atrophy in sporadic AD (sAD). This case-control association study was conducted in an Italian cohort consisting of 297 sAD patients and 316 controls. Seven tag-SNPs were selected and genotyped. Linear and logistic regression analyses were used to assess the association between parameters of interest and the genetic variability of ADAM17/TACE. After Bonferroni correction, our findings underscore the complexity of genetic influences of ADAM17/TACE on sAD, particularly the roles of rs12692385 in modulating sAD risk and the performance on the Rey Auditory Verbal Learning Test - delayed recall. In addition, rs13008101 significantly affected the performance on the Clock Drawing Test. Moreover, rs10179642 and rs35280016 were associated with a higher frequency and severity of hallucinations and agitation/aggression, respectively. These results contribute to a deeper understanding of the genetic underpinnings of sAD and may be useful for examining the risk of developing sAD, assessing cognitive deficits, neuropsychiatric symptoms, and informing new therapeutic strategies and future research targeting ADAM17/TACE.

Genomic evidence for behavioral adaptation of herding dogs

Herding dogs exhibit a distinct constellation of behaviors marked by inherent instinct and motor skills that manipulate and guide livestock in response to instructive commands and cues. Comparison of the whole-genome sequences of herding and nonherding breeds reveals signatures of positive selection associated with pathways underlying social interaction and cognitive functions. Of the strong selective sweep signals, haplotypes within ephrin type-B receptor 1 (EPHB1), which is linked to locomotor hyperactivity and spatial memory, show evidence of segregation within breed lineages for the conformation versus working lines of border collies and introgression with a genetically and geographically distant herding breed of Entlebucher mountain dogs. We show that a working line-specific haplotype of EPHB1 is associated with elevated levels of chase-bite motor patterns based on a well-validated behavior survey. These findings indicate that functional selection has shaped the genetic architecture of herding breeds, which may relate to their proficiency in addressing diverse tasks and challenges in maintaining control over the herd.

Genetic variants in the IFNGR2 locus associated with severe chronic Q fever

Q fever is a highly contagious zoonosis capable of causing large outbreaks of important health and economic consequences. Host genetic factors are believed to influence the development of severe chronic Q fever following the infection by the etiological agent, Coxiella burnetii. Targetted next generation sequencing (NGS) was performed in a case-control genetic association study on 53 confirmed Q fever cases, including 38 compatible with acute and 15 with chronic disease, and 29 samples from the general Portuguese population. Four SNPs in the IFNGR2 locus, rs78407108 G > A, rs17879956 C > T, rs7277167 C > T, and rs9974603 C > A, showed a statistically significant association to chronic Q fever, resisting the Bonferroni correction. These belonged to haplotypes significantly associated with chronic Q fever. The individual SNPs are referenced in the GTEx database as possible eQTLs. Given the direct bearing of IFNGR2 on IFN-γ signaling, the possible involvement of the associated variants with higher IFNGR2 expression could be in line with observations suggesting that IFN-γ production in chronic Q fever patients is significantly higher than in healthy controls. Further investigations are required to clarify the role of IFNGR2 signaling in association with chronic Q fever.

Influence of WWOX/MAF genes on cognitive performance in patients with Parkinson's disease

BACKGROUND

Beyond its hallmark motor symptoms, Parkinson's disease (PD) encompasses a range of non-motor disturbances, particularly cognitive impairment, which significantly affects patients' quality of life. Cognitive impairment is a shared manifest in both PD and Alzheimer's disease (AD), two prevalent neurodegenerative disorders. Existing literature has identified the WWOX/MAF genes as potential risk factors for AD, but their role in cognitive functions among PD remains unclear.

OBJECTIVES

This study examines the influence of AD-associated risk genes, specifically WWOX/MAF, on cognitive function in PD, aiming to bridge the neuropathological gap between AD and PD.

PARTICIPANTS

A total of 402 participants were included in this study, comprising 150 individuals with PD and 252 healthy controls (HC).

MEASUREMENTS

Participants underwent comprehensive neuropsychological assessment and genotyping. A moderation regression model was employed to assess the impact of WWOX/MAF single nucleotide polymorphisms on cognitive function and the potential modulatory effect of PD.

RESULTS

The WWOX gene was found to influence verbal fluency performance across the entire cohort. Additionally, PD significantly moderated the effect of genetic variants on attention (p = 0.000040), non-verbal memory (p = 0.000007), and visuospatial function (p = 0.000303), suggesting a distinct impact within this group. Further analysis indicated that cognitive status moderated the effect of genetic variants on verbal memory across the entire cohort (p < 0.001). Among individuals with PD, genetic variants also influenced verbal fluency (p = 0.000113) and verbal memory (p = 0.000440 and p = 0.000032).

CONCLUSIONS

These findings underscore the critical role of WWOX/MAF genes in cognitive impairments associated with PD, enhancing our understanding of their connection to AD and providing deeper insights into neurodegenerative disease progression.

Whole plant transpiration responses of common bean (Phaseolus vulgaris L.) to drying soil: Water channels and transcription factors

Common bean (Phaseolus vulgaris L.) is the main legume crop for direct human consumption worldwide. Among abiotic factors affecting common bean, drought is the most limiting. This study aimed at characterizing genetic variability and architecture of transpiration, stomatal regulation and whole plant water use within the Mesoamerican germplasm. A critical fraction of transpirable soil water (FTSWc) was estimated as the inflection point at which NTR starts decreasing linearly. Genome-wide association (GWA) analyses for mean NTR and FTSWc were performed. High variation on mean NTR and FTSWc was found among genotypes. Unreported genomic signals controlling the variation of these traits were identified on Pv01 and Pv07 some located in intergenic, intronic and exonic regions. A set of novel candidate genes and putative regulatory elements located in these QTL were identified. Some of the genes have been previously reported to be involved in abiotic tolerance in model species, including some of the five transcription factors (TF) identified. Four candidate genes, one with potential water transportation activity and three TFs were validated. The gene Phvul.001G108800, an aquaporin SIP2-1 related gene, showed water channel activity through oocyte water assays. Mutant Arabidopsis thaliana (Ath) lines for the homologous genes of common bean were evaluated in transpiration experiments. Two of the three evaluated TFs, UPBEAT1 and C2H2-type ZN finger protein, were involved in the control of transpiration responses to drying soil. Our results provide evidence of novel genes to accelerate the drought tolerance improvement in the crop and study the physiological basis of drought response in plants.

A case-control association study of APOE promoter region variants with glaucoma in North Indian population

PURPOSE

Genetic variants in apolipoprotein E (APOE) are reported as risk factors for glaucoma in different ethnic populations, however, there is a scarcity of data from North India. Therefore, the present study aimed to investigate the association of APOE promoter region variants c.-219T > G, c.-427T > C, and c.-491A > T with glaucoma in the North Indian population.

METHODS

286 primary glaucoma patients and 300 healthy controls were included in the present study. Promoter region variants (c.-219T > G, c.-427T > C, c.-491A > T) of APOE were genotyped by Sanger sequencing followed by statistical analyses.

RESULTS

Present case-control association analysis indicated that the GG genotype of the c.-219T > G variant is more common in glaucoma patients (18.53 %) than in controls (11.33 %) and conferred a 1.9-fold increased risk of glaucoma (OR = 1.92, 95 % CI 1.16-3.16, p = 0.010). This risk is particularly higher in females, showing a 2.7-fold increase (OR = 2.66, 95 % CI 1.10-6.41, p = 0.028). In the recessive model, the GG genotype also exhibited a 1.8-fold increased risk of glaucoma development (OR = 1.78, 95 % CI 1.12-2.83, p = 0.014). During sub-group analysis, GG genotype was more prevalent in POAG group compared to controls, with a 2.3-fold increased risk (OR = 2.27, 95 % CI 1.32-3.89, p = 0.002). However, no significant differences in genotype distribution were found between PACG and PCG vs. controls. Additionally, the genotype and allele frequency distributions for the c.-427T > C and c.-491A > T variants were not statistically significant between cases and controls.

CONCLUSION

Our study shows the association of the c.-219T > G variant in the development of glaucoma in the analyzed Indian population. The present study analyzed the genotype-phenotype correlation between APOE promoter region variants and glaucoma characteristics in the Indian population.

Genetic polymorphisms in HMGCS1 gene and its association with slaughter characteristics, meat quality, and organ coefficients in Guizhou white goats

OBJECTIVE

This study aimed to identify polymorphisms in the gene encoding the 3-hydroxy-3-methylglutaryl-CoA synthase 1, HMGCS1, and analyze their association with slaughter characteristics, meat quality, and organ coefficients in Guizhou white goats.

METHODS

A total of 153 twelve-month-old Guizhou white goats (78 male and 75 female) were included in the study. Slaughter characteristics, meat quality, and organ coefficients were assessed. Association analyses between genotypes and phenotypic traits were conducted using a generalized linear model.

RESULTS

Four polymorphic loci were identified, i.e., g.15523T>C, g.15530G>C, g.18413T>C, g.19711G>A in exons 5, 8, and 9 of the HMGCS1 gene. Across all polymorphic loci, males of the same genotype generally exhibited significantly better slaughter traits compared to females of the same genotype (p<0.05). At the g.18413T>C locus, differences in shear force were observed between males and females of the same genotype and within the same sex across different genotypes (p<0.05). Organ coefficients were significantly higher in males of the same genotype compared to females (p<0.05). The g.15523T>C and g.15530G>C loci were found in strong linkage disequilibrium and significantly associated with intramuscular fat content (p<0.05). Fat content in diploid Hap2/2 individuals was significantly higher than in Hap1/1 and Hap1/2 (p<0.05). At the g.19711G>A locus, female goats with the CC genotype showed significantly higher levels of dry matter compared to male goats of the same genotype and female goats of other genotypes within the group. Organ coefficients for the liver and hooves in male goats were significantly higher than in females of the same genotype (p<0.05).

CONCLUSION

The strongly linked loci g.15523T>C and g.15530G>C were significantly associated with intramuscular fat content and could be used as molecular markers for enhancing this trait in goat breeding programs, fostering the development of goat production.

An alternative splicing caused by a natural variation in BnaC02.VTE4 gene affects vitamin E and glucosinolate content in rapeseed (Brassica napus L.)

Vitamin E (VE) is essential for plants and animals. Rapeseed oil is rich in α-tocopherol (α-T), which is the most bioactive form of VE in human body. This study demonstrated that VE in rapeseed seeds was mainly controlled by embryo genotype through incomplete diallel hybridization. By genome-wide association study, the QTL-qVE.C02 associated with VE and α-T contents was detected in a Brassica napus association population, and the phenotypic contribution rate was up to 18.71%. BnaC02.VTE4, encoding gama-tocopherol methyltransferase, was proved as the target gene of qVE.C02 by genetic complementation. Two BnaC02.VTE4 haplotypes were identified in the population. Compared with BnaC02.VTE4HapH, a point mutation from A to G at the 3' splicing site of the second intron were found in BnaC02.VTE4HapL, resulting in alternative splicing and early termination of translation. HapL1052(G-A), the site-directed mutagenesis fragment of BnaC02.VTE4HapL, was introduced into Arabidopsis vte4 mutant and 8S088 (a BnaC02.VTE4HapL accession), and the contents of VE and α-T in atvte4-4 and 8S088 seeds were increased by 90.10% to 307.29%. These demonstrated the point mutation as the causal for the difference in VE biosynthesis in rapeseed. Further, this variation also led to the significant difference in glucosinolate content between BnaC02.VTE4HapH and BnaC02.VTE4HapL accessions. Multi-omics analysis suggested that the expression of some genes and the accumulation of several metabolites related to the glucosinolate biosynthesis pathway were significantly increased in BnaC02.VTE4HapL group. Moreover, by functional marker identification, the BnaC02.VTE4HapH was found to be selected during domestication. Our findings offered promising opportunities for enhancing rapeseed quality traits.

Statistical Analysis of Reproductive Traits in Jinwu Pig and Identification of Genome-Wide Association Loci

BACKGROUND

The Jinwu pig is a novel breed created by crossbreeding Jinhua and Duroc pigs, displaying superior meat quality, strong adaptability to coarse feed, high production performance, and a rapid growth rate. However, research on its reproductive traits and genomic characteristics has not been systematically reported.

METHODS

In this study, we investigated the genetic basis of reproductive traits in Jinwu pigs us-ing a genome-wide association study. We analyzed 2831 breeding records from 516 Jinwu sows to evaluate the effects of fixed factors (farrowing season, parity, and mated boar) on six reproductive traits: the total number of births (TNB), number born alive (NBA), number of healthy offspring produced (NHOP), weak litter size (WLS), number of stillbirths (NS), and number of mummies (NM).

RESULTS

A total of 771 genome-wide significant single-nucleotide polymorphisms (SNPs) and ten potential candidate genes associated with pig reproductive traits were identified: VOPP1, PGAM2, TNS3, LRFN5, ORC1, CC2D1B, ZFYYE9, TUT4, DCN, and FEZF1. TT-genotype-carrier individuals of the pleiotropic SNP rs326174997 exhibited significantly higher TNB, NBA, and NHOP trait-related phenotypic values.

CONCLUSIONS

These findings provide a foundation for the reproductive breeding of Jinwu pigs and offer new insights into molecular genetic breeding in pigs.

Genomic evidence of the blood virome and bacteriome provides insights into prevalence, evolution, and susceptibility-related genes across Eurasian pigs

BACKGROUND

Infectious diseases are among the primary constraints to pig production, and the globalization of the pig industry has contributed to the emergence and spread of pathogens. However, there is a lack of comprehensive genomic surveillance on the Eurasian scale, resulting in the prevalence and evolution of pig pathogenic viruses and bacteria are still unknown.

RESULTS

In this study, we proposed a protocol to identify viral and bacterial sequences and estimate the abundance accurately based on the whole-genome sequencing data of the blood samples. Through whole-genome analysis of 685 Eurasian pigs, we constructed the blood virome and bacteriome landscape. There were a total of 15 pathogenic bacteria, 12 pathogenic viruses, and porcine endogenous retrovirus were identified. We divided 685 Eurasian pigs into three subgroups and discovered significant differences in the viral and bacterial composition, prevalence, and abundance among subgroups. Besides, we performed the quantitative Polymerase Chain Reaction experiment to quantify the copy number of porcine endogenous retrovirus and confirm the reliability of the proposed protocol. Furthermore, we constructed the phylogenetic tree of porcine parvovirus 6 and the results suggested that large-scale transportation across China provides viral connectivity between geographically distinct localities, potentially facilitating the spread of viruses. We also discovered the ADAM28 and ADAMDEC1 genes that may relate to porcine lymphotropic herpesvirus, and the ATF4 gene that may correlate with porcine cytomegalovirus.

CONCLUSIONS

Our study provides new insights into the genomic investigation and epidemiology of viruses and bacteria, in turn helping to prevent viral and bacterial infectious diseases in pigs.

Analysis of the DYNC1H1 Gene Polymorphic Variants' Association with ASD Occurrence and Clinical Phenotype of Affected Children

OBJECTIVES

To analyze potential associations between three polymorphisms (rs3818188, rs941793, rs2403015) of the DYNC1H1 gene and the occurrence of autism spectrum disorder as well as the clinical phenotype of affected individuals.

METHODS

This family-based study included 206 children diagnosed with ASD and 364 of their biological parents. To examine the potential association between three polymorphisms of the DYNC1H1 gene and ASD occurrence, a transmission disequilibrium test was performed. Additionally, associations between the studied polymorphisms and the clinical phenotype of affected individuals were analyzed using the χ2 test.

RESULTS

None of the polymorphisms studied showed an association with ASD in the overall patient group. However, an association between the rs3818188 polymorphic variant and ASD was observed in a subgroup of girls, with the G allele being transmitted more than 2.5 times as frequently as the A allele. Moreover, several associations between the tested variants and features related to neuromotor development, communication, and social skills were observed in univariate analysis. However, after correction for multiple comparisons, only the association between the rs2403015 polymorphism and transient increase in muscle tone during infancy remained statistically significant.

CONCLUSIONS

This study demonstrated an association between the rs3818188 polymorphism and ASD in a subgroup of girls. Additionally, the rs2403015 polymorphism was found to be associated with transient increase in muscle tone during infancy.

Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination

Objective

Coat color is a complex trait and plays an important role in breed identification. However, information regarding genes associated with coat color in cattle is limited, especially at the skin transcriptome level.

Methods

We investigated the differential expressed genes (DEGs) and genomic selection signal underlying the coat color variation between black and brown cattle breeds. A total of 19 cattle (Brangus, Angus, Simmental, and Guanling) were performed skin transcriptome analysis and 262 cattle (Angus and Simmental) were performed whole genome analysis.

Results

Angus cattle (black coat) had a significantly higher melanin content in both their hair and skin compared to that of Simmental and Guanling cattle (brown coat). Transcriptomic analysis identified 14,118 expressed genes, with principal component analysis and hierarchical clustering revealing clear differences between black and brown cattle. DEGs analysis across four pairwise breed comparisons highlighted 343 downregulated and 54 upregulated genes common to all comparisons, with the ASIP gene (agouti signaling protein) emerging as a key gene linked to melanogenesis. The ASIP expression was several dozen-fold higher in brown cattle than in black cattle, suggesting a crucial role in coat color determination. Path-way enrichment and gene set enrichment analysis (GSEA) identified the "Melanogenesis" pathway as significantly enriched and central to coat color variation. Genes such as FZD10, WNT6, and ASIP showed differential expression patterns that correlated with coat color. Genomic analysis revealed strong selection signals in the ASIP gene region, with several SNPs exhibiting high linkage disequilibrium. Notably, the mutation type was predominant in Simmental cattle, while the reference allele was more common in Angus cattle.

Conclusion

Based on the skin transcriptomic and genomic analyses, we found that ASIP was significantly differential expressed between black and brown cattle breeds and under strong positive selection. These findings provide valuable insights into the genetic basis of coat color variation in cattle and highlight the ASIP gene as a critical determinant of this trait.

Genome-wide association analyses identify single-nucleotide polymorphisms associated with in vitro embryo cleavage and blastocyst rates in Holstein bulls

Reproductive success is an essential component of profitable and sustainable dairy operations. Although selection for production traits such as milk yield has led to a decline in fertility in dairy cattle, strategies including assisted reproductive technologies such as in vitro fertilization and embryo transfer, as well as genomic selection for fertility traits, are being implemented to help mitigate this loss. Previous studies have identified genetic markers associated with fertility traits such as daughter pregnancy rate, conception rate, and interval to first conception. However, genetic markers associated with in vitro embryo development have yet to be explored. Therefore, this study aimed to identify genetic markers associated with in vitro embryo cleavage and blastocyst rates with the future goal of creating an index to select bulls with superior abilities to produce embryos in vitro. Rigorous in vitro fertilization trials identified Holstein bulls with divergent abilities to produce embryos that successfully cleave and develop into blastocysts in vitro. A total of 40 bulls with embryo cleavage and blastocyst rate phenotypes were whole genome sequenced. Sequencing was performed on an Illumina platform with PE150 reads followed by cleaning, mapping to ARS-UCD1.2, variant calling with GATK HaplotypeCaller, and quality control following the 1000 Bulls Genomes Project best practices. Genome-wide association analyses identified 819 and 442 SNPs associated with embryo cleavage and blastocyst rates, respectively. Significant regions on chromosomes 15, 18, 21, 22, and 23 were in linkage disequilibrium with QTL previously associated with reproductive traits in cattle. Further, a region on chromosome 28 with the most significant variant associated with cleavage rate contained several synonymous variants in EGLN1, which is a critical component of the hypoxia inducible pathway. An additional region on chromosome 18 associated with cleavage rate contained a missense variant in SMG9, a gene involved in the nonsense-mediated mRNA decay pathway. A region on chromosome 21 associated with blastocyst rate also contained variants in regulatory regions downstream from AEN, a gene required for efficient DNA fragmentation during the p53-dependent apoptosis pathway. In summary, this study identified a preliminary collection of genomic regions associated with embryo cleavage and blastocyst rates in vitro that contain relevant genes and other QTL associated with reproductive traits in cattle. These regions, after validation, could contribute to a selection index for identification of bulls with genetic predispositions to produce a greater number of embryos in vitro for use in assisted reproduction techniques.

Single-Nucleotide Polymorphisms of BRCA1 and BRCA2 and Risk of Papillary Thyroid Carcinoma

Background/Objectives: We sought to evaluate the association between the risk of papillary thyroid carcinoma (PTC) and single-nucleotide polymorphisms (SNPs) of breast cancer genes 1 (BRCA1) and 2 (BRCA2). Methods: We prospectively recruited 515 cases with PTC and 296 controls without cancer. The genotypes of five BRCA1 SNPs (rs8176318, rs1799966, rs799917, rs16940, rs1799949) and three BRCA2 SNPs (rs15869, rs1799943, rs1799955) were determined using the TaqMan assay. We evaluated the association of haplotypes with the risk of PTC due to linkage disequilibrium (LD). Results: The five BRCA1 SNPs were significantly associated with the risk of PTC. The AC genotype of rs8176318 (OR = 0.69, p = 0.02) and the CT and CC genotypes of rs1799966 (OR = 0.70, p = 0.02 and OR = 0.67, p = 0.01, respectively) were associated with a decreased risk of PTC. The AG genotype of rs16940 (OR = 0.67, p = 0.01) and the AG genotypes of rs799917 and rs1799949 (both OR = 0.70, p = 0.02) decreased the risk of PTC. Haplotype 1 [rs8176318(C)-rs1799966(T)-rs799917(G)-rs16940(A)-rs1799949(G)] ± (OR = 0.69, p = 0.02) and haplotype 2 [rs8176318(A)-rs1799966(C)-rs799917(A)-rs16940(G)-rs1799949(A)] ± (OR = 0.71, p = 0.03) of BRCA1 reduced the risk of PTC. Conclusions: Our findings suggest that the polymorphisms of BRCA1 may contribute to the susceptibility to PTC in the Korean population.

Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice

BACKGROUND

Pre-harvest sprouting (PHS), which adversely impacts grain yield and quality, is controlled by seed dormancy genes. However, only a few dormancy-related genes have been characterized, and the effects of allelic variation in genes and the genetic basis of seed dormancy in rice remain largely unknown. Here, we performed a whole-genome meta-quantitative trait loci study to elucidate the genetic basis of seed dormancy in rice.

RESULT

One hundred and sixty-seven QTL were identified for PHS from which 134 were successfully projected onto the reference map yielding 20 consensus regions, meta-QTL (mQTL). The mean confidence interval of the mQTL was narrower (9.56-fold reduction) than that of the initial QTL. Six of the 20 identified mQTL were designated as breeders' mQTL based on their small confidence intervals, large phenotypic variance explained, and the involvement of high number of QTL. Further, we retrieved 559 high-confidence genes from breeders' mQTL regions conferring resistance to PHS. Comparative analysis of genes found in breeders' mQTL loci and an RNA-seq-based transcriptomic dataset discovered 34 common genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed a significant enrichment of the common genes in amino sugar and nucleotide sugar metabolism, carbon metabolism, and carbon fixation in photosynthetic organs. Combined in silico expression profiling and qRT-PCR validation showed that LOC_Os10g18364, LOC_Os10g21940, LOC_Os10g22590, and LOC_Os10g25140 exhibited high fold-change expression in PHS resistant cultivar (23xS-261) than PHS susceptible cultivar (23xS-262). Association analysis of these genes with germination rate index demonstrated that LOC_Os10g18364Hap1, LOC_Os10g21940Hap1, LOC_Os10g22590Hap1, and LOC_Os10g25140Hap1/Hap3 exhibited low germination rate (GR) in cultivars carrying these haplotypes.

CONCLUSION

In summary, this study delineates the genetic basis of PHS and provides a new set of target genes for improving PHS resistance. The natural variants identified in these genes and markers associated with breeders' mQTL serve as potential resources for incorporating PHS resistance in rice.

Improved Litter Size in Thin-Tailed Indonesian Sheep Through Analysis of TGIF1 Gene Polymorphisms

Reproductive traits, particularly the litter size, are crucial for sheep husbandry. Molecular genetic selection methods, including single-nucleotide polymorphism (SNP) analyses, offer potential avenues for enhancing these traits. This study investigated the association between TGIF1 SNPs and litter size in thin-tailed Indonesian sheep. A total of 47 sheep were sampled, and their genomic DNA was analyzed. Bioinformatics, sequencing, and statistical analyses were conducted to identify SNPs, assess genetic parameters, and examine their association with litter size. Nine SNPs, including nonsynonymous variants, were successfully identified through targeted sequencing and Sanger sequencing within exon 3 of TGIF1. Noteworthy polymorphisms at g. 42725867 G>A, g. 42725886 G>A, g. 42725932 A>C, g. 42725950 A>G, g. 42726009 G>A, g.42726036 C>T, g.42726042 A>C, g. 42726051 A>G, and g. 42726059 G>A were revealed. Genetic parameter assessments indicated moderate diversity although no significant association was observed between the TGIF1 SNPs and litter size. This lack of association highlights the potential influence of environmental factors, polygenic effects, or the need for larger sample sizes in future studies. In addition, linkage disequilibrium analysis highlighted strong interconnectivity among six of the nine TGIF1 SNPs, designating them as potential Tag SNPs. Data analysis further demonstrated that the haplotype combination of H3 and Hap 6 within the identified blocks exhibited the highest litter size. This study unveils novel TGIF1 SNPs in thin-tailed Indonesian sheep, prompting the need for additional research to unravel their functional implications and potential impacts on reproductive traits. While no significant associations were found, these findings contribute to the growing body of knowledge on genetic factors influencing litter size and underscore the need for broader investigations, including whole-genome sequencing and validation in larger populations. This investigation provides valuable insights into the genetic factors that influence litter size in this breed and lays the foundation for future genetic improvement strategies.

Impact of age, HIV1, sickle-cell genotypes, and interferon-gamma gene upstream variants on malaria disease outcomes in a longitudinal pediatric cohort

This prospective cohort study explored the association between two upstream IFN-γ variants (rs2069709: G > T and rs2069705: A > G) and hazard factors for malaria outcomes in a longitudinal cohort of children (n = 941, 3-36 mos.), followed for three years. The impact of age, sex, previous malaria exposure, HIV1 infection, and sickle-cell genotypes (HbAA, HbAS, and HbSS) was also investigated. Reduced malaria episodes were associated with older age at enrollment [HR = 0.957 (95% CI = 0.953-0.961) per month, P < 2.2e-16], HIV1 infection [0.687 (0.545-0.866), P = 0.001], being female [0.910 (0.859-0.964), P = 0.040], and HbAS [0.823 (0.754-0.898), P = 0.005]. The GA/TA diplotype [0.376 (0.230-0.614), P = 0.002] also reduced the hazard of malaria, while TA haplotype increased susceptibility [1.749 (1.159-2.640), P = 0.029]. Factors protecting against the development of SMA [Hemoglobin (Hb < 6.0 g/dL)] included older age [0.927 (0.913-0.942) per month, P < 2.2e-16], previous malaria episodes [0.576 (0.542-0.614, P = 9.5e-32)], HbAS [0.553 (0.400-0.766), P = 0.015]. The rs2069705AG genotype increased the hazard of SMA [1.697 (1.002-2.875), P = 0.042]. Reduced hazard of mortality was observed for older children [0.898 (0.857-0.941), P < 2.2e-16], while a higher hazard was present in HIV-infected children [12.475 (6.380-24.392), P < 2.2e-16], and in those with HbSS [6.341 (1.944-20.686), P = 0.007]. The GG haplotype increased the mortality hazard [1.817 (0.936-3.527), P = 0.078]. The results here highlight critical factors influencing the hazard of malaria, SMA, and mortality.

PRED-LD: efficient imputation of GWAS summary statistics

BACKGROUND

Genome-wide association studies have identified connections between genetic variations and diseases, but they only examine a small portion of single nucleotide polymorphisms. To enhance genetic findings, researchers suggest imputing genotypes for unmeasured SNPs to improve coverage and statistical power. When this is not possible, summary statistics imputation can be used as an alternative. The available summary statistics imputation tools rely on reference panels, such as the 1000 Genomes Project, to estimate linkage disequilibrium (LD) between variants for accurate imputation. Tools like FAPI and SSIMP use these reference panels in variant call format (VCF) for this purpose, though this process can be time-consuming. A more effective approach for processing reference panels in summary statistics imputation was proposed in RAISS. In this approach, the LD among the variants is precomputed from the reference panel, prior to imputation, thereby reducing computational time.

RESULTS

We present PRED-LD, an imputation method for GWAS summary statistics that aims to enhance the resolution of genetic association analyses. The proposed method uses precomputed linkage disequilibrium statistics from HapMap, Pheno Scanner and TOP-LD to impute summary statistics, given beta coefficients and standard errors. The single-point approach that we describe provides a fast and accurate way to estimate associations for untyped single nucleotide polymorphisms that exhibit high linkage disequilibrium (LD). The proposed method is faster, provides accurate imputation compared to existing tools, and has been implemented in both a web service ( https://compgen.dib.uth.gr/PRED-LD/ ) and a command-line tool ( https://github.com/pbagos/PRED-LD ), making it a useful resource for the research community.

CONCLUSIONS

PRED-LD offers an efficient and accurate method for GWAS summary statistics imputation, providing faster performance, direct result interpretation, and the ability to use multiple reference panels. Also, the online version of PRED-LD simplifies obtaining LD information and performing imputation tasks without downloading reference panels and will be continuously updated to support tools for meta-analysis and fine-mapping in GWAS.

Molecular study of vitamin D metabolism-related single nucleotide polymorphisms in cardiovascular risk: a case-control study

Cardiovascular diseases (CVDs) constitute a major global health problem, being the leading cause of death. Several risk factors for CVDs have been identified, including tobacco use, unhealthy diet, and physical inactivity. However, the role of genetic factors in CVDs remains unclear. Recent studies suggest that vitamin D deficiency is associated with an increased risk of CVDs. Therefore, the aim of this study is to assess the impact of 13 single nucleotide polymorphisms (SNPs) located in genes involved in vitamin D metabolism (VDR, GC, CYP27B1, CYP2R1, and CYP24A1) on the risk of developing CVDs. A retrospective case-control study was conducted in 766 Caucasian individuals from southern Spain: 383 diagnosed with CVDs and 383 without cardiovascular complications, matched based on age and sex. The 13 SNPs were identified by real-time PCR using TaqMan™ probes at the Virgen de las Nieves University Hospital and the University of Granada. According to statistical analysis the allele G and genotype GG of the SNP CYP2R1 rs10741657 and the allele C and CC genotype of the SNP CYP27B1 rs3782130 are associated with a decreased risk of CVDs and diabetes in three of the five heritage models studied. Thus, it can be concluded that CYP2R1 rs10741657 and CYP27B1 rs3782130 could be used as risk biomarkers for CVDs in the future, although studies with a larger number of participants are needed.

An Expression Quantitative Trait Locus of Fc Gamma Receptor Genes Is Associated With Antimalarial IgG Responses and Infection Levels in Burkinabe Families

BACKGROUND

The interaction between antibodies and Fcγ receptors (FcγRs) plays a critical role in regulating immune responses to Plasmodium falciparum. Polymorphisms in genes encoding FcγRs influence the host's capacity to control parasite infection. This study investigates whether noncoding variants influencing FcγR expression are associated with antimalarial immunization and infection traits.

METHODS

We utilized eQTL databases and functional annotations to identify noncoding variants, specifically rs1771575, rs2099684, and rs6700241, within the FCGR gene cluster. In addition, we examined the coding variants rs1801274 (p.His167Arg) and rs1050501 (p.Ile231Thr), which affect the affinity of FcγRIIa and FcγRIIb for IgG. These variants were genotyped in 163 individuals from Burkinabe families. Family-based linear mixed regression and Quantitative Transmission Disequilibrium Tests (QTDT) analyses were performed to assess associations with IgG levels and malaria infection, accounting for relevant covariates.

RESULTS

Linear mixed models identified rs1771575 as associated with total IgG levels, while both rs1771575 and rs1801274 were linked to IgG2, and rs1050501 to IgG1 levels. A haplotype combining rs2099684 and rs6700241 was positively associated with IgG1. The rs1771575-CC and rs1050501-TT genotypes correlated with higher infection levels in children. QTDT models confirmed the association of rs1771575 with IgG2 and infection in children.

CONCLUSIONS

Our findings suggest that the intergenic variant rs1771575 serves as an independent marker for IgG levels and blood infection in children. This highlights the interplay between regulatory variants and coding mutations in FCGR, which may influence immune function and antibody production. These results underscore the potential for personalized strategies to monitor humoral responses in malaria-endemic regions.

Genome-wide association meta-analyses of drug-resistant epilepsy

BACKGROUND

Epilepsy is one of the most common neurological disorders, affecting over 50 million people worldwide. One-third of people with epilepsy do not respond to currently available anti-seizure medications, constituting one of the most important problems in epilepsy. Little is known about the molecular pathology of drug resistance in epilepsy, in particular, possible underlying genetic factors are largely unknown.

METHODS

We performed a genome-wide association study (GWAS) in two epilepsy cohorts of European ancestry, comparing drug-resistant (N = 4208) to drug-responsive individuals (N = 2618) followed by meta-analyses across the studies. Next, we performed subanalyses split into two broad subtypes: acquired or non-acquired focal and genetic generalized epilepsy.

FINDINGS

Our drug-resistant versus drug-responsive epilepsy GWAS meta-analysis showed no significant loci when combining all epilepsy types. Sub-analyses on individuals with focal epilepsy (FE) identified a significant locus on chromosome 1q42.11-q42.12 (lead SNP: rs35915186, P = 1·51 × 10-8, OR[C] = 0·74). This locus was not associated with any epilepsy subtype in the latest epilepsy GWAS (lowest uncorrected P = 0·009 for FE vs. healthy controls), and drug resistance in FE was not genetically correlated with susceptibility to FE itself. Seven genome-wide significant SNPs within this locus, encompassing the genes CNIH4, WDR26, and CNIH3, were identified to protect against drug-resistant FE. Further transcriptome-wide association studies (TWAS) imply significantly higher expression levels of CNIH3 and WDR26 in drug-resistant FE than in drug-responsive FE. CNIH3 is implicated in AMPA receptor assembly and function, while WDR26 haploinsufficiency is linked to intellectual disability and seizures. These findings suggest that CNIH3 and WDR26 may play a role in mediating drug response in focal epilepsy.

INTERPRETATION

We identified a contribution of common genetic variation to drug-resistant focal epilepsy. These findings provide insights into possible mechanisms underlying drug response variability in epilepsy, offering potential targets for personalised treatment approaches.

FUNDING

This work is part of the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 279062 (EpiPGX) and the Centers for Common Disease Genomics (CCDG) program, funded by the National Human Genome Research Institute (NHGRI) and the National Heart, Lung, and Blood Institute (NHLBI).

Toll-like Receptor Gene Polymorphisms as Predictive Biomarkers for Response to Infliximab in Japanese Patients with Crohn's Disease

Objectives: To explore the possible relationship between Toll-like receptor (TLR) gene encoding and a predictive outcome for the loss of response (LOR) to IFX treatment among Japanese patients with Crohn's disease (CD). Methods: An association analysis that involved 25 single-nucleotide polymorphisms (SNPs) across the TLR1, TLR2, TLR4, TLR6, TLR9, and TLR10 genes was performed on a cohort of 127 Japanese patients with CD. The therapeutic responses were evaluated at 10 weeks, 1 year, and 2 years using three different inheritance models. Results: The CD patients with a G/G genotype of rs5743565 in TLR1 were significantly less likely in the responders at 10 weeks compared with the non-responders (p = 0.023, OR = 0.206). The frequencies of the C/T or T/T genotypes of rs5743604 in the TLR1, G/A, or A/A genotypes of rs13105517 in TLR2, both in the minor allele dominant model, were significantly higher in the responders at 10 weeks as compared with those in the non-responders (p = 0.035, OR = 4.401; p = 0.017, OR = 5.473). The patients with an A/A genotype of rs13105517 in TLR2 in the minor allele recessive model were significantly less likely in the responders at one year of IFX treatment compared with those in the non-responders (p = 0.004, OR = 0.195). Conclusions: The polymorphisms of TLR1 and TLR2 can be useful as biomarkers for predicting initial and secondary LOR to IFX in Japanese CD patients. The IFX response in genetic testing may target molecules for new drugs to overcome the non-response and LOR to IFX.

Association of Lower COMT Activity Alleles with Aggressive Traits in Male Youth with Conduct Disorder Living in a Correctional Facility

Aggression constitutes a significant behavioral issue associated with delinquent behavior, commonly observed in youth diagnosed with conduct disorder (CD) and living in correctional facilities. Catechol-o-methyl-transferase (COMT) gene variants modify the environmental sensitivity associated with the risk of aggression. This study evaluated the association of COMT rs4680 and rs4818 polymorphisms with aggressive behavior in 341 male adolescents living inside and outside a correctional facility, with or without a diagnosis of CD. Aggression was assessed using the Hare Psychopathy Checklist: Youth Version (PCL-YV), Modified Overt Aggression Scale (MOAS) and Swanson, Nolan and Pelham Questionnaire. COMT rs4680 and rs4818 polymorphisms were genotyped using TaqMan SNP Genotyping Assays. A similar prevalence of the COMT genotypes or haplotypes was found between adolescents with or without CD, suicidal behavior, or detention in correctional facility. In youth with CD, the COMT rs4680 A allele was associated with higher MOAS verbal aggression, aggression toward objects, irritability (subjective and open), and PCL-YV interpersonal domain scores compared with carriers of the COMT rs4680 G allele. COMT rs4818 GC carriers with CD had higher scores on the MOAS subjective irritability than GG heterozygotes. These novel findings revealed the association of lower COMT rs4680 and rs4818 activity alleles with aggression in detained male adolescents with CD.

Frequency of Tumor Necrosis Factor-α, Interleukin-6, and Interleukin-10 Gene Polymorphisms in Mexican Patients with Diabetic Retinopathy and Diabetic Kidney Disease

BACKGROUND/OBJECTIVES

Two of the microvascular complications in type 2 diabetes (T2D) are diabetic retinopathy (DR), which is the most common cause of non-traumatic blindness, and diabetic kidney disease (DKD); the latter generally requires renal replacement therapy. The aim of the present study was to determine the frequency of polymorphisms of Tumor Necrosis Factor-α, interleukin-6, and interleukin-10 (TNF-α, IL-10, and IL-6), as well as to describe the clinical and laboratory characteristics of T2D association with these microvascular complications.

METHODS

This study included 203 patients with T2D, of which 102 had microvascular complications: 95 with DR, 50 with DKD, and 15 with diabetic neuropathy (the latter were not included in the statistical analysis); those with T2D without confirmed microvascular complications were considered as controls. Clinical and laboratory data were collected from the patient's medical records. Polymorphism typing of TNF-α rs361525 and rs1800629 and IL-10 rs1800872 and rs1800871 were obtained using MALDI-TOF MS. IL-10 rs1800896 and IL-6 rs1800795 were typed using a quantitative real-time polymerase chain reaction.

RESULTS

The results of age, HbA1c, fasting glucose, and arterial hypertension are significantly associated in every group. The TNF-α rs1800629A allele and TNF-α rs1800629G/A genotype were associated with microvascular complications and DR. For IL-10-rs1800896, all the models were associated in DKD. The TNF-α rs361525-rs1800629GA haplotype was associated with microvascular complications and DR, while the IL-10 haplotype, rs1800872-rs1800871-rs1800896 GGC, showed susceptibility in every group.

CONCLUSIONS

Our results show the contributions of the variants of these cytokines to these microvascular complications, but more studies are required to reach relevant conclusions.

Genome-Wide Association Studies of Body Weight and Average Daily Gain in Chinese Dongliao Black Pigs

In the domain of swine production, body weight (BW) and average daily gain (ADG) are recognized as the primary performance indicators. Nevertheless, the genetic architecture of ADG and BW in Dongliao black (DLB) pigs remains to be fully elucidated. In this study, we performed a genome-wide association analysis of BW, ADG, and body mass index (BMI) in 358 DLB pigs of different days of age. The genome-wide association study (GWAS) showed the following: (1) The most significant single nucleotide polymorphism (SNP) detected for BW was on Sus scrofa chromosome (SSC) 11:100,808 (p-value = 1.16 × 10-6) that was also the most significant SNP for ADG. (2) The most significant SNP associated with BMI was SSC17:51,463,521 (p-value = 5.16 × 10-8). (3) SNPs SSC10:6,523,844 and SSC17:23,852,682 were identified in both BW and ADG. A meta-analysis was conducted on BW at different days and demonstrated SSC5:39,028,335 (p-value = 8.37 × 10-6) which was not identified in the results of each single trait. The regions of two SNPs (SSC11:100,808, SSC4:10,703,277) exhibited considerable influence on both BW and ADG and the related regions were selected for linkage disequilibrium (LD) analyses that exhibited a notable linkage. In addition, several genes were identified that are associated with obesity and play roles in lipid metabolism, including MACROD2, PHLPP2, CYP2E1, and STT3B.

Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses

Soybean domestication has been essential for crop evolution, adaptation, and modern breeding. Despite advancements in understanding soybean genetics, the genetic basis of DRTs has yet to be fully explored, particularly in the context of genome-wide association studies (GWASs) and gene interaction analyses (epistasis). This study evaluated 198 diverse soybean accessions using 23,574 high-quality SNPs obtained via ddRAD-seq. Nine key DRTs-including those related to seed size (length, width, and thickness), seed coat color, cotyledon color, hypocotyl color, stem growth habit, flower color, pod color, pubescence, and pod-shattering-were phenotyped in two environments. A GWASs conducted via the FarmCPU and BLINK models identified 78 significant SNPs, 14 consistently detected across both environments and models, demonstrating stability. Notably, the SNP rs.Gm16.29778273 linked to pod-shattering resistance. The functional annotation linked three known quantitative trait loci /genes and revealed 11 novel candidate genes associated with DRTs, providing insights into their roles via Gene Ontology (GO) terms. The main effect SNP × SNP interaction analysis revealed that the significant SNP rs.Gm13.16695800 exhibits a pleiotropic effect, controlling both hypocotyl and flower color. Furthermore, 324 epistatic interactions were identified, influencing the expression of DRTs, thereby highlighting the complex genetic architecture underlying these traits. These findings offer valuable insights into domestication and the traits linked to higher yield. They provide a solid foundation for developing marker-assisted selection (MAS) strategies and functional studies to improve soybean breeding for resilient, high-yielding varieties.