Significant Linkage Disequilibrium Research Articles

Identification and tagging of QTLs for arjunolic acid in Terminalia arjuna among Indian sub populations by association mapping and linkage disequilibrium

The content of cardiotonic arjunolic acid in Terminalia arjuna vary among the population. We studied the population structure and the association between the molecular markers and its active ingredient among 140 plants collected from various agroclimatic zones in India. Large variation was detected for the arjunolic acid in this study showing suitableness of the genotypes. The maximum arjunolic acid content was approximately 238 per cent higher than the lowest value for the genotypes and was found to be considerably correlated to bark thickness, bark fresh weight and bark dry weight. The population structure studies described the existence of nine subpopulations. As the distance increased between the associated markers, Linkage disequilibrium (LD) reduction and a considerable reduction in LD decay was ascertained. Eleven QTL regions associated with arjunolic acid were identified from a genome-wide marker-trait association study. Fine-scale resolution detected significant LD among 3.4 per cent RAPD paired loci and 8.7 per cent ISSR paired loci and 6.7 per cent RAPD paired loci and 13.3 per cent ISSR paired loci. Importantly LD decay found to start at a distance of >20bp from the loci on the genome of T. arjuna accessions. Finally, association mapping (AM) in arjun tightly linked to OPT09 which can be a possible substitute to QTL mapping methodology.

Development of microsatellite markers in Betula costata (Betulaceae) by next-generation sequencing and cross-species transferability test.

This study was conducted to develop the first species-specific microsatellite markers in Betula costata. A total of 178 primers were designed from 95,755 contigs and screened in two B. costata populations sampled from Mt. Hwaaksan and Mt. Gyebangsan. A total of 16 polymorphic microsatellite loci were selected and used for population genetic characterization. The average values of observed heterozygosity (HO) and expected heterozygosity (HE) of the Mt. Hwaaksan population were 0.488 and 0.493, respectively. The average values of HO and HE in the Mt. Gyebangsan population were 0.492 and 0.481, respectively. The null allele frequency was less than 0.2 in all loci. No significant linkage disequilibrium was detected in all combinations of loci. In addition, 26 polymorphic markers were selected by cross-species transferability test to B. costata using the microsatellite markers developed in four other Betula species. The cross-species transferability of the microsatellite markers developed in B. costata was conducted in two other Betula species. The transferability was 75% in B. ermanii and 100% in B. davurica. Therefore, the microsatellite markers developed and characterized in this study were expected to be useful for further genetic studies in B. costata and related species in the genus Betula.

Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species.

BackgroundThe presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with ~ 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesii Mirb. (Franco)) and Interior spruce (Picea glauca (Moench) Voss x Picea engelmannii Parry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200–50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F1 families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada.ResultsAs marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000–15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size.ConclusionsAlthough possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits.

Assessment of risk conferred by coding and regulatory variations of TMPRSS2 and CD26 in susceptibility to SARS-CoV-2 infection in human

At present, more than 200 countries and territories are directly affected by the coronavirus disease-19 (COVID-19) pandemic. Incidence and case fatality rate are significantly higher among elderly individuals (age > 60 years), type 2 diabetes and hypertension patients. Cellular receptor ACE2, serine protease TMPRSS2 and exopeptidase CD26 (also known as DPP4) are the three membrane bound proteins potentially implicated in SARS-CoV-2 infection. We hypothesised that common variants from TMPRSS2 and CD26 may play critical role in infection susceptibility of predisposed population or group of individuals. Coding (missense) and regulatory variants from TMPRSS2 and CD26 were studied across 26 global populations. Two missense and five regulatory SNPs were identified to have differential allelic frequency. Significant linkage disequilibrium (LD) signature was observed in different populations. Modelled protein‒protein interaction (PPI) predicted strong molecular interaction between these two receptors and SARS-CoV-2 spike protein (S1 domain). However, two missense SNPs, rs12329760 (TMPRSS2) and rs1129599 (CD26), were not found to be involved physically in the said interaction. Four regulatory variants (rs112657409, rs11910678, rs77675406 and rs713400) from TMPRSS2 were found to influence the expression of TMPRSS2 and pathologically relevant MX1. rs13015258 a 5′ UTR variant from CD26 have significant role in regulation of expression of key regulatory genes that could be involved in SARS-CoV-2 internalization. Overexpression of CD26 through epigenetic modification at rs13015258-C allele was found critical and could explain the higher SARS-CoV-2 infected fatality rate among type 2 diabetes.Electronic supplementary materialThe online version of this article (10.1007/s12041-020-01217-7) contains supplementary material, which is available to authorized users.

Multilocus sequence typing of Enterocytozoon bieneusi in crab-eating macaques (Macaca fascicularis) in Hainan, China

BackgroundEnterocytozoon bieneusi is one of common intestinal pathogens in humans and animals including non-human primates (NHPs). Many zoonotic pathogens including E. bieneusi have been found in these animals. However, there are few studies on the population structure of E. bieneusi in NHPs. To infer the gene diversity and population genetics of E. bieneusi, we selected 88 E. bieneusi-positive samples from crab-eating macaques for multilocus characterizations in this study.MethodsThe E. bieneusi isolates examined belonged to three common genotypes with different host ranges by sequence analysis of the ribosomal internal transcribed spacer (ITS): Type IV (n = 44), Macaque3 (n = 24) and Peru8 (n = 20). They were further characterized by sequence analysis at four microsatellite and minisatellite loci (MS1, MS3, MS4 and MS7). DnaSP, Arlequin and LIAN were used to analyze the sequence data together with those from the ITS locus to infer the population genetics. Subpopulation structure was inferred using phylogenetic and STRUCTURE analyses.ResultsSeventy-two (81.8%), 71 (80.7%), 76 (86.4%) and 79 (89.8%) samples were amplified and sequenced successfully at the MS1, MS3, MS4 and MS7 loci, respectively, with 53 having sequence data at all five MLST loci including ITS. Altogether, 33 multilocus genotypes (MLGs) were produced based on concatenated sequences from the 53 samples. In phylogenetic analyses of sequences and allelic data, four major subpopulations (SPs) were observed with different ITS genotypes in each of them: Type IV and Peru8 in SP1 and SP2; Type IV, Macaque3 and Peru8 in SP3; and Type IV and Macaque3 in SP4. SP3 and SP4 were phylogenetically related and might be NHP-specific based on the fact that Macaque3 is mostly found in NHPs. A strong linkage disequilibrium (LD) was observed among the multilocus sequences and allelic data.ConclusionsThe significant LD in the multilocus sequence analysis indicated the presence of an overall clonal population structure of E. bieneusi in crab-eating macaques. The inconsistent segregation of MLGs among ITS genotypes suggested some occurrence of genetic recombination. These observations should improve our understanding of the population genetics of E. bieneusi in NHPs.

DNA methylation profiling identifies a high effect genetic variant for lipoprotein(a) levels

ABSTRACT Changes in whole blood DNA methylation levels at several CpG sites have been associated with circulating blood lipids, specifically high-density lipoprotein and triglycerides. This study performs a discovery and validation epigenome-wide association study (EWAS) for circulating lipoprotein(a) [Lp(a)], an independent risk factor for cardiovascular diseases. Whole-blood DNA methylation profiles were assessed in a cohort of 1020 elderly individuals using the Illumina EPIC array and independent validation in 359 elderly males using the Illumina 450 k array. Plasma Lp(a) was measured using an apolipoprotein(a)-size-independent ELISA. Epigenome-wide rank regression analysis identified and validated a single CpG site, cg17028067 located in intron 1 of the LPA gene, that was significantly associated with plasma Lp(a) levels after correction for multiple testing. Genotyping of the site identified a relatively uncommon SNP (rs76735376, MAF <0.02) at the CpG site that largely explained the observed methylation effect. Rs76735376 is an expression quantitative trait loci for the LPA gene and could affect expression by altering enhancer activity. This EWAS for plasma Lp(a) identified a single CpG site within LPA. This association is due to an uncommon, but highly effective genetic variant, which was not in significant linkage disequilibrium with other variants known to influence Lp(a) levels or apo(a) isoform size. This study highlights the utility of CpG site methylation to identify potentially important genetic associations that would not be readily apparent in a comparable size genetic association study.

A small NGS-SNP panel of ancestry inference designed to distinguish African, European, East, and South Asian populations.

In this study, a small set of ancestry informative SNPs was selected to differentiate African, European, East and South Asian samples, which was detected by the next-generation sequencing technology. A total of 127 Chinese Shaanxi Han individuals were collected as test samples. No statistically significant linkage disequilibrium of any pair of loci or departure from Hardy-Weinberg equilibrium of each locus was observed in the test population. To evaluate the performance of ancestry assignment using this panel, admixture analysis, principal component analysis, and likelihood ratio calculations were conducted based on the 1000 genome data and test samples. All populations were clustered into four groups, African, European, South and East Asian populations, which were consistent with their geographical origins. The pairwise fixation index (FST ) between populations from different continental groups ranged from 0.140 to 0.621 with average 0.415, and the pairwise FST between populations from the same continent ranged from 0.000 to 0.056 with average 0.012. The likelihood ratio results of 125 test individuals indicated that their ancestry components were highly possible from East Asia. In conclusion, this small set of ancestry informative SNPs can be used as a reliable tool to identify and quantify ancestry components of unknown samples.

Genome survey and development of polymorphic microsatellite loci for Sillago sihama based on Illumina sequencing technology.

In this study, we first conducted a genome survey assay for Sillago sihama by Illumina sequencing platform, and then developed 15 polymorphic microsatellite loci in a wild population. A total of 129.46Gb raw data were obtained, of which 115.07Gb were clean data, with a sequencing depth of 179.3-folds. This genome was estimated to be 522.6Mb in size, with the heterozygosity, repeat content and GC content being 0.63%, 21% and 44%. A total of 630,028 microsatellites were identified from the genome, of which, dinucleotide repeat was the most abundant (56.80%), followed by mononucleotide repeat (30.23%). Furthermore, 60 pairs of primers were designed and synthesized based on microsatellite sequences, of which 15 were polymorphic in a wild population. A total of 91 alleles were found, with an average of 6.07 per locus. Number of alleles, observed and expected heterozygosity per locus ranged from two to 13, from 0.250 to 0.862, and from 0.396 to 0.901, respectively. Twelve loci were highly informative (PIC > 0.5), and the others were medium informative (0.25 < PIC < 0.5). Seven loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0033). No significant linkage disequilibrium was detected between loci pairs. This study provided a large number of genomic resources and 15 polymorphic microsatellite loci that should be helpful for the further genetic studies in S. sihama.

Isolation and characterization of 30 SNP markers in Guangdong bream (Megalobrama terminalis) by next-generation sequencing

Guangdong bream (Megalobrama terminalis) is an economically important species. However, wild Guangdong bream resources have declined sharply in recent years as a result of human disturbance and habitat destruction. Thus, it is crucial that the current resources of Guangdong bream are protected. In this study, 30 novel single nucleotide polymorphism (SNP) markers were developed based on restriction site-associated DNA sequencing (RAD-seq). The results showed that the minor allele frequency varied from 0.021 to 0.489 and that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.043 to 0.638 and 0.042 to 0.506, respectively. The PIC ranged from 0.041 to 0.375. Seven loci showed significant deviations from the HWE after Bonferroni correction (p < 0.05), but no significant linkage disequilibrium was found. These SNP markers will serve as a useful tool for genetic studies and population evaluation aimed at the conservation of Guangdong bream.

Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection

In order to integrate genomics in breeding and development of drought-tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used 3249 diversity array technology sequencing (DArTSeq) markers for a genetic analysis of 125 ICRISAT groundnut mini core collection evaluated in 2015 and 2017 for genome-wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD). Marker-trait association (MTA) analysis, probability values, and percent variation modelled by the markers were calculated using the GAPIT package via the KDCompute interface. The LD analysis showed that about 36% of loci pairs were in significant LD (p &lt; 0.05 and r2 &gt; 0.2) and 3.14% of the pairs were in complete LD. The MTAs studies revealed 20 significant MTAs (p &lt; 0.001) with 11 markers. Four MTAs were identified for leaf area index, 13 for canopy temperature, one for chlorophyll content and two for normalized difference vegetation index. The markers explained 20.8% to 6.6% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. This could be due to a common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance after further validation.

HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies and phylogenetic analysis of Bahraini population

The origin of Arab-speaking population is classified according to their geographical location, ethnic background, and historical influx of nearby and distant populations. Data on HLA class I and class II loci in (Arabian Peninsula) Bahraini population are lacking. We analyzed HLA genetic profile of Bahrainis with neighboring communities, and with Levantines, North Africans, Sub-Saharans, Europeans, and Asians, using genetic distances, neighbor-joining dendrograms, correspondence and haplotype analysis. HLA class I and class II genotyping were done by high resolution PCR-SSP in 175 Bahraini subjects. In total, 19 HLA-A, 33 HLA-B, 15 HLA-C, 14 DRB1 and 7 DQB1 alleles were identified. The most common class I alleles were A*02:01:01 (18.3%), A*01:01:01(15.4%), B*35:01:02 (12.9%), C*12:01:01 (15.1%), and C*04:01:01 (14.9%), while DRB1*03:01:01 (18.0%), DQB1*02:01:01 (29.1%), and DQB1*05:01:01 (24.9%) were the most frequent class II alleles. Significant linkage disequilibrium was seen between all HLA loci pairs. DRB1*03:01:01-DQB1*02:01:01 (15.18%) was the most frequent two-locus haplotype. Significant negative Fnd values were observed, indicating balancing selection at studied loci. Bahrainis appear to be related to Western Mediterranean (North Africans, Iberians and French), but relatively distinct from Levantines (Palestinians, Lebanese, and Jordanians) and Sub-Saharans. This indicates limited genetic contribution of Levantine Arabs and Sub-Saharans to the Bahraini gene pool.

Cross-species testing of nuclear markers in Pelophylax water frogs in Greece and examination of their power to detect genetic admixture

Abstract The genus Pelophylax has been considered a model organism for understanding hybridization. Despite being the most diverse within the Western Palearctic group of Pelophylax, the ridibundus/bedriagae lineage that includes six species, remains largely understudied, revealing many knowledge gaps in regards to their evolution and conservation. Using genetic data from populations among species inhabiting contact zones could prove vital in filling these gaps. We tested 17 microsatellite markers for cross-species amplification in mainland Pelophylax species distributed in southern Balkans and evaluated their power to successfully detect population/species structure. Importantly, we examined their potential for identifying hybrids and backcrosses between known hybridized species. We detected 12 highly polymorphic loci that cross-amplified all species that showed no significant Linkage Disequilibrium and were able to discriminate among species and between parental and hybrids. We suggest their future use in genetic studies for the genus Pelophylax in Greece, including the identification of contact zones.

Triple Haplotypes of the TP53 Gene in Patients with Diffuse Small B-Cell Lymphoma

The role of genetic susceptibility to the development of lymphoma is confirmed by the accumulating data on common genetic variants of the genes involved in lymphomogenesis. The varieties of disease variants, as well as the small effect of each of the polymorphisms, require the analysis of these markers in individual histological lymphoma subtypes in haplotype groups. This study was carried out to analyze the frequencies of rs1042522, rs1625895, and rs17878362, their triple haplotypes, and linkage disequilibrium in patients with diffuse small B-cell lymphoma and a control group. The absence of pronounced linkage disequilibrium between the rs17878362, rs1042522, and rs1625895 markers of the TP53 gene in the population control sample was revealed. At the same time, data on significant linkage disequilibrium between rs1625895 and rs1042522, as well as rs1625895 and rs17878362, and on moderate linkage disequilibrium between rs17878362 and rs1042522 in the group of patients with lymphoma were obtained. An association of the haplotype wArgG in the homozygous state with a predisposition to the development of diffuse small B-cell lymphoma was found.

Interleukin-1 single nucleotide polymorphisms and risk of systemic lupus erythematosus among Iraqi patients

Present case-control study explored the association between five single nucleotide polymorphisms (SNPs) of interleukin-1 (IL-1) gene family (IL1A−889; rs1800587, IL1B−511; rs16944, IL1B+3962; rs1143634, IL1Rpsti 1970; rs2234650 and IL1RAmspa 11,100; rs315952) and SLE. A sample of 103 Iraqi female patients and 113 healthy matched females were investigated. Serological testing revealed that 91.1 and 88.9% of patients were seropositive for anti-nuclear and anti-double-stranded DNA antibodies, respectively, while none of the control females were seropositive. Serum level of C3 (54 vs. 108 mg/dL) and C4 (5 vs. 21 mg/dL) showed a significant decreased median in patients compared to control. Inspecting IL1 gene SNPs demonstrated a significant increased frequency of IL1A−889C allele in patients compared to control (72.8 vs.56.0%, odds ratio = 1.94, 95% confidence interval = 1.30–2.91), while T allele frequency was significantly decreased (27.2 vs.42.0%). For IL1B−511, IL1B+3962, IL1Rpsti 1970 and IL1RAmspa 11,100 SNPs, allele and genotype frequencies showed no significant variation between patients and control. A significant two-locus linkage disequilibrium (LD) was recorded between IL1B−511 and IL1RAmspa 11,100 SNPs in SLE patients only (log of likelihood odds ratio = 5.69, correlation coefficient = 0.241, LD coefficient = 0.517). Five-locus haplotype frequency estimation revealed that CCCTC and CCTCT haplotypes were positively associated with SLE risk. It is concluded that IL1A−889 SNP is associated with susceptibility to SLE, while, IL1B−511, IL1B+3962, IL1Rpsti 1970 and IL1RAmspa 11,100 SNPs may have no influence on SLE risk. Specific allelic combinations (haplotypes) between the five SNPs may also have a susceptibility role in SLE.

The genome-wide risk alleles for psychiatric disorders at 3p21.1 show convergent effects on mRNA expression, cognitive function, and mushroom dendritic spine.

Schizophrenia and bipolar disorder (BPD) are believed to share clinical features, etiological factors, and disease pathologies (such as impaired cognitive functions and dendritic spine pathology). Meanwhile, there is growing evidence of shared genetic risk between schizophrenia and BPD, despite that our knowledge of the functional risk variations and biological mechanisms is still limited. Here, we conduct summary data-based Mendelian randomization (SMR) analyses through combining the statistical data from genome-wide association studies (GWAS) of both schizophrenia and BPD and multiple expression quantitative trait loci (eQTL) datasets of the human brain dorsolateral prefrontal cortex (DLPFC) tissues. These integrative investigations identify a lead risk locus at the chromosome 3p21.1 region, which contains numerous single-nucleotide polymorphisms (SNPs) in varied linkage disequilibrium (LD) and encompasses more than 20 genes. Further analyses suggest that many SNPs at 3p21.1 are significantly associated with both schizophrenia and BPD, and even depression, and the psychiatric risk alleles at 3p21.1 are correlated with mRNA expression of multiple genes such as NEK4, GNL3, and PBRM1. We also identify a 335-bp functional Alu polymorphism rs71052682 in significant LD with the psychiatric GWAS risk SNP rs2251219, and confirm the regulatory effects of this Alu polymorphism on transcription activities. We then explore the involvement of the 3p21.1 locus in the common clinical features and etiology of these illnesses. We reveal that psychiatric risk alleles at 3p21.1 in low-to-high LD consistently predict worse cognitive functions in humans, and manipulating the gene expression (NEK4, GNL3, and PBRM1) linked with higher genetic risk could reduce the density of mushroom dendritic spines in rat primary cortical neurons, mirroring the spine pathology in the prefrontal cortex of psychiatric patients. Our results find that, although the risk alleles at 3p21.1 are in low-to-moderate LD spanning a large genomic area, their underlying biological mechanisms in psychiatric disorders likely converge. These results provide essential insights into the neural mechanisms underlying the chromosome 3p21.1 risk locus in the shared pathological and etiological features of both schizophrenia and BPD.

&lt;p class="Body"&gt;&lt;strong&gt;Development and characterization of five microsatellite loci for the hard tick &lt;em&gt;Hyalomma marginatum&lt;/em&gt; (Acari: Ixodidae), through next generation sequencing&lt;/strong&gt;&lt;/p&gt;

Hyalomma marginatum is a hard tick species of medical and veterinary importance that is widely distributed throughout Turkey. In this study, five novel polymorphic microsatellite markers were isolated and developed from partial genome information using the Hiseq Illumina paired end technology. A total of 20,943,321 reads were obtained from vegetation collected specimens, 103 primer pairs were randomly selected for the analysis and 62 of them were tested for polymorphism. Seventy five specimens from nine different localities of Turkey were genotyped. Markers for selected loci were tested using labeled primers on capillary electrophoresis. Five loci were successfully scored and used to analyze genetic diversity. The number of alleles per locus ranged from 4 to 7, with an average of 5.4 alleles per locus. The average observed and expected heterozygosity values were 0.314 and 0.468, respectively. Two loci deviated significantly from Hardy-Weinberg expectations. No significant linkage disequilibrium was detected between loci. This study is the first attempt to generate genome sequence data and to develop SSR markers for H. marginatum. These markers will be useful to understand the taxonomic status of this vector, its population dynamics, and spatial distributions as well as mechanisms underlying Crimean Congo Heamorrhagic Fever transmission and the development and implementation of well-designed prevention strategies.

The biology of IncI2 plasmids shown by whole-plasmid multi-locus sequence typing

IncI2 type plasmids are medium-sized (~55–80 kb) conjugative plasmids that have been found carrying important antimicrobial resistance genes but have also been frequently found as cryptic plasmids. The DNA sequences for 147 fully sequenced IncI2 plasmids were studied by a whole-plasmid multi-locus sequence typing (wpMLST) scheme. A total of 171 loci were identified of which 52 were considered core (carried by greater than 95% of the plasmids). Most of the plasmids carrying the antimicrobial gene mcr-1 were in a distinct clade while most of the antimicrobial gene free plasmids were more distantly related. However, the host strains of bacteria were disparate for both groups of plasmids, showing that conjugal transfer of IncI2 plasmid is frequent. The mcr-1 gene was likely to have been introduced into IncI2 plasmids multiple times. It was also observed that the genes for conjugation showed significant linkage disequilibrium despite substantial diversity for most of those genes. Genes associated with biofilm formation were also among the core genes. The core genes can be considered the cohesive unit that defines the IncI2 plasmid group. Given the role conjugation can play in biofilm formation, it was concluded that conjugation is an active survival strategy for IncI2 plasmids. The IncI2 plasmid will have selective advantage when the plasmid-bearing bacteria are introduced to a new animal host that carries potential conjugal mates.

A multilocus sequence typing scheme of Pseudomonas putida for clinical and environmental isolates

Pseudomonas putida is a bacterium commonly found in soils, water and plants. Although P. putida group strains are considered to have low virulence, several nosocomial isolates with carbapenem- or multidrug-resistance have recently been reported. In the present study, we developed a multilocus sequence typing (MLST) scheme for P. putida. MLST loci and primers were selected and designed using the genomic information of 86 clinical isolates sequenced in this study as well as the sequences of 20 isolates previously reported. The genomes were categorised into 68 sequence types (STs). Significant linkage disequilibrium was detected for the 68 STs, indicating that the P. putida isolates are clonal. The MLST tree was similar to the haplotype network tree based on single nucleotide morphisms, demonstrating that our MLST scheme reflects the genetic diversity of P. putida group isolated from both clinical and environmental sites.

Programmed cell death 1 gene polymorphism as a possible risk for systemic lupus erythematosus in Egyptian females.

Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease with a suggested genetic basis. The newly identified human programmed cell death 1 gene could be associated with SLE susceptibility. We aimed to investigate the association between programmed cell death 1 polymorphism (PD1.3G/A (rs11568821) and PD1.5C/T (rs2227981)) with the risk of SLE in the Egyptian female population. This retrospective case-control study included 150 Egyptian females; 70 patients diagnosed to have SLE and 80 age-matched healthy controls. The two single nucleotide polymorphisms of the pdcd1 gene were genotyped by allelic discrimination through TaqMan real-time polymerase chain reaction. The PD1.3GG genotype and G allele as well as the PD1.5CC genotype were significantly more frequent in SLE patients (67.1%; p = 0.023, 82.1%; p = 0.0021, 62.9%; p = 0.0287 respectively). The GC haplotype was the most common haplotype among SLE patients (70.77%) with a reported significant linkage disequilibrium between the two studied polymorphisms (p = 0.0041). Although most of the studies showed significant association of SLE with the minor alleles, we reported a significant association between the dominant genotypes (PD1.3GG and PD1.5CC) as well as the major G allele with the risk of SLE among Egyptian females.

Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia

While many studies have been undertaken of Middle Eastern populations using autosomal STR profiling by capillary electrophoresis, little has so far been published from this region on the forensic use of massively parallel sequencing (MPS). Here, we carried out MPS of 27 autosomal STRs and 91 identity-informative SNPs (iiSNPs) with the Verogen ForenSeq™ DNA Signature Prep Kit on a representative sample of 89 Saudi Arabian males, and analysed the resulting sequence data using Verogen’s ForenSeq Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0. This revealed sequence variation in the composition of complex STR arrays, and SNPs in their flanking regions, which raised the number of STR alleles from 238 distinct length variants to 357 sequence sub-variants. Similarly, between one and three additional polymorphic sites were observed within the amplicons of 37 of the 91 iiSNPs, forming up to six microhaplotypes per locus. These further enhance discrimination compared to the biallelic target SNP data presented by the primary UAS interface. In total, we observed twenty-two STR alleles previously unrecognised in the STRait Razor v3.0 default allele list, along with nine SNPs flanking target iiSNPs that were not highlighted by the UAS. Sequencing reduced the STR-based random match probability (RMP) from 2.62E-30 to 3.49E-34, and analysis of the iiSNP microhaplotypes reduced RMP from 9.97E-37 to 6.83E-40. The lack of significant linkage disequilibrium between STRs and target iiSNPs allowed the two marker types to be combined using the product rule, yielding a RMP of 2.39E-73. Evidence of consanguinity was apparent from both marker types. While TPOX was the only locus displaying a significant deviation from Hardy-Weinberg equilibrium, 23 out of 27 STRs and 63 out of 91 iiSNPs showed fewer than expected heterozygotes, demonstrating an overall homozygote excess probably reflecting the high frequency of first-cousin marriages in Saudi Arabia. We placed our data in a global context by considering the same markers in the Human Genome Diversity Panel (HGDP), revealing that the Saudi sample was typical of Middle Eastern populations, with a higher level of inbreeding than is seen in most European, African and Central/South Asian populations, correlating with known patterns of endogamy. Given reduced levels of diversity within endogamous groups, the ability to combine the discrimination power of both STRs and SNPs offers significant benefits in the analysis of forensic evidence in Saudi Arabia and the Middle East region more generally.