Differences In Allele Frequencies Research Articles

CACNA1C Gene rs1006737 Polymorphism Affects Cognitive Performance in Chinese Han Schizophrenia.

ObjectiveTo investigate the relationship between L-type calcium channel α1C subunit (CACNA1C) gene polymorphism and schizophrenia (SCZ) and cognitive function in the Han nationality, the main nationality in China.MethodsGenotyping of CACNA1C SNP (rs1006737, rs1024582, rs2007044) in SCZ patients (n = 312) and healthy controls (n = 305) was performed. Cognitive function was assessed in the SCZ patients using Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). Then, the correlation between SNP and SCZ, as well as cognition, was calculated.ResultsThere was no significant difference in allele frequency and genotype distribution frequency of the three polymorphic loci of CACNA1C gene between the two groups. In cognitive tests, delayed memory scores in RBANS were significantly lower in rs1006737 “A” risk allele carriers than in non-carriers.ConclusionThere is no significant difference in allele and genotype frequency of CANCA1C Gene rs1006737, rs1024582 and rs2007044 between the schizophrenia patients and healthy controls. The cognitive function of schizophrenia patients is correlated with the rs1006737, and the delayed memory of “A” allele carriers is significantly reduced.

Difference in Risk Allele Frequencies and Reported Clinical Severity of COVID-19 in Different Countaries

Difference in Risk Allele Frequencies and Reported Clinical Severity of COVID-19 in Different Countaries

Association of SLC30A8 (rs13266634) and GLIS3 (rs7034200) gene variant in development of type 2 diabetes mellitus in Indian population: A case-control study

ObjectiveType 2 diabetes mellitus (T2DM) is a chronic disorder characterized by pancreatic beta-cell dysfunction and insulin resistance because of unsettled hyperglycemia. The present study was designed to understand the association of genetic variations in SLC30A8 and GLIS3 genes with T2DM. MethodA total of 600 samples were taken with 400 T2DM cases (240 males and 160 females; mean age 42.4 ± 9.3) and 200 control cases (130 males and 70 females; mean age 40.7 ± 8.2) in the study from regions across North India. A genetic study was conducted by PCR-RFLP methods. P parametric and non-parametric tests were used to analyze the data based on the qualitative and quantitative data. ResultsSignificant difference was found in biochemical parameters and sedentary lifestyle compared between T2DM patients and healthy controls such as triglycerides, HbA1c, T-cholesterol, LDL-C, BMI, systolic and diastolic BP, PPG, FPG, weight loss, fatigue, slow wound healing, blur vision, urination, appetite, urination, consumption of alcohol, non-veg, fast food and sugary drink, excessive consumption of calorie, normal and brisk (20 min) walk, prolonged sitting 3 h work, leisure sitting (3 h) and standing work (3 h) while no significant differences were observed in parameters such as HDLC, WHR, family history, household chores and exercise among T2DM patients and controls. In SLC30A8 rs13266634 variant, it was observed that TC and CC genotypes frequencies were significantly higher in T2DM cases as compared to healthy controls (OR- 2.88; 95%CI- 1.93–4.31; p < 0.0001 and OR- 5.6; 95%CI- 2.33–13.55; p = 0.0001). C allele frequency was higher as compared to healthy controls. For the GLIS3 rs7034200 variant, no significant difference was found in allelic frequency in cases and controls (p-0.434). We did not find any significant association of T2DM with GLIS3 gene variant under dominant as well as recessive models. ConclusionPresent study concludes that the association of genetic variations between T2DM cases and control was found to have a significant difference and play a vital role in T2DM risk based on odds ratio. However, the difference in frequency of alleles in the GLIS3 variant was non-significant among T2DM patients and healthy controls.

Quantitative evaluation of nonlinear methods for population structure visualization and inference.

Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations in a population as a result of nonrandom mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics, it is an important confounding variable in genome-wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this article, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is known a priori either through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to principal component analysis, while neural network-based methods fall behind.

Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments

IntroductionInvestigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. ObjectChicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. MethodHere, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). ResultsOur results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation. ConclusionOur findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.

Common polymorphisms of protein tyrosine phosphate non-receptor type 2 gene are not associated with risk of Crohn's disease in Indian.

BACKGROUNDMultiple genetic risk factors for Crohn’s disease (CD) have been identified. However, these observations are not consistent across different populations. The protein tyrosine phosphate non-receptor type 2 (PTPN2) gene plays a role in various aspects of host defense including epithelial barrier function, autophagy, and innate and adaptive immune response. Two common polymorphisms in the PTPN2 gene (rs2542151 and rs7234029) have been associated with risk of CD in Western countries. AIMTo evaluate the association of PTPN2 gene polymorphisms with risk of CD in Indian population.METHODSWe conducted a prospective case-control study. Patients with CD were recruited, and their clinical and investigation details were noted. Controls were patients without organic gastrointestinal disease or other comorbid illnesses. Two common polymorphisms in the PTPN2 gene (rs2542151 and rs7234029) were assessed. DNA was extracted from peripheral blood samples of cases and controls and target DNA was amplified using specific sets of primers. The amplified fragments were digested with restriction enzymes and the presence of polymorphism was detected by restriction fragment length polymorphism. The frequency of alleles was determined. The frequencies of genotypes and alleles were compared between cases and controls to look for significant differences.RESULTSA total of 108 patients with CD (mean age 37.5 ± 12.7 years, females 42.6%) and 100 controls (mean age 39.9 ± 13.5 years, females 37%) were recruited. For the single nucleotide polymorphism (SNP) rs7234029, the overall frequency of G variant genotype (AG or GG) was noted to be significantly lower in the cases compared to controls (35.2% vs 50%, P = 0.05). For the SNP rs2542151, the overall frequency of G variant genotype (GT or GG) was noted to be similar in cases compared to controls (43.6% vs 47%, P = 0.73). There were no significant differences in minor allele (G) frequency for both polymorphisms between the cases and controls. Both the SNPs had no significant association with age of onset of illness, gender, disease location, disease behaviour, perianal disease, or extraintestinal manifestations of CD.CONCLUSIONUnlike observation form the West, polymorphisms in the PTPN2 gene (rs7234029 and rs2542151) are not associated with an increased risk of developing CD in Indian patients.

FNDC5/Irisin polymorphisms are associated with osteopenia in postmenopausal Mayan-Mestizo women

Objective This study aimed to analyze the association between rs3480 and rs16835198 of FNDC5/Irisin and their haplotypes with variations in bone mineral density (BMD) and osteopenia/osteoporosis in postmenopausal Mayan-Mestizo women. Methods We studied 547 postmenopausal women of Maya-Mestizo origin. BMD was measured in the lumbar spine and total hip by dual-energy X-ray absorptiometry. DNA was obtained from blood leukocytes. rs3480 and rs16835198 of FNDC5/Irisin were studied using real-time PCR allelic discrimination. Differences between the means of BMD according to genotype were analyzed with covariance. Allele frequency differences were assessed by χ 2 and logistic regression was used to test for associations. Pairwise linkage disequilibrium between polymorphisms was calculated by direct correlation r 2, and haplotype analysis was conducted. Results Under a recessive model, we observed a significant association of rs3480 with the presence of osteopenia at the total hip and femoral neck (p = 0.008 and p = 0.003, respectively). For rs16835198, we found an association with osteopenia at the total hip and femoral neck in a dominant model (p = 0.043 and p = 0.009, respectively). Conclusions We found an association of rs3480 with risk to present osteopenia at the total hip and femoral neck, while rs16835198 was associated as a protector for presence of osteopenia only at the femoral neck.

Association of RAAS gene polymorphisms with susceptibility to essential hypertension in military secret service personnel

Objective: To analyze the relationship between renin-angiotensin-aldosterone system (RAAS) gene polymorphisms and susceptibility to essential hypertension (EH) in military secret service personnel. Methods: In October 2019, military secret service personnel (162 people) who were recuperating in a sanatorium from January to December 2017 were selected as the research subjects, all of whom were Han and male. The patients (79 people) who were diagnosed with EH according to the diagnostic criteria of hypertension in the "Chinese Guidelines for the Prevention and Treatment of Hypertension" (2016 Revised Edition) were the case group, and the people with normal blood pressure (83 people) were the control group. Occupational epidemiological investigation was conducted, 5 ml of fasting cubital venous blood was collected, genomic DNA was extracted by phenol-chloroform method, and RAAS gene polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism method. The distribution differences of genotype and allele frequency between groups were compared, and the relationship between genotype, allele frequency and EH was analyzed. Results: The average age of military secret service personnel was (38.2±5.3) years old, and there was no statistical significance in the average age and the age distribution over 40 years old of the case group and the control group (P>0.05) . There were significant differences in the distribution of AGT gene M235T locus, ACE gene I/D polymorphism genotype and allele between the case group and the control group (P<0.05) . The TT genotype with AGT gene M235T locus (OR=3.28, 95%CI: 1.21-8.91) and DD genotype with ACE gene (OR=2.86, 95%CI: 1.17-7.00) were risk factors for EH in military secret service personnel. Conclusion: The TT genotype of AGT gene M235T and the DD genotype of ACE gene may be the susceptibility genotypes of military secret service personnel for EH.

The DDT‐induced decline influenced genetic diversity in naturally recovered Peregrine falcons (Falco peregrinus) nesting within the Alaska Arctic and eastern interior

We assessed the influence of the severe mid‐20th century population decline on genetic diversity in non‐augmented Peregrine Falcon Falco peregrinus populations nesting within the Alaska Arctic and eastern Interior. Microsatellite and mitochondrial DNA (mtDNA) data were analysed for Peregrine Falcons sampled from three periods: pre‐decline, decline and post‐decline. The influence of the decline on genetic diversity differed between the two locales. The Alaska Arctic was characterized by shifts in mtDNA haplotype frequencies, increased inbreeding coefficient, reduction in effective population size and increase in private haplotypes, and a signature of post‐decline population growth was detected; by contrast, the eastern Interior showed a reduction in haplotype diversity and no differences in allelic or haplotypic frequencies between pre‐ and post‐decline periods, though pre‐decline birds clustered away from the other two periods and allelic frequency differences were observed between decline and post‐decline periods. Patterns in genetic diversity suggest populations recovered through recruitment from within and immigration.

The association of vitamin D binding protein levels and genotypes with type 1 diabetes in the black South African population

BackgroundVitamin D deficiency and the vitamin D pathway have previously been associated with type 1 diabetes (T1D). The majority of vitamin D is transported through the blood bound to the vitamin D binding protein (VDBP). Two polymorphisms in the VDBP gene (rs4588 and rs7041) result in different VDBP variants and have been associated with T1D, however the results are not consistent. The association of VDBP levels and its polymorphisms with T1D have not been investigated in the black South African population. Therefore, this study aimed to determine whether rs4588, rs7041 or serum VDBP levels were associated with T1D in this population.MethodsParticipants with type 1 diabetes and controls were recruited from the greater Johannesburg area, South Africa. Participants were genotyped for rs4588 and rs7041 using PCR-RFLP and serum VDBP levels were determined by ELISA.ResultsThere was no difference in VDBP allelic or genotypic frequencies between participants with T1D and controls (rs4588 C allele frequency 0.92 vs. 0.94; p = 0.390 and rs7041 T allele frequency 0.95 vs. 0.95; p = 0.890). In univariate analysis, the rs4588 CC genotype was associated with increased serum VDBP levels, however, this association was lost with multivariate analysis. The VDBP genotypes were not associated with any other study variables. In logistic regression analysis, higher VBDP levels were associated with T1D (OR: (95% CI): 6.58 (1.45–29.9); p = 0.015), and within a linear regression analysis, T1D disease status was found to be associated with 0.044 mg/ml higher VDBP levels (p = 0.028).ConclusionsThese data suggest that serum VDBP levels are positively associated with the presence of T1D in the African population. Whether VDBP lies in the causal pathway or its elevation is an effect of T1D is uncertain and requires further investigation.

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.

Effects of TIMP1 rs4898 Gene Polymorphism on Early-Onset Preeclampsia Development and Placenta Weight.

Introduction: Some evidence indicates that the improper trophoblast invasion of maternal spiral arteries could be caused by an imbalance between matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs), leading to preeclampsia (PE) development. This study aimed to assess the potential role of MMP1, MMP9, TIMP1 and TIMP2 gene polymorphisms in the pathogenesis of PE. Materials and methods: A total of 308 Polish women, 115 preeclamptic (55 with early-onset preeclampsia [EOPE], 60 with late-onset preeclampsia [LOPE]) and 193 healthy pregnant women, all of Caucasian origin, were recruited to the study. PE was diagnosed following the ACOG criteria. The polymorphic variants of the MMP-TIMP pathway (MMP1 rs1799750, MMP9 rs17576, MMP9 rs17577, TIMP1 rs4898, TIMP2 rs2277698, TIMP2 rs55743137) were genotyped by polymerase chain reaction and restriction fragment length polymorphism. Results: Analyzing all SNPs in the MMP-TIMP pathway, no significant differences in allele frequencies between preeclamptic women and controls were observed. However, comparing the EOPE and LOPE groups with each other, we observed a statistically significant difference between them for the TIMP1 rs4898 variant. In the whole group of 308 women, the mean placenta weight was the lowest in carriers of the rs4898 CC genotype. Post hoc analysis revealed significant differences between CC-CT (p = 0.0209) and CC-TT (p = 0.0469). Additionally, during allele analysis, a statistically significant difference in the mean placenta weight (for C allele 529.32 ± 157.11 g, for T allele 560.24 ± 162.24 g, p = 0.021) was also observed. Conclusion: Our findings suggest a relationship between TIMP1 rs4898 (372T > C) polymorphism and increased risk of early-onset preeclampsia in a population of pregnant Polish women. Our data suggest that the TIMP1 rs4898 C allele might be associated with increased risk for early-onset, but not for late-onset preeclampsia. To evaluate the role of the TIMP1 polymorphic variants in the etiopathology of preeclampsia, further studies with a larger sample size are needed.

Association of RB1 rs9568036 and CDKN1A rs1801270 Polymorphisms with Retinoblastoma Susceptibility.

To investigate the association of polymorphisms (rs9568036 and rs1801270) in the RB1 and P21 genes with susceptibility to retinoblastoma (RB). This case-control study was designed with 50 patients with RB and 50 controls. Polymerase chain reaction was performed to amplify the intron 17 of RB1 rs9568036 and exon 2 of P21 rs1801270. Then, all the amplified fragments were subjected to directional sequencing, and finally, the association between genotypes and the development of RB risk and invasion was studied. A statistically significant difference in genotypic or allele frequencies of single-nucleotide polymorphisms (SNPs) (rs1801270 and rs9568036) was found between Iranian RB patients and the controls (P > 0.05). However, the frequency of genotype RB1 rs9568036 observed a statically significant difference in the RB patients compared to the control group, and the nonwild-type allele A increased the chance of susceptibility to developing RB by 2.92 times. The rs9568036 SNP in the RB1 gene may increase susceptibility to the development of RB in the affected patients. In spite of that, this polymorphism does not influence RB patient's invasion. Further investigation with a large enough sample size is recommended to validate this hypothesis.

Glucocerebrosidase variant T369M is not a risk factor for Parkinson’s disease in Sweden

IntroductionGenetic variants in the Beta-glucocerebrosidase gene (GBA1) is a known risk factor for Parkinson’s disease. The GBA1 mutations L444P, N370S and many other have been shown to associate with the disease in populations with diverse background. Some GBA1 polymorphisms have a less pronounced effect, and their pathogenicity has been debated. We have previously found associations with L444P, N370S and E326K and Parkinson’s disease in Sweden. MethodIn this study we used pyrosequencing to genotype the T369M variant in a large Swedish cohort consisting of 1,131 patients with idiopathic Parkinson’s disease, and 1,594 control subjects to evaluate the possibility of this variant conferring an increased risk for Parkinson’s disease. ResultsThe minor allele frequency was 2.15% in patients and 1.76% in controls. Statistical analysis showed that there was no significant difference in allele frequency between patients and control subjects, p-value 0.37, Odds Ratio 1.23 with a 95% confidence interval of 0.82–1.83. ConclusionOur results suggest that T369M is not a risk factor for Parkinson’s disease in the Swedish population.

ASSOCIATION BETWEEN VASCULAR ENDOTHELIAL GROWTH FACTOR GENE POLYMORPHISMS AND THE RISK OF PREECLAMPSIA IN IRAQI PREGNANT WOMEN

Background: Vascular endothelial growth factor (VEGF) is an essential factor for angiogenesis and plays important role in placental development. Objective: To investigate the association between VEGF single nucleotide polymorphisms (SNPs) +936 Cytosine/Thymine (C/T) and -634 Guanine/Cytosine (G/C) and preeclampsia risk. Methods: A total of 50 cases of pregnant women with preeclampsia and 50 healthy pregnant women (as a control) were involved in this case control study. Blood samples were collected form each woman and the Deoxyribonucleic acid (DNA) was extracted. Amplification of VEGF gene was done by conventional polymerase chain reaction (PCR) and then detection of SNPs-634 G/C and +936 C/T were carried out by restriction fragment length polymorphism PCR (PCR-RFLP). Results: The frequency of different genotypes of VEGF SNPs +936 C/T &amp;-634 G/C are in accordance with Hardy Weinberg equilibrium. VEGF polymorphism +936 C/T appeared in 3 genotypes after digestion with restriction enzymes Cytosine Cytosine (CC), Cytosine Thymine (C/T) &amp; Thymine Thymine (TT). VEGF SNP -634 G/C appeared in 3 genotypes after digestion with restriction enzymes; those were Guanine Guanine (GG), Guanine Cytosine (GC) and CC. The heterozygous genotype CT of polymorphism +936 C/T was more frequent among preeclamptic patients than the controls (26% versus 16%). Likewise, TT genotype was more frequent among preeclamptic patients (8% versus 2%) with no significant differences. At the allelic level, the difference was more prominent. The frequency of mutant allele (T allele) was much more frequent in preeclamptic patients than controls (21% versus 10%) with a statistically significant difference (p=0.049). Although CC genotype of polymorphism -634 G/C was more frequent among preeclamptic patients than controls (14% versus 10%), the difference was not significant (p=0.704). Likewise, there were no significant differences in allele frequency. Conclusion: The study suggested that the mutant T allele of VEGF +936 C/T polymorphism was associated with increased preeclampsia risk and disease development. Keywords: Vascular endothelial growth factor, polymorphisms, preeclampsia Citation: Khaleel MF, Al-Moayad HA. Association between vascular endothelial growth factor gene polymorphisms and the risk of preeclampsia in Iraqi pregnant women. Iraqi JMS. 2022; 20(1): 106-112. doi: 10.22578/IJMS.20.1.14

A Synonymous Variant, GABRG2 rs211037 might be a Predictive Genetic Marker of Migraine: A Case Control Study from Pakistan

Background: Migraine is a severe neurovascular disease with some temporary symptoms like unilateral headache attacks associated with sensory and autonomic disturbances. It affects 12% of the general population worldwide. Females are more susceptible to migraine than males. The genetic and environmental factors contribute as a causative agent to its symptomatology. Gamma-aminobutyric acid (GABA) neurotransmitter plays a potential role in migraine pathophysiology that prompted us to evaluate the association between gamma-aminobutyric acid type a receptor gamma two subunit gene (GABRG2) polymorphisms and the risk of a migraine attack. Methods The present case-control study included 220 subjects (100 control; 120 patients). Blood samples were taken from all the participants and DNA was isolated. The selected SNPs (rs211037, rs121909672, and T813C) of exons 5, 7, and 8 of the GABRG2 gene were genotyped for cases and controls. Results: A silent polymorphism was found at the rs211037 polymorphic site, while no variation was found on other targeted sites either in the case or control population. Statistical analysis indicated significant differences in genotypic (p=&lt;0.05) and allelic frequencies (p = &lt;0.001; OR 2.039; 95% CI 1.346-3.089) and for dominant model (p = &lt;0.001; OR 2.836; 95% CI 1.618-4.970). Conclusion: The result of our study showed that rs211037 polymorphism of the GABRG2 gene was significantly associated with migraines in the Pakistani population.

HLA-G, LILRB1 and LILRB2 Variants in Zika Virus Transmission from Mother to Child in a Population from South and Southeast of Brazil.

During the 2015–2016 epidemic, Brazil was the country with the highest rate of Zika virus (ZIKV) infection in the Americas. Twenty-nine percent of pregnant women positive for ZIKV exhibited ultrasound scans with fetus anomalies. Human leukocyte antigen-G (HLA-G) exerts immunoregulatory effects by binding to inhibitory receptors, namely LILRB1 and LILRB2, thus preventing mother–fetus rejection and vertical pathogen transmission. The binding of HLA-G to one of its receptors modulates both innate and adaptive immunity. However, in a viral infection, these molecules may behave as pathogenic mediators shifting the pregnancy environment from an anti-inflammatory profile to a pro-inflammatory phenotype. Genetic mutations might be associated with the change in phenotype. This study aimed to explore the possible role of polymorphic sites in HLA-G, LILRB1 and LILRB2 in mother–fetus ZIKV transmission. Polymorphisms were detected by direct sequencing. Differences in allele and/or genotype frequencies for each SNP analyzed among ZIKV non-transmitting and transmitting mother–child pairs, among ZIKV-transmitting and non-transmitting mothers and between ZIKV-infected and non-infected children were compared by Mid-P exact test or Yates’ correction. Significant susceptibility of ZIKV vertical transmission is suggested in ZIKV-transmitting and non-transmitting mothers and ZIKV-infected and non-infected children for LILRB1_rs1061684 T/T (p = 0.03, Pc = 0.06, OR = 12.4; p = 0.008, Pc = 0.016, OR = 16.4) and LILRB1_rs16985478 A/A (p = 0.01, Pc = 0.02, OR = 19.2; p = 0.008, Pc = 0.016, OR = 16.4). HLA-G_rs1710 (p = 0.04, Pc = 0.52, OR = 4.30) was also a susceptibility factor. LILRB2_rs386056 G/A (p = 0.02, Pc = 0.08, OR = 0.07), LILRB2_rs7247451 G/G (p = 0.01, Pc = 0.04, OR = 0.04) and HLAG_rs9380142 T/T (p = 0.04, Pc = 0.52, OR = 0.14) were suggested as protective factors against vertical transmission. The current study suggests that polymorphic sites in the LILRB1 and HLA-G genes might be associated with mother-to-child ZIKV transmission while LILRB2 might be associated with protection against ZIKV transmission in the womb in a population from the south and southeast of Brazil.

Accurate recombination estimation from pooled genotyping and sequencing: a case study on barley

Sexual reproduction involves meiotic recombination and the creation of crossing over between homologous chromosomes, which leads to new allele combinations. We present a new approach that uses the allele frequency differences and the physical distance of neighboring polymorphisms to estimate the recombination rate from pool genotyping or sequencing. This allows a considerable cost reduction compared to conventional mapping based on genotyping or sequencing data of single individuals. We evaluated the approach based on computer simulations at various genotyping depths and population sizes as well as applied it to experimental data of 45 barley populations, comprising 4182 RIL. High correlations between the recombination rates from this new pool genetic mapping approach and conventional mapping in simulated and experimental barley populations were observed. The proposed method therefore provides a reliable genetic map position and recombination rate estimation in defined genomic windows.

Genetic relationships and genome selection signatures between soybean cultivars from Brazil and United States after decades of breeding

Soybean is one of the most important crops worldwide. Brazil and the United States (US) are the world’s two biggest producers of this legume. The increase of publicly available DNA sequencing data as well as high-density genotyping data of multiple soybean germplasms has made it possible to understand the genetic relationships and identify genomics regions that underwent selection pressure during soy domestication and breeding. In this study, we analyzed the genetic relationships between Brazilian (N = 235) and US soybean cultivars (N = 675) released in different decades and screened for genomic signatures between Brazilian and US cultivars. The population structure analysis demonstrated that the Brazilian germplasm has a narrower genetic base than the US germplasm. The US cultivars were grouped according to maturity groups, while Brazilian cultivars were separated according to decade of release. We found 73 SNPs that differentiate Brazilian and US soybean germplasm. Maturity-associated SNPs showed high allelic frequency differences between Brazilian and US accessions. Other important loci were identified separating cultivars released before and after 1996 in Brazil. Our data showed important genomic regions under selection during decades of soybean breeding in Brazil and the US that should be targeted to adapt lines from different origins in these countries.

Promoter polymorphisms in STK35 and IFT27 genes and their associations with boar sperm freezability

We have shown that STK35 and IFT27 genes are differentially expressed in spermatozoa from boars with good and poor semen freezability (GSF and PSF, respectively). STK35 is a stress-related gene that is implicated in spermatogenesis, whereas IFT27 is a motility-related gene that is mainly involved in intracellular protein transport. In this study we hypothesized that polymorphic variants in the 5′-flanking regulatory regions of STK35 and IFT27 genes could contribute to differences in semen freezability. We also predicted the interactions of the polymorphic variants with transcription factors on the gene promoter activity, using bioinformatics. The 5′-flanking region sequences of the STK35 and IFT27 were PCR amplified and analyzed by Sanger sequencing method. Protein expression in STK35 and IFT27 was determined in pre-freeze (PF) and frozen-thawed (FT) spermatozoa, using western blotting analysis. Sanger sequencing revealed a single nucleotide polymorphism (SNP) rs327863835 (C > T) in STK35 promoter, while two SNPs (rs337563873, A > T; rs331520020, T > C) were detected in IFT27 promoter. STK35 and IFT27 promoter polymorphisms showed significant allele frequency differences between the GSF and PSF groups. Using bioinformatics approaches, we predicted that SNPs resulted in the generation of additional transcription factor binding sites for NFATC2, ELK1 and GR-β, which appeared to enhance or repress the promoter activity of STK35 or IFT27 in either freezability group. Wide variations in STK35 and IFT27 protein expression were observed among the boars, however, significantly higher protein expression was detected in IFT27 in FT spermatozoa of the GSF group. We suggest that the upstream variants, detected in STK35 and IFT27 promoters, might regulate the transcriptional activity of the genes by affecting their potential binding of transcription factors. The results indicate that the allelic variants in STK35 and IFT27 could be considered as potential genetic markers for predicting boar sperm freezability.