Haplotype Effects Research Articles

Genetic basis of vascular bundle variations in rice revealed by genome-wide association study

The vascular bundles play important roles in transportation of photoassimilate, and the number, size, and capacity of vascular bundles influence the transportation efficiency. Dissecting the genetic basis may help to make better use of naturally occurring vascular bundle variations. Here, we conducted a genome-wide association study (GWAS) of the vascular bundle variations in a worldwide collection of 529 Oryza sativa accessions. A total of 42 and 93 significant association loci were identified in the neck panicle and flag leaf, respectively. The introgression lines showing extreme values of the target traits harbored at least one GWAS signal, indicating the reliability of the GWAS loci. Based on the data of near-isogenic lines and transgenic plants, Grain number, plant height, and heading date7 (Ghd7) was identified as a major locus for the natural variation of vascular bundles in the neck panicle at the heading stage. In addition, Narrow leaf1 (NAL1) was found to influence the vascular bundles in both the neck panicle and flag leaf, and the effects of the major haplotypes of NAL1 were characterized. The loci or candidate genes identified would help to improve vascular bundle system in rice breeding.

Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats.

Simple SummaryAlthough the casein complex has been reported to condition economically important traits in dairy species, information in goats is scarce. The analysis of haplotypic sequences has been suggested to maximize the results obtained after the assessment of other genetic units, such as SNPs. We studied the association between haplotype sequences for αS1-, αS2-, β-, and κ-casein loci and milk yield, protein, fat, dray matter, lactose, somatic cells count, and the curve shape parameters that they describe during lactation (peak and persistence). This aimed to provide basic research data for the integration of haplotype monitoring in the selection strategies of dairy goats.Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used using a Bayesian inference for ANOVA. We identified 48 single nucleotide polymorphisms (SNPs) present in the casein complex of 159 unrelated individuals of diverse ancestry, which were organized into 86 haplotypes. The Ali and Schaeffer model was chosen as the best fitting model for milk yield (Kg), protein, fat, dry matter, and lactose (%), while parabolic yield-density was chosen as the best fitting model for somatic cells count (SCC × 103 sc/mL). Peak and persistence for all traits were computed respectively. Statistically significant differences (p < 0.05) were found for milk yield and components. However, no significant difference was found for any curve shape parameter except for protein percentage peak. Those haplotypes for which higher milk yields were reported were the ones that had higher percentages for protein, fat, dry matter, and lactose, while the opposite trend was described by somatic cells counts. Conclusively, casein complex haplotypes can be considered in selection strategies for economically important traits in dairy goats.

Functional polymorphisms and transcriptional analysis in the 5\u2032 region of the human serotonin receptor 1B gene (HTR1B) and their associations with psychiatric disorders

BackgroundThe 5-hydroxytryptamine 1B receptor (5-HT1B) plays an essential role in the serotonin (5-HT) system and is widely involved in a variety of brain activities. HTR1B is the gene encoding 5-HT1B. Genome-wide association studies have shown that HTR1B polymorphisms are closely related to multiple mental and behavioral disorders; however, the functional mechanisms underlying these associations are unknown. This study investigated the effect of several HTR1B haplotypes on regulation of gene expression in vitro and the functional sequences in the 5′ regulatory region of HTR1B to determine their potential association with mental and behavioral disorders.MethodsSix haplotypes consisting of rs4140535, rs1778258, rs17273700, rs1228814, rs11568817, and rs130058 and several truncated fragments of the 5′ regulatory region of HTR1B were transfected into SK-N-SH and HEK-293 cells. The relative fluorescence intensities of the different haplotypes and truncated fragments were detected using a dual-luciferase reporter assay system.ResultsCompared to the major haplotype T-G-T-C-T-A, the relative fluorescence intensities of haplotypes C-A-T-C-T-A, C-G-T-C-T-A, C-G-C-A-G-T, and C-G-T-A-T-A were significantly lower, and that of haplotype C-G-C-A-G-A was significantly higher. Furthermore, the effects of the rs4140535T allele, the rs17273700C-rs11568817G linkage combination, and the rs1228814A allele made their relative fluorescence intensities significantly higher than their counterparts at each locus. Conversely, the rs1778258A and rs130058T alleles decreased the relative fluorescence intensities. In addition, we found that regions from − 1587 to − 1371 bp (TSS, + 1), − 1149 to − 894 bp, − 39 to + 130 bp, + 130 to + 341 bp, and + 341 to + 505 bp upregulated gene expression. In contrast, regions − 603 to − 316 bp and + 130 to + 341 bp downregulated gene expression. Region + 341 to + 505 bp played a decisive role in gene transcription.ConclusionsHTR1B 5′ regulatory region polymorphisms have regulatory effects on gene expression and potential correlate with several pathology and physiology conditions. This study suggests that a crucial sequence for transcription is located in region + 341 ~ + 505 bp. Regions − 1587 to − 1371 bp, − 1149 to − 894 bp, − 603 to − 316 bp, − 39 to + 130 bp, and + 130 to + 341 bp contain functional sequences that can promote or suppress the HTR1B gene expression.

Discovery of beneficial haplotypes for complex traits in maize landraces

Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources of diversity, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make their native diversity for early development traits accessible for elite germplasm improvement. A comparative genomic analysis of the discovered haplotypes in the landrace-derived lines and a panel of 65 breeding lines, both genotyped with 600k SNPs, points to untapped beneficial variation for target traits in the landraces. The superior phenotypic performance of lines carrying favorable landrace haplotypes as compared to breeding lines with alternative haplotypes confirms these findings. Stability of haplotype effects across populations and environments as well as their limited effects on undesired traits indicate that our strategy has high potential for harnessing beneficial haplotype variation for quantitative traits from genetic resources.

Characterizing Clinical and Neuropathological Traits of APOE Haplotypes in African Americans and Europeans.

The APOEɛ4 allele is the largest genetic risk factor for late-onset Alzheimer's disease (AD). Recent literature suggested that the contribution of APOEɛ4 to AD risk could be population-specific, with ɛ4 conferring a lower risk to Blacks or African Americans. To investigate the effect of APOE haplotypes on AD risk in individuals with European ancestry (EU) and Blacks or African Americans (AA). We selected data from 1) the National Alzheimer's Coordinating Center: a total of 3,486 AD cases and 4,511 controls (N = 7,997, 60% female) with genotypes from the Alzheimer's Disease Genetics Consortium (ADGC), and 2) the Rush University Religious Orders Study and Memory and Aging Project (ROSMAP) cohort with 578 AD and 670 controls (N = 1,248, 60% female). Using ɛ3 homozygotes as the reference, we compared the association of various APOE haplotypes with the clinical and neuropathological correlates of dementia in AA and EU. In both cohorts, we find no difference in the odds or age of onset of AD among the ɛ4-linked haplotypes defined by rs769449 within either AA or EU. Additionally, while APOEɛ4 was associated with a faster rate of decline, no differences were found in rate of decline, clinical or neuropathological features among the ɛ4-linked haplotypes. Further analysis with other variants near the APOE locus failed to identify any effect modification. Our study finds similar effects of the ɛ4-linked haplotypes defined by rs769449 on AD as compared to ɛ3 in both AA and EU. Future studies are required to understand the heterogeneity of APOE conferred risk of AD among various genotypes and populations.

Statistically efficient association analysis of quantitative traits with haplotypes and untyped SNPs in family studies

BackgroundAssociations between haplotypes and quantitative traits provide valuable information about the genetic basis of complex human diseases. Haplotypes also provide an effective way to deal with untyped SNPs. Two major challenges arise in haplotype-based association analysis of family data. First, haplotypes may not be inferred with certainty from genotype data. Second, the trait values within a family tend to be correlated because of common genetic and environmental factors.ResultsTo address these challenges, we present an efficient likelihood-based approach to analyzing associations of quantitative traits with haplotypes or untyped SNPs. This approach properly accounts for within-family trait correlations and can handle general pedigrees with arbitrary patterns of missing genotypes. We characterize the genetic effects on the quantitative trait by a linear regression model with random effects and develop efficient likelihood-based inference procedures. Extensive simulation studies are conducted to examine the performance of the proposed methods. An application to family data from the Childhood Asthma Management Program Ancillary Genetic Study is provided. A computer program is freely available.ConclusionsResults from extensive simulation studies show that the proposed methods for testing the haplotype effects on quantitative traits have correct type I error rates and are more powerful than some existing methods.

Estimation of NAM-A1 haplotypes effect on the level of quantitative traits and grain protein content in wheat

Aim. NAM-A1 gene plays an important role in the regulation of metabolic processes, the remobilization of nutrients from the wheat vegetative organs to grain. The aim of this work is the genotyping of SNP polymorphisms of the NAM-A1 gene in introgression lines derived from the cross of bread wheat varieties with species of genus Triticum, as well as estimation of NAM-A1 haplotypes effect on quantitative traits and grain protein content of the studied genotypes. Methods. NAM-A1 gene polymorphisms were identified using the TaqMan - Real-time PCR. Statistical data analysis was carried out using MS Excel 2007, Statistica 10.0. Results. NAM-A1c haplotype is mainly found in the studied genus Triticum species, NAM-A1d - in bread wheat varieties, and mixed haplotypes - in the introgression wheat lines. Statistically significant associations among NAM-A1 gene haplotypes and productive tillering of plants, the length of the main spike, the number of spikelets in the main spike and the thousand kernel weight were revealed. Conclusions. A significant effect of the NAM-A1 haplotypes was established for the traits «productive tillering» and «thousand kernel weight». The highest thousand kernel weight was reached in plants carrying the haplotype NAM-A1d.&#x0D; Keywords: T. aestivum L., species of genus Triticum, NAM-A1, SNP, quantitative characters.

Effects of ‘Candidatus Liberibacter Solanacearum’ Haplotype on Atlantic Potato Tuber Emergence Rate in South Texas

The bacterium ‘Candidatus Liberibacter solanacearum’ (Lso) is a phloem-restricted plant pathogen associated with different diseases worldwide. In North America, two haplotypes, LsoA and LsoB, are vectored by the potato psyllid, Bactericera cockerelli Sulc that causes zebra chip (ZC) in potato (Solanum tuberosum L.) and other solanaceous plants. In potato, both haplotypes cause similar symptoms albeit with different severities: LsoB-infected potato plants exhibit more severe ZC tuber symptoms compared to LsoA-infected plants. Previous research suggested that Lso-infected plants could produce viable seed tubers, potentially creating a reservoir for Lso propagation. The current study evaluated the effect of Lso haplotype on the emergence rate of tubers produced by infected potato plants (var. ‘Atlantic’) grown in the Lower Rio Grande area during the 2018 and 2019 growing seasons. Five Lso treatments were evaluated: uninfested controls, plants infested with uninfected psyllids (LsoFree), plants infested with LsoA- or LsoB-infected psyllids (LsoA and LsoB, respectively), and plants infested with psyllids co-infected with both Lso haplotypes (LsoAB). A portion of harvested tubers were evaluated for ZC symptom severity using a visual score. The remaining tubers were placed in cold storage for six months and then used as seed tubers to compare emergence and plant development rates among the treatments. This study confirms the previously reported differences in ZC symptom severity between Lso haplotypes. Furthermore, this study showed that tubers produced by Lso-infected plants were 90.1 ± 8.2% inviable. Importantly, all plants developing from these seed tubers tested negative for the presence of Lso. The results of this study suggest that while seed tubers produced by Lso-infected plants can germinate, the daughter plant was not infected by Lso. Therefore, Atlantic tubers produced by previously infected plants with Lso haplotypes A and B in South Texas do not represent a reservoir for Lso disease.

Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency.

Mouse embryonic stem cells (mESCs) cultured in the presence of LIF occupy a ground state with highly active pluripotency-associated transcriptional and epigenetic circuitry. However, ground state pluripotency in some inbred strain backgrounds is unstable in the absence of ERK1/2 and GSK3 inhibition. Using an unbiased genetic approach, we dissect the basis of this divergent response to extracellular cues by profiling gene expression and chromatin accessibility in 170 genetically heterogeneous mESCs. We map thousands of loci affecting chromatin accessibility and/or transcript abundance, including 10 QTL hotspots where genetic variation at a single locus coordinates the regulation of genes throughout the genome. For one hotspot, we identify a single enhancer variant ∼10 kb upstream of Lifr associated with chromatin accessibility and mediating a cascade of molecular events affecting pluripotency. We validate causation through reciprocal allele swaps, demonstrating the functional consequences of noncoding variation in gene regulatory networks that stabilize pluripotent states invitro.

Training Population Design With the Use of Regional Fusarium Head Blight Nurseries to Predict Independent Breeding Lines for FHB Traits.

Fusarium head blight (FHB) is a devastating disease in cereals around the world. Because it is quantitatively inherited and technically difficult to reproduce, breeding to increase resistance in wheat germplasm is difficult and slow. Genomic selection (GS) is a form of marker-assisted selection (MAS) that simultaneously estimates all locus, haplotype, or marker effects across the entire genome to calculate genomic estimated breeding values (GEBVs). Since its inception, there have been many studies that demonstrate the utility of GS approaches to breeding for disease resistance in crops. In this study, the Uniform Northern (NUS) and Uniform Southern (SUS) soft red winter wheat scab nurseries (a total 452 lines) were evaluated as possible training populations (TP) to predict FHB traits in breeding lines of the UK (University of Kentucky) wheat breeding program. DON was best predicted by the SUS; Fusarium damaged kernels (FDK), FHB rating, and two indices, DSK index and DK index were best predicted by NUS. The highest prediction accuracies were obtained when the NUS and SUS were combined, reaching up to 0.5 for almost all traits except FHB rating. Highest prediction accuracies were obtained with bigger TP sizes (300–400) and there were not significant effects of TP optimization method for all traits, although at small TP size, the PEVmean algorithm worked better than other methods. To select for lines with tolerance to DON accumulation, a primary breeding target for many breeders, we compared selection based on DON BLUES with selection based on DON GEBVs, DSK GEBVs, and DK GEBVs. At selection intensities (SI) of 30–40%, DSK index showed the best performance with a 4–6% increase over direct selection for DON. Our results confirm the usefulness of regional nurseries as a source of lines to predict GEBVs for local breeding programs, and shows that an index that includes DON, together with FDK and FHB rating could be an excellent choice to identify lines with low DON content and an overall improved FHB resistance.

Association Between FoxO1, A2M, and TGF-β1, Environmental Factors, and Major Depressive Disorder.

IntroductionInvestigations of gene-environment (G×E) interactions in major depressive disorder (MDD) have been limited to hypothesis testing of candidate genes while poly-gene-environmental causation has not been adequately address. To this end, the present study analyzed the association between three candidate genes, two environmental factors, and MDD using a hypothesis-free testing approach.MethodsA logistic regression model was used to analyze interaction effects; a hierarchical regression model was used to evaluate the effects of different genotypes and the dose-response effects of the environment; genetic risk score (GRS) was used to estimate the cumulative contribution of genetic factors to MDD; and protein-protein interaction (PPI) analyses were carried out to evaluate the relationship between candidate genes and top MDD susceptibility genes.ResultsAllelic association analyses revealed significant effects of the interaction between the candidate genes Forkhead box (Fox)O1, α2-macroglobulin (A2M), and transforming growth factor (TGF)-β1 genes and the environment on MDD. Gene-gene (G×G) and gene-gene-environment (G×G×E) interactions in MDD were also included in the model. Hierarchical regression analysis showed that the effect of environmental factors on MDD was greater in homozygous than in heterozygous mutant genotypes of the FoxO1 and TGF-β1 genes; a dose-response effect between environment and MDD on genotypes was also included in this model. Haplotype analyses revealed significant global and individual effects of haplotypes on MDD in the whole sample as well as in subgroups. There was a significant association between GRS and MDD (P = 0.029) and a GRS and environment interaction effect on MDD (P = 0.009). Candidate and top susceptibility genes were connected in PPI networks.ConclusionsFoxO1, A2M, and TGF-β1 interact with environmental factors and with each other in MDD. Multi-factorial G×E interactions may be responsible for a higher explained variance and may be associated with causal factors and mechanisms that could inform new diagnosis and therapeutic strategies, which can contribute to the personalized medicine of MDD.

Inter-individual variation in the diet within a group of Japanese macaques and its relationship with social structure investigated by stable isotope and DNA analyses.

We investigated individual variation in diet in relation to age-sex class and kin relationship in 28 of 40 members of a small group of wild Japanese macaques (Macaca fuscata). We used stable isotope ratios from hair as an index of individual dietary profiles, genetic relatedness as an index of kin relationship, and mitochondrial DNA (mtDNA) haplotype as a marker of being an immigrant or native member of the group. The range of carbon and nitrogen stable isotope ratios from hair of individual macaques (δ13C: -24.1‰ to -22.6‰, δ15N:3.8-5.5‰), which reflected their diet over a period of ~ 6months, implied small individual variation in diet. The results of PERMANOVA implied that there were no significant effects of age class, sex, or mtDNA haplotype on hair stable isotope ratios between individuals, or on the variation in individual diet. However, the isotope values of males with mtDNA haplotypes that differed from those of the native females appeared to differ from those of other group members, which implies that immigrant males might have had a different diet profile from that of native group members. Furthermore, there was a weak correlation trend between genetic relatedness and differences in stable isotope ratios between pairs of individuals. Differences in stable isotope values were more marked in pairs with a more distant genetic relationship. This implies that within the group, closely related kin tended to forage together to avoid competing for food. However, this effect might have been weak because the size of the group was small relative to the size of the food patches, thereby reducing competition.

Effects of genetic variations in Acads gene on the risk of chronic obstructive pulmonary disease.

Short-chain acyl-CoA dehydrogenase (SCAD), encoded by the Acads gene, functions in the mitochondrial β-oxidation of saturated short-chain fatty acids. SCAD deficiency results in mitochondrial dysfunction, which is one underlying biological mechanism of chronic obstructive pulmonary disease (COPD) pathogenesis. In this case-control study, we aimed to examine the effects of Acads gene polymorphisms on the susceptibility to COPD. A total of 16 tagging single-nucleotide polymorphisms (SNPs) in Acads gene region was identified and genotyped in 646 unrelated ethnic Chinese Han individuals including 279 patients with COPD and 367 healthy controls, their allelic and genotypic associations with COPD were determined by different genetic models. Furthermore, we estimated the linkage disequilibrium and haplotypes from these tested variants and determined the effects of haplotypes on the risk of COPD. The allelic and genotypic frequencies of SNPs rs2239686 and rs487915 in Acads gene were significantly different between COPD patients and controls, no statistically significant results were observed for other SNPs. Minor alleles A of rs2239686 and T of rs487915 were associated with a decreased pulmonary function and an increased COPD risk in a dominant manner. Functional analysis indicated that the risk allele A of rs2239686 could increase Acads expressions and the intracellular reactive oxygen species content. Haplotype analysis revealed that the haplotypes CTCCT in block 2 (rs3794216-rs3794215-rs34491494-rs558314-rs7312316) as well as GC in block 3 (rs2239686-rs487915) were protective against COPD, while haplotypes CTCGC in block 2 and AT in block 3 exhibited significant associations with the increased susceptibility to COPD. Our results suggest that Acads gene could potentially be a risk factor of COPD and thus its genetic variants might be as genetic biomarkers to predict the COPD susceptibility.

PON-1 haplotype (-108C>T, L55M, and Q192R) modulates the serum levels and activity PONase promoting an atherogenic lipid profile in rheumatoid arthritis patients.

Paraoxonase 1 (PON1) promotes antioxidant and antiatherogenic activity related to the hydrolysis of oxidized lipids of low-density lipoproteins. In rheumatoid arthritis (RA) patients, it has been reported that low PON1 activity is related to an impaired lipid profile, increasing cardiovascular risk (CVR). The goal of this study was to analyze the effect of common PON1 polymorphisms and haplotypes on enzymatic activity, PON1 serum levels (PON1s), and lipid parameters related to atherogenic profile in RA patients. A cross-sectional study was carried out on 250 Mexican patients with RA. The lipid profile was determined by colorimetric tests. The PON1 activity (CMPAase) was measured by spectrophotometry. The levels of PON1s were determined by ELISA, and the polymorphisms in the PON-1 gene (-108C>T, L55M, and Q192R) were genotyped by the PCR-RFLP method. The haplotypes were estimated and statistical analysis was performed. The median of the CMPAase activity and PON1 levels was 13.91U/mL and 24.75ng/mL, respectively. The CMPAase activity was significantly lower in carriers of -108TT and 192QQ genotypes (β = - 4.09, P = 0.001 and β = - 3.73, P = 0.002, respectively); moreover, the PON1 levels were lower in 192Q allele carriers (P < 0.01). The TLQ haplotype was associated with CMPAase activity < 13.91U/mL (OR = 2.29, P < 0.001), as well as with levels of PON1s < 24.75ng/mL (OR = 1.65, P = 0.017). In this study, the CMPAase activity (< 13.91U/mL) showed a positive association with lower levels of high-density lipoprotein cholesterol (HDL-c; < 40/50mg/dL), and with a triglycerides/HDL-c ratio > 3%, and a total cholesterol/HDL-c ratio > 4.5/5%, all representatives of an atherogenic risk lipid profile. PON1 polymorphisms modulate the CMPAase activity and PON1 levels in Mexican patients with RA. The CMPAase activity < 13.91U/mL is associated with an atherogenic lipid profile, independently of inflammation markers and treatment with anti-rheumatic drugs. Key Points •The haplotype TLQ is a marker for low PONase activity in rheumatoid arthritis. •The haplotype TLQ is a marker for low PON1 serum levels in rheumatoid arthritis. •The enzymatic PON1 activity represents the best marker for an atherogenic lipid profile in rheumatoid arthritis, in comparison with PON1 levels. •The haplotype TLQ is a marker of low PON1 activity, levels of PON1s, and atherogenic lipid profile, independent of treatment therapy in rheumatoid arthritis.

The effect of the AKT1 gene and cannabis use on cognitive performance in healthy subjects.

Evidence suggests that the AKT1 gene may modulate the degree to which cannabis use induces cognitive alterations in patients with a psychotic disorder. To examine the interplay between AKT1 and cannabis use in terms of the cognitive performance of the general population. Our sample consisted of 389 Spanish university students. Sustained attention was measured via the Continuous Performance Test-Identical Pairs, immediate and delayed verbal memory with the Logical Memory subtest of the Wechsler Memory Scale, and working memory with the Wisconsin Card Sorting Test. Lifetime cannabis use frequency was assessed and individuals were classified as cannabis users or non-users. Two single nucleotide polymorphisms of the AKT1 gene were genotyped and, according to previous studies, each subject was defined as a carrier of two, one or no copies of the haplotype (rs2494732(C)-rs1130233(A)). Multiple linear regressions were conducted to test the effect of the genetic variability and cannabis use (and their interaction) on cognitive performance. An effect of the AKT1 haplotype was found on attention scores: individuals with two copies of the haplotype performed better (β=0.18, p<0.001 (adjusted for false discovery rate)), while neither cannabis nor the AKT1-cannabis interaction was associated with attention. No effect of AKT1, cannabis or the AKT1-cannabis interaction was found on verbal memory or working memory. Our study provides additional evidence that AKT1 modulates cognitive performance. However, in our non-clinical sample, the previously reported interaction between cannabis use and the AKT1 gene was not replicated.

In silico features of ADAMTS13 contributing to plasmatic ADAMTS13 levels in neonates with congenital heart disease

IntroductionRisk factors contributing to heightened thrombosis in pediatric congenital heart disease (CHD) patients are not fully understood. Among the neonatal CHD population, those presenting with single ventricular physiology are at the highest risk for perioperative thrombosis. The von Willebrand factor and ADAMTS13 interactions have emerged as causative risk factors for pediatric stroke and could contribute to heightened thrombosis in CHD neonates. MethodsThis study investigates a cohort of children with single ventricle physiology and undergoing cardiac surgery, during which some patients developed thrombosis. In this cohort, we analyzed the relationship of several molecular features of ADAMTS13 with the plasma and activity levels in patients at risk of thrombosis. Additionally, in light of the natural antithrombotic activity of ADAMTS13, we have sequenced the ADAMTS13 gene for each patient and evaluated the role of genetic variants in determining the plasma ADAMTS13 levels using a series of in silico tools including Hidden Markov Models, EVmutation, and Rosetta. ResultsLower ADAMTS13 levels were found in patients that developed thrombosis. A novel in silico analysis to assess haplotype effect of co-occurring variants identified alterations in relative surface area and solvation energy as important contributors. Our analysis suggested that beneficial or deleterious effect of a variant can be reasonably predicted by comprehensive analysis of in silico assessment and in vitro and/or in vivo data. ConclusionFindings from this study add to our understanding the role of genetic features of ADAMTS13 in patients at high risk of thrombosis related to an imbalanced relation between VWF and ADAMTS13.

The SLC16A11 Risk Haplotype for Type 2 Diabetes (T2D) Is Associated to Differentiated Responses in Weight Loss, and Glucose Metabolism After Treatments to Prevent T2D

Abstract Objectives A haplotype in SLC16A11 is associated with decreased insulin action, and risk for type 2 diabetes (T2D) in Mexicans. We aim to determine the impact of the risk haplotype on SLC16A11 on early therapeutic responses in treatments to prevent T2D. Methods We recruited subjects with at least one prediabetes criteria according to the American Diabetes Association, and body mass index 25–45 kg/m2. Subjects were randomized in two groups: lifestyle intervention (LSI): hypocaloric diet, 25 kcal/kg of ideal weight, 45% of the total intake of carbohydrates, 30% lipids and 15% protein sources + physical activity (&amp;gt;150 min medium intensity per week), or LSI + metformin (750 mg prolonged release twice a day). Interventions were prescribed by standardized dietitians. The goal was to achieve &amp;gt;3% weight loss. We evaluated the early treatment response in a follow-up period of 12 weeks with intermediate visits each 3 weeks to reinforce knowledge and treatment goals. Evaluations (baseline and post-treatment) included an oral glucose tolerance test (OGTT), and dual-energy X-ray absorptiometry. Adherence to treatment was measured trough electronic recordings. Participants were genotyped for the risk allele rs13342232. Researchers remained blinded to the genotype results. The effects of the risk haplotype were evaluated with linear and logistic regressions adjusted by age, sex, and baseline body fat %. Results We evaluated 61 subjects, 30 carriers, and 31 non-carriers. Most of participants (57%) achieved ≥3% weight loss. The LSI + metformin treatment increased in carriers, 2 times OR 3 IC95% (1.07 – 8.6) (P = 0.04) the probability to reach the ≥3% weight loss goal compared with LSI and non-carriers. In the same treatment, carriers had a greater decrease in the total and incremental area under the curve of insulin in the OGTT IC95% (−1.75 −0.11) (P = 0.02) compared with non-carriers and LSI. Carriers also had higher decrease in postprandial glucose compared with non-carriers regardless of treatment −12.63 + 30.38 vs 0.71 30.24 (P = 0.02). Conclusions After 12 weeks of treatment, carriers with prediabetes showed a higher probability achieve weight loss and to improve insulin secretion with metformin. Regardless of the treatment, carriers were prone to improve postprandial glucose. Funding Sources Miguel Aleman Medical Research Award.

Genetic dissection of Rift Valley fever pathogenesis: Rvfs2 locus on mouse chromosome 11 enables survival to early-onset hepatitis

Infection of mice with Rift Valley fever virus (RVFV) reproduces major pathological features of severe human disease, notably the early-onset hepatitis and delayed-onset encephalitis. We previously reported that the Rvfs2 locus from the susceptible MBT/Pas strain reduces survival time after RVFV infection. Here, we used BALB/cByJ (BALB) mice congenic for Rvfs2 (C.MBT-Rvfs2) to investigate the pathophysiological mechanisms impacted by Rvfs2. Clinical, biochemical and histopathological features indicated similar liver damage in BALB and C.MBT-Rvfs2 mice until day 5 after infection. However, while C.MBT-Rvfs2 mice succumbed from acute liver injury, most BALB mice recovered and died later of encephalitis. Hepatocytes of BALB infected liver proliferated actively on day 6, promoting organ regeneration and recovery from liver damage. By comparison with C.MBT-Rvfs2, BALB mice had up to 100-fold lower production of infectious virions in the peripheral blood and liver, strongly decreased RVFV protein in liver and reduced viral replication in primary cultured hepatocytes, suggesting that the BALB Rvfs2 haplotype limits RVFV pathogenicity through decreased virus replication. Moreover, bone marrow chimera experiments showed that both hematopoietic and non-hematopoietic cells are required for the protective effect of the BALB Rvfs2 haplotype. Altogether, these results indicate that Rvfs2 controls critical events which allow survival to RVFV-induced hepatitis.

A Gilbert syndrome-associated haplotype protects against fatty liver disease in humanized transgenic mice

UDP-glucuronosyltransferases 1 A (UGT1A) enzymes are capable of detoxifying a broad range of endo- and xenobiotic compounds, which contributes to antioxidative effects, modulation of inflammation and cytoprotection. In the presence of low-function genetic UGT1A variants fibrosis development is increased in various diseases. This study aimed to examine the role of common UGT1A polymorphisms in NASH. Therefore, htgUGT1A-WT mice and htgUGT1A-SNP mice (carrying a common human haplotype present in 10% of the white population) were fed a high-fat Paigen diet for 24 weeks. Serum aminotransferase activities, hepatic triglycerides, fibrosis development and UGT1A expression were assessed. Microscopic examination revealed higher hepatic fat deposition and a significant induction of UGT1A gene expression in htgUGT1A-WT mice. In agreement with these observations, lower serum aminotransferase activities and lower expression levels of fibrosis-related genes were measured in htgUGT1A-SNP mice. This was accompanied by reduced PPARα protein levels in htgUGT1A-WT but not in SNP mice. Our data demonstrate a protective effect of a UGT1A SNP haplotype, leading to milder hepatic steatosis and NASH. Higher PPARα protein levels in animals with impaired UGT1A activity are the likely result of reduced glucuronidation of ligands involved in PPARα-mediated fatty acid oxidation and may lead to the observed protection in htgUGT1A-SNP mice.

Incorporating Genome Annotation Into Genomic Prediction for Carcass Traits in Chinese Simmental Beef Cattle.

Various methods have been proposed for genomic prediction (GP) in livestock. These methods have mainly focused on statistical considerations and did not include genome annotation information. In this study, to improve the predictive performance of carcass traits in Chinese Simmental beef cattle, we incorporated the genome annotation information into GP. Single nucleotide polymorphisms (SNPs) were annotated to five genomic classes: intergenic, gene, exon, protein coding sequences, and 3′/5′ untranslated region. Haploblocks were constructed for all markers and these five genomic classes by defining a biologically functional unit, and haplotype effects were modeled in both numerical dosage and categorical coding strategies. The first-order epistatic effects among SNPs and haplotypes were modeled using a categorical epistasis model. For all makers, the extension from the SNP-based model to a haplotype-based model improved the accuracy by 5.4–9.8% for carcass weight (CW), live weight (LW), and striploin (SI). For the five genomic classes using the haplotype-based prediction model, the incorporation of gene class information into the model improved the accuracies by an average of 1.4, 2.1, and 1.3% for CW, LW, and SI, respectively, compared with their corresponding results for all markers. Including the first-order epistatic effects into the prediction models improved the accuracies in some traits and genomic classes. Therefore, for traits with moderate-to-high heritability, incorporating genome annotation information of gene class into haplotype-based prediction models could be considered as a promising tool for GP in Chinese Simmental beef cattle, and modeling epistasis in prediction can further increase the accuracy to some degree.