Differences In Allele Frequency Distributions Research Articles

Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding.

Rapeseed (Brassica napus L.) is an important oil-producing crop for the world. Its adaptation, yield and quality have been considerably improved in recent decades, but the genomic basis underlying successful breeding selection remains unclear. Hence, we conducted a comprehensive genomic assessment of rapeseed in the breeding process based on the whole-genome resequencing of 418 diverse rapeseed accessions. We unraveled the genomic basis for the selection of adaptation and agronomic traits. Genome-wide association studies identified 628 associated loci-related causative candidate genes for 56 agronomically important traits, including plant architecture and yield traits. Furthermore, we uncovered nonsynonymous mutations in plausible candidate genes for agronomic traits with significant differences in allele frequency distributions across the improvement process, including the ribosome recycling factor (BnRRF) gene for seed weight. This study provides insights into the genomic basis for improving rapeseed varieties and a valuable genomic resource for genome-assisted rapeseed breeding.

Deleterious effect of angiotensin-converting enzyme gene polymorphism in vitiligo patients.

Vitiligo is a rare skin condition caused by an immune reaction. Vitiligo can occur anywhere on the body. This proposed explanation of vitiligo makes it clear that vitiligo is not linked to any other autoimmune diseases. The polymorphisms of some genes present in the immune system play a major function in susceptibility of vitiligo. Meta-analysis studies have shown that the Angiotensin converting enzyme (ACE) gene insertion and deletion polymorphism is closely associated with vitiligo in many ethnicities. The connection between ACE gene and vitiligo is connected through the auto immune diseases and there are no genetic polymorphism studies have been carried out with ACE gene with vitiligo in the Saudi population. Previous studies show that vitiligo patients are more likely to also have an autoimmune disorder. The current study aims to investigate the I/D polymorphism in the ACE gene with diagnosed patients with vitiligo subjects. This is a case-control study carried out in the Saudi population with 100 vitiligo cases and 100 healthy controls. Genotyping was performed through polymerase chain reaction followed by 3% agarose gel electrophoresis. Genotype and allele frequencies were carried out with genetic mode of inheritances. Statistical analysis was performed considering p < 0.05 as significant association. There was a substantial difference in allele frequency distribution between vitiligo patients and healthy controls (OR-1.70 (95%CI: 1.14–2.53); p = 0.008). Additionally, DD genotype (OR-4.71 (95%CI: 1.42–15.61); p = 0.008) and recessive model (OR-2.66 (95%CI: 1.41–5.02); p = 0.002) was strongly associated. Both dominant and co-dominant showed the negative association (p > 0.05) when compared between the vitiligo cases and controls. The correlation between age and genotyping was performed with Anova analysis and current study results confirmed the substantial link between 11 and 20 years (p = 0.01) and 31–40 years (p = 0.04) with the defined age groups. In conclusion, in Saudi populations, the ACE gene I/D polymorphism was identified as being correlated with vitiligo. This is the first study in Saudi Arabia to report the risk factors of vitiligo with the ACE gene polymorphism.

HLA diversity in the Argentinian Umbilical Cord Blood Bank: frequencies according to donor\u2019s reported ancestry and geographical distribution

Umbilical cord blood (UCB) is a suitable source for hematopoietic stem cell transplantation. The study of HLA genes by next generation sequencing is commonly used in transplants. Donor/patient HLA matching is often higher within groups of common ancestry, however “Hispanic” is a broad category that fails to represent Argentina’s complex genetic admixture. Our aim is to describe HLA diversity of banked UCB units collected across the country taking into consideration donor’s reported ancestral origins as well as geographic distribution. Our results showed an evenly distribution of units mainly for 2 groups: of European and of Native American descent, each associated to a defined geographic location pattern (Central vs. North regions). We observed differences in allele frequency distributions for some alleles previously described in Amerindian populations: for Class I (A*68:17, A*02:11:01G, A*02:22:01G, B*39:05:01, B*35:21, B*40:04, B*15:04:01G, B*35:04:01, B*51:13:01) and Class II (DRB1*04:11:01, DRB1*04:07:01G/03, DRB1*08:02:01, DRB1*08:07, DRB1*09:01:02G, DRB1*14:02:01, DRB1*16:02:01G). Our database expands the current knowledge of HLA diversity in Argentinian population. Although further studies are necessary to fully comprehend HLA heterogeneity, this report should prove useful to increase the possibility of finding compatible donors for successful allogeneic transplant and to improve recruitment strategies for UCB donors across the country.

Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm.

Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm Mauritia flexuosa. We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events. Functional annotation of SNPs with selection footprints identified loci affecting genes related to adaptation to environmental stress, plant development, and primary metabolic processes. The strong differences in climatic and soil variables between ecosystems matched the high differentiation and low admixture in population Bayesian clustering. Further, we found only small differences in allele frequency distribution in loci putatively under selection among widespread populations from different ecosystems, with fixation of a single allele in most populations. Taken together, our results indicate that adaptive selective sweeps related to environmental stress shaped the spatial pattern of genetic diversity in M. flexuosa, leading to high similarity in allele frequency among populations from different ecosystems.

Polymorphism of Transcription Factor 7-Like 2 in Obese Patients with Type 2 Diabetes Mellitus

Objective: The article is to investigate the relationship between the polymorphism of transcription factor 7-like 2 (TCF7L2) gene rs7903146 and type 2 diabetes mellitus with obesity in Chinese Han population. Methods: 216 patients with type 2 diabetes mellitus (T2DM), 92 males, 124 females, 194 normal controls, 89 males and 105 females. The polymorphism of TCF7L2 gene rs7903146 was measured by PCR-RFLP. PCR amplifier was used for amplification reaction, followed by polymorphism analysis of TCF7L2 gene: the reaction system was 20 μl, among which restriction endonuclease was 0.5 μl and PCR product was 7.5 μl. Restriction enzyme SspI (Fermentas) was used for PCR product and was bathed at 37°C for 16 h. The enzyme digestion products were detected and genotypes were identified by 2% agarose gel electrophoresis. The genotyping was repeated in 10% of the samples, and the genotyping rate was 100%. Height and weight were measured and BMI calculated. According to BMI, the experimental group was further divided into the obese group (n = 137, BMI > 25 kg/m2) and the normal body mass group (n = 79, BMI 2). Normal control group: BMI 2: FBG P P > 0.05). There was a significant difference in genotype frequency between the control group and the experimental group (χ2 = 17.382, P P > 0.05). Genotype frequency at BMI level was significantly different between the control group and the T2DM group (χ2 = 20.427, P = 0.001), but there was no significant difference in allele frequency distribution (P > 0.05). The TT type and TC + CC type were significantly different between the T2DM group and the control group (χ2 = 78.154, P = 0.006) and the T2DM obesity group and the control group (χ2 = 7.247, P = 0.009), but there was no significant difference between the T2DM normal body mass group and the control group (P > 0.05). In addition, there was no significant difference between TC type + TT type and CC type between the T2DM group and the control group and the T2DM obesity group and the control group (P > 0.05). Conclusion: There were significant differences in the genotype frequency and recessive inheritance pattern (TT/CC + TC) of rs7903146, suggesting that this SNP may be associated with the incidence of T2DM in obesity and insulin resistance.

Study on the polymorphism of PPAR-γ gene and preeclampsia susceptibility

Objective To investigate the correlation between peroxisome proliferator-activated receptor-gamma (PPAR-γ) gene polymorphism and preeclampsia (PE). Methods 110 PE patients and 110 normal pregnants who delivered in our hospital from May 2016 to October 2018 were selected as the study subjects. Detection of two loci of PPAR-γ gene by SNaPshot technique: rs10865710 and rs4684847. Results ⑴ rs10865710: The genotype frequencies of CC, CG and GG in the control group were 44.55%, 42.73% and 12.73%, respectively, and those in the PE group were 31.82%, 44.55% and 23.64%, respectively. There was a critical difference in the distribution of genotype frequencies between the two groups (χ2=5.975, P=0.050); The frequencies of C and G alleles were 65.91% and 34.09% in the control group, 54.09% and 45.91% in the PE group, respectively. There was significant difference in the frequency distribution of C and G alleles between the two groups (χ2=6.402, P=0.015). ⑵ rs4684847: the genotype frequencies of CC, CT and TT in control group were 94.55%, 5.45%, 0, and those in PE group were 84.55%, 15.45% and 0, respectively, with significant difference in the distribution of genotype frequencies between the two groups (χ2=5.875, P=0.015). The frequencies of C and T alleles in control group were 97.27%, 2.73% and those in PE group were 92.27% and 7.73%, respectively, with significant difference in allele frequency distribution between the two groups (χ2=5.551, P=0.030). ⑶ The frequency of GG genotype and G allele at rs10865710 locus in PE group was significantly higher than that in control group [OR (95% CI)=2.600 (1.190-5.679), P=0.021; OR (95% CI)=1.64 (1.117-2.411), P=0.015]. The frequencies of CT genotype and T allele at rs4684847 locus in PE group were significantly higher than those in control group [OR (95% CI)=3.168 (1.199-8.374), P=0.026; OR (95% CI)=2.987 (1.155-7.726), P=0.030]. Conclusions The single nucleotide polymorphisms of PPAR-γ gene rs10865710 and rs4684847 may be related to the susceptibility to preeclampsia in Chinese population. Key words: Pre-eclampsia; PPAR gamma; Polymorphism, genetic

A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree

The role of natural selection in shaping patterns of diversity is still poorly understood in the Neotropics. We carried out the first genome-wide population genomics study in a Neotropical tree, Handroanthus impetiginosus (Bignoniaceae), sampling 75,838 SNPs by sequence capture in 128 individuals across 13 populations. We found evidences for local adaptation using Bayesian correlations of allele frequency and environmental variables (32 loci in 27 genes) complemented by an analysis of selective sweeps and genetic hitchhiking events using SweepFinder2 (81 loci in 47 genes). Fifteen genes were identified by both approaches. By accounting for population genetic structure, we also found 14 loci with selection signal in a STRUCTURE-defined lineage comprising individuals from five populations, using Outflank. All approaches pinpointed highly diverse and structurally conserved genes affecting plant development and primary metabolic processes. Spatial interpolation forecasted differences in the expected allele frequencies at loci under selection over time, suggesting that H. impetiginosus may track its habitat during climate changes. However, local adaptation through natural selection may also take place, allowing species persistence due to niche evolution. A high genetic differentiation was seen among the H. impetiginosus populations, which, together with the limited power of the experiment, constrains the improved detection of other types of soft selective forces, such as background, balanced, and purifying selection. Small differences in allele frequency distribution among widespread populations and the low number of loci with detectable adaptive sweeps advocate for a polygenic model of adaptation involving a potentially large number of small genome-wide effects.

Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers.

Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources.

Increased Insulin following an Oral Glucose Load, Genetic Variation near the Melatonin Receptor MTNR1B, but No Biochemical Evidence of Endothelial Dysfunction in Young Asian Men and Women.

AimTo identify biochemical and genetic variation relating to increased risk of developing type 2 diabetes mellitus and cardiovascular disease in young, lean male and female adults of different ethnicities.MethodFasting blood and urine and non-fasting blood following oral glucose intake were analysed in 90 Caucasians, South Asians and South East/East Asians.ResultsThere were no differences in age, birthweight, blood pressure, body mass index, percent body fat, total energy, percentage of macronutrient intake, microalbumin, leptin, cortisol, adrenocorticotropic hormone, nitric oxide metabolites, C-reactive protein, homocysteine, tumor necrosis factor-α, interleukin-6, von Willebrand factor, vascular cell adhesion molecule-1, plasminogen activator inhibitor-1, and tissue plasminogen activator. Fasting total cholesterol (P = .000), triglycerides (P = .050), low density lipoprotein (P = .009) and non-fasting blood glucose (15 min) (P = .024) were elevated in South Asians compared with Caucasians, but there was no significant difference in glucose area under curve (AUC). Non-fasting insulin in South Asians (15–120 min), in South East/East Asians (60–120 min), and insulin AUC in South Asians and South East/East Asians, were elevated compared with Caucasians (P≤0.006). The molar ratio of C-peptide AUC/Insulin AUC (P = .045) and adiponectin (P = .037) were lower in South Asians compared with Caucasians. A significant difference in allele frequency distributions in Caucasians and South Asians was found for rs2166706 (P = 0.022) and rs10830963 (P = 0.009), which are both near the melatonin receptor MTNR1B.ConclusionsElevated non-fasting insulin exists in young South Asians of normal fasting glucose and insulin. Hepatic clearance of insulin may be reduced in South Asians. No current biochemical evidence exists of endothelial dysfunction at this stage of development. MTNR1B signalling may be a useful therapeutic target in Asian populations in the prevention of type 2 diabetes mellitus.

Association between LOXL1 gene polymorphisms and primary open angle glaucoma in Sichuan population

To investigate association between the lysyl oxidase-like 1 (LOXL1) gene single nucleotide polymorphism (SNP) and primary open-angle glaucoma (POAG) in Sichuan population. In this study,416 subjects with primary open-angle glaucoma and 997 normal controls were recruited.Three reported LOXL1 tag SNPs (rs1048661,rs3825942 and rs2165241) were genotyped by SNaPshot method. The study showed that the genotypes of LOXL1 rs1048661,rs3825942 and rs2165241 between POAG and control groups were not statistically significant (OR=1.085, 95%CI 0.92-1.28, P=0.578 for rs1048661; OR=1.059, 95%CI 0.82-1.37, P=0.846 for rs3825942; OR=1.006, 95%CI 0.77-1.32, P=0.966 for rs2165241, respectively). There were no significant difference in allele frequency distribution of LOXL1 rs1048661、rs3825942 and rs2165241 between POAG and normal controls (P=0.322, P=0.660, P=0.965). The results from the present study do not indicate the association of LOXL1 SNPs (rs1048661, rs3825942 and rs2165241) with POAG in Sichuan population.

Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)

Ex situ germ plasm collections of woody crops are necessary to ensure the optimal use of plant genetic resources. The fig tree (Ficus carica L.) germ plasm bank, consisting of 229 accessions, is located in Centro de Investigacion ‘La Orden’. Despite great progress in conservation, ex situ collections face size and organization problems. Core collections obtained from structured samples of bigger collections are a useful tool to improve germ plasm management. In this work, we used simple sequence repeat (SSR) markers to establish a core collection in this underutilised Mediterranean fruit tree species. Four approaches have been carried out (random sampling, maximization, simulated annealing and stepwise clustering) to determine the best method to develop a core collection in this woody plant. The genetic diversity obtained with each subset was compared with that of the complete collection. It was found that the most efficient way to achieve the maximum diversity was the maximization strategy, which, with 30 accessions, recovers all the SSR alleles and does not show significant differences in allele frequency distribution in any of the loci or in the variability parameters (H O, H E) between the whole and core collections. Thus, this core collection, a representative of most fig diversity conserved in the germ plasm bank, could be used as a basis for plant material exchange among researchers and breeders.

Genetic diversity within 5′upstream region of Toll-like receptor 8 gene reveals differentiation of riverine and swamp buffaloes

In this study the nucleotide diversity in the 5′untranslated region (UTR) of TLR8 gene in riverine as well as swamp buffaloes has been described. Analysis of the 5′UTR of TLR8 gene showed presence of two SNPs in this region, g.-139G>T and g.-128A>G. A PCR–RFLP assay designed for genotyping of g.-139G>T SNP across 667 samples from 2 buffalo populations revealed a striking difference in allele frequency distribution across the swamp and riverine buffaloes. The frequency of T allele was higher in swamp buffalo as compared to riverine buffalo, ranging from 0.71 to 1. The G allele on the other hand exhibited a higher frequency across all the Indian riverine buffalo breeds/populations. The principal component analysis revealed separate clusters for the riverine and swamp buffaloes, as expected; however, the riverine type Assamese buffalo population of eastern India formed a distinct cluster. Since most of the buffalo populations in the eastern region are swamp type, this demarcation may be related to the difference in immune response in riverine and swamp buffaloes. These preliminary results indicate that the genetic variation observed in 5′upstream region of TLR8 gene, which differentiates swamp and riverine buffalo, needs to be further explored for association with disease susceptibility in buffalo, an important dairy and meat animal of Southeast Asia.

DC-SIGN gene promoter variants and IVIG treatment response in Kawasaki disease

BackgroundGenetic variants in the inhibiting FcγRIIB mediate anti-inflammatory responses and influence IVIG refractoriness (IVIG-R). However, these variants are rare in Asian and Hispanic populations so other genes in the pathway could be potentially involved. IVIG is ineffective in mice lacking SIGN-R1, a related molecule to human DC-SIGN. Further, DC-SIGN is a known receptor for sialylated Fc, the component responsible for the anti-inflammatory action of IVIG. Thus, we hypothesized that DC-SIGN would also be involved in the pathway of IVIG response in Kawasaki Disease (KD) patients.FindingsA case-control approach was performed to examine the differential distribution of five single nucleotide polymorphisms (SNPs) in DC-SIGN promoter with IVIG-R among White (158 vs. 62), Asian (64 vs. 12) and Hispanic (55 vs. 20) KD patients. Distinct differences in allele frequency distributions of several variants in the DC-SIGN promoter were observed in the three ethnic groups. Further, Asians with the major allele “A” in rs2287886 were more likely (OR = 1.76, p = 0.04) to be IVIG non-responder, but this allele is a minor allele in other two ethnic groups, where the association was not apparent.ConclusionsDC-SIGN can potentially complement the role of FcγRIIB in the anti-inflammatory cascade involved in the IVIG response mechanism.

Association between MYH9 gene polymorphisms and membranous glomerulonephritis patients in Taiwan

Membranous glomerulonephritis (MGN) is a common cause of idiopathic nephrotic syndrome in adults end- stage renal disease in 25% of patients. MYH9 gene polymorphisms have been reported to be associated with several types of renal diseases. The objective of this study was to clarify the relationship between MYH9 gene polymorphisms and the pathogenesis of MGN. We investigated MYH9 gene polymorphisms (rs7078 and rs12107) and their association with MGN susceptibility in 400 Taiwanese individuals (135 MGN patients and 265 healthy controls). The results revealed a statistically significant difference in allele frequency distribution at the rs12107 between MGN patients and the control group (p = 0.04). In addition, individuals with the AA genotype at the rs12107 SNP who become MGN patients may have a higher risk of kidney failure than other MGN patients (adjusted odds ratio: 1.63; 95% confidence interval: 1.08-2.48, p = 0.02). A C-A haplotype was susceptible for development of MGN. Our data show that MYH9 (rs12107) polymorphism may be the underlying cause of MGN; hence the polymorphism examined in this study warrant further investigation.

Association of angiotensin-converting enzyme gene 2350 G/A polymorphism with diabetic retinopathy in Chinese Han population

The angiotensin-converting enzyme (ACE) gene is one of the most studied candidate genes related to diabetic retinopathy (DR). ACE 2350 G/A polymorphism (rs4343) is known among the polymorphisms of this gene to have the most significant effect on plasma ACE concentrations. The aim of the present study was to investigate the relationship between 2350 G/A polymorphism of ACE gene and the susceptibility of DR in Chinese Han population. A case-control study for 145 type 2 diabetes mellitus (DM) patients, including 63 type 2 DM without DR (NDR) and 82 type 2 DM with DR (DR), and 90 subjects of age, gender matched normal controls (NC group) was performed. ACE 2350 G/A genotypes were identified by polymerase chain reaction and restriction digestion in all study participants. The distribution of the ACE 2350 G/A genotypes (GG, GA, and AA) was 35.56, 45.55, and 18.89 % in the NC group, 28.57, 46.03, and 25.40 % in the NDR group, and 15.85, 46.34, and 37.81 % in the DR group, respectively. There were no significant differences in either genotype frequency distribution (P = 0.5266) or allele frequency distribution (P = 0.2425) between the NC group and NDR group. However, the distribution of genotype frequency (P = 0.0026) and allele frequency (P = 0.0003) in the DR group showed a significant difference when compared to that of NC group (P = 0.0075). Moreover, there was statistical difference in allele frequency distribution (P = 0.0328) between the DR group and the NDR group. No statistical differences were observed between ACE 2350 G/A polymorphism and the diabetes duration or types of DR. Results obtained in this study indicate that ACE 2350 G/A polymorphism is associated with DR in Han Chinese patients with type 2 DM.

CYP2D6Genotyping in Natives and Immigrants from the Emilia-Romagna Region (Italy)

Pharmacogenetic testing of drug metabolizing enzyme polymorphisms provides an important tool to improve prescribing decisions, avoiding therapeutic failure and adverse drug reactions. Cytochrome P450 2D6 isoform plays an important role in the metabolism of about 20%-25% of widely used clinical drugs. Interethnic differences in allele frequency distribution of the CYP2D6 gene are well established, but interethnic admixture, introducing variations in population ancestry and resulting in distinct levels of population structure, should be acknowledged in pharmacogenomic studies to avoid inappropriate extrapolation of CYP2D6 data. The aim of the present research was to characterize CYP2D6 polymorphism in a random sample of 122 natives and 175 immigrants from Africa, Asia, and South America living in the Emilia-Romagna region (Italy), considering the present scenario of immigration and back migration events, which is a source of admixture. The results are today consistent with the known interethnic genetic variation, but the observed significant divergence between natives and Africans or South-East Asians predicts that admixture will reshape the population structure and the native metabolic ratio curve requiring, for drug prescription and pharmacogenetics studies, an interdisciplinary approach applied in an appropriate biogeographical and anthropological frame.

A new single-nucleotide mutation (rs362719) of the reelin (RELN) gene associated with schizophrenia in female Chinese Han

Reelin is an extracellular signaling protein that plays an important role in the development of the central nervous system. Post-mortem studies have shown lower reelin protein levels in the brains of patients with schizophrenia and bipolar disorder compared with controls. Genetic studies have also shown that mutations in the reelin gene (RELN) increase the risk for schizophrenia and bipolar disorder. We evaluated whether an RELN gene variant, rs362719, which has been associated with increased susceptibility to bipolar disorder, is also associated with susceptibility to schizophrenia. We included 405 Chinese Han schizophrenia patients and 390 controls in our study. The polymorphism was genotyped by PCR and RFLP methods. We found a significant difference in allele frequency distribution (P< 0.05) between schizophrenia patients and controls. The frequency of the A allele was significantly higher in schizophrenia patients than in healthy controls. The effect of SNP rs362719 on allele distribution was significant in female (P < 0.05) but not in male participants (P = 0.473). Besides the gender factor, demographic and clinical characteristics of the rs362719 genotype groups were also analyzed using the chi-square test, but no significant differences were found. We conclude that rs362719 of the RELN gene is associated with susceptibility to schizophrenia in Chinese Han, possibly through a gender-specific mechanism. Further studies will be needed to confirm this genetic risk factor for schizophrenia.

Allele Frequencies of 10 Autosomal STR Loci from Chakma and Tripura Tribal Populations in Bangladesh

Allele frequencies of ten autosomal STR loci, D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, and FGA were investigated in Chakma and Tripura tribal populations of Bangladesh. In both the populations, all loci were in Hardy-Weinberg equilibrium except for FGA locus in Chakma and D21S11 in Tripura. All the loci were highly polymorphic in Chakma population with an observed heterozygosity (Ho) of >0.7 and moderately polymorphic in Tripura population (Ho > 0.6). However, both the population showed least polymorphism at TH01 locus (Ho < 0.6). A comparison between Chakma and Tripura population data revealed statistically significant differences in allele frequency distribution for most of the loci. A similar comparison with the mainstream Bengali population using previously published data from this lab also showed significant difference in allele frequency with these two tribal populations.

Evolutionary and Functional Analysis of Celiac Risk Loci Reveals SH2B3 as a Protective Factor against Bacterial Infection

Celiac disease (CD) is an intolerance to dietary proteins of wheat, barley, and rye. CD may have substantial morbidity, yet it is quite common with a prevalence of 1%-2% in Western populations. It is not clear why the CD phenotype is so prevalent despite its negative effects on human health, especially because appropriate treatment in the form of a gluten-free diet has only been available since the 1950s, when dietary gluten was discovered to be the triggering factor. The high prevalence of CD might suggest that genes underlying this disease may have been favored by the process of natural selection. We assessed signatures of selection for ten confirmed CD-associated loci in several genome-wide data sets, comprising 8154 controls from four European populations and 195 individuals from a North African population, by studying haplotype lengths via the integrated haplotype score (iHS) method. Consistent signs of positive selection for CD-associated derived alleles were observed in three loci: IL12A, IL18RAP, and SH2B3. For the SH2B3 risk allele, we also show a difference in allele frequency distribution (Fst) between HapMap phase II populations. Functional investigation of the effect of the SH2B3 genotype in response to lipopolysaccharide and muramyl dipeptide revealed that carriers of the SH2B3 rs3184504*A risk allele showed stronger activation of the NOD2 recognition pathway. This suggests that SH2B3 plays a role in protection against bacteria infection, and it provides a possible explanation for the selective sweep on SH2B3, which occurred sometime between 1200 and 1700 years ago.

A study of East Timor variability using the SNP forID 52-plex SNP panel

A set of 52 autosomal single nucleotide polymorphism (SNP) loci was analyzed in 46 unrelated individuals from the East Timor population using the forensic assay previously described by Sanchez et al. (2006) [J.J. Sanchez, C. Phillips, C. Børsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe Court, PM. Schneider, Á. Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713–1724]. Allele frequencies are presented for the 52 SNPs with all loci in Hardy–Weinberg equilibrium for the study population. Comparison with African, European, East Asian and Oceanian populations of the CEPH human genome diversity panel (CEPH-HGDP) revealed significant differences in allele frequency distributions between East Timor and each of the above population groups. Statistical parameters measuring forensic informativeness were also calculated and the values obtained reached comparable levels to those previously described for the other global population groups. This is the first study of variability in these SNPs in an Oceanian population outside of the CEPH-HGDP.