Evidence For Genetic Variation Research Articles

Molecular Genetic Screening of Neonatal Intensive Care Units: Hyperbilirubinemia as an Example.

ObjectiveTo explore the clinical value of newborn genomic screening (nGS) for neonatal intensive care units (NICU) infants (taking neonatal hyperbilirubinemia as an example).MethodsDried blood spots (DBSs) were collected after 72 hours of birth. The tandem mass spectrometry (TMS) screening and Angel Care genomic screening (GS, based on Targeted next-generation sequencing) were performed at the same time.ResultsNinety-six hyperbilirubinemia newborns were enrolled in this study and none was identified with inborn errors of metabolism (IEM) by TMS, while 6 infants (6.25%, 6/96) were suspected to have a genetic disorder by Angel Care, including 2 cases of glucose-6-phosphate dehydrogenase deficiency (G6PD), and 1 case of maple syrup urine disease type 1B (MSUD1B), autosomal recessive deafness 1A (DFNB1A), Leber hereditary optic neuropathy (LHON), thyroid dyshormonogenesis 6 (TDH6) each. In addition, 44 infants (45.8%) were detected having at least one variant which conferred a carrier status for a recessive childhood-onset disorder. A total of 33 out of 60 variants (55.0%) reported for carrier status were pathogenic (P), 24 (40.0%) were likely pathogenic (LP), and 3 variants were variant of uncertain significance (VUS). Top six common genes of carrier status were GJB2, DUOX2, PRODH, ATP7B, SLC12A3, SLC26A4. Two newborns showed abnormalities in elementary screening of TMS, but were confirmed as false positive after recall. Their results of Angel Care did not found abnormality.ConclusionUsing neonatal hyperbilirubinemia as an example, genome sequencing screening can find more evidence of genetic variation in NICU newborns, and “Angel Care” is an effective method.

Comparative genomics of ST5 and ST30 methicillin-resistant Staphylococcus aureus sequential isolates recovered from paediatric patients with cystic fibrosis

Staphylococcus aureus chronic airway infection in patients with cystic fibrosis (CF) allows this pathogen to adapt over time in response to different selection pressures. We have previously shown that the main sequence types related to community-acquired methicillin-resistant S. aureus (MRSA) infections in Argentina – ST5 and ST30 – are also frequently isolated from the sputum of patients with CF, but in these patients they usually display multi-drug antimicrobial resistance. In this study, we sequenced the genomes of MRSA from four paediatric CF patients with the goal of identifying mutations among sequential isolates, especially those possibly related to antimicrobial resistance and virulence, which might contribute to the adaptation of the pathogen in the airways of patients with CF. Our results revealed genetic differences in sequential MRSA strains isolated from patients with CF in both their core and accessory genomes. Although the genetic adaptation of S. aureus was distinct in different hosts, we detected independent mutations in thyA, htrA, rpsJ and gyrA – which are known to have crucial roles in S. aureus virulence and antimicrobial resistance – in isolates recovered from multiple patients. Moreover, we identified allelic variants that were detected in all of the isolates recovered after a certain time point; these non-synonymous mutations were in genes associated with antimicrobial resistance, virulence, iron scavenging and oxidative stress resistance. In conclusion, our results provide evidence of genetic variability among sequential MRSA isolates that could be implicated in the adaptation of these strains during chronic CF airway infection.

An Overview of Genomic Biomarker Use in Cardiovascular Disease Clinical Trials.

Clinical trial designs targeting patient subgroups with certain genetic characteristics may enhance the efficiency of developing drugs for cardiovascular disease (CVD). To evaluate the extent to which genetic knowledge translates to the CVD pipeline, we analyzed how genomic biomarkers are utilized in trials. Phase II and III trial protocols for investigational new drugs for CVD and risk factors were evaluated for prospective and exploratory genomic biomarker use; drug targets were evaluated for the presence of evidence that genetic variations can impact CVD risk or drug response. We identified 134 programs (73 unique drug targets) and 147 clinical trials. Less than 1% (n=1/147) trials used a genomic biomarker prospectively for in-trial enrichment despite 32% (n=23/73) of the drug targets having evidence of genetic variations. Additionally, 46% (n=68/147) of the trials specified exploratory biomarker use. The results highlight an opportunity for more targeted CVD drug development by leveraging genomic biomarker knowledge.

Pharmacogenetic Factors Affecting Asthma Treatment Response. Potential Implications for Drug Therapy

Asthma is a frequent disease, mainly characterized by airway inflammation, in which drug therapy is crucial in its management. The potential of pharmacogenomics testing in asthma therapy has been, to date, little explored. In this review, we discuss pharmacogenetic factors affecting asthma treatment, both related to drugs used as controller medications for regular maintenance, such as inhaled corticosteroids, anti-leukotriene agents, long-acting beta-agonists, and the new biologic agents used to treat severe persistent asthma. In addition, we discuss current pharmacogenomics knowledge for rescue medications provided to all patients for as-needed relief, such as short-acting beta-agonists. Evidence for genetic variations as a factor related to drugs response has been provided for the following genes and groups of drugs: Inhaled corticosteroids: FCER2; anti-leukotriene agents: ABCC1, and LTC4S; beta-agonists: ADRB2. However, the following genes require further studies confirming or rejecting association with the response to asthma therapy: ADCY9, ALOX5, ARG1, ARG2, CRHR1, CRHR2, CYP3A4, CYP3A5, CYSLTR1, CYSLTR2, GLCCI1, IL4RA, LTA4H, ORMDL3, SLCO2B1, SPATS2L, STIP1, T, TBX21, THRA, THRB, and VEGFA. Although only a minority of these genes are, at present, listed as associated with drugs used in asthma therapy, in the Clinical Pharmacogenomics Implementation Consortium gene-drug pair list, this review reveals that sufficient evidence to start testing the potential of clinical pharmacogenomics in asthma therapy already exists. This evidence supports the inclusion in pilot pharmacogenetics tests of at least four genes. Hopefully these tests, if proven useful, will increase the efficiency and the safety of asthma therapy.

Evidence for Genetic Contribution to Variation in Posttraumatic Osteoarthritis in Mice.

Recombinant inbred mouse strains generated from an LG/J and SM/J intercross offer a unique resource to study complex genetic traits such as osteoarthritis (OA). We undertook this study to determine the susceptibility of 14 strains to various phenotypes characteristic of posttraumatic OA. We hypothesized that phenotypic variability is associated with genetic variability. Ten-week-old male mice underwent surgical destabilization of the medial meniscus (DMM) to induce posttraumatic OA. Mice were killed 8 weeks after surgery, and knee joints were processed for histology to score cartilage degeneration and synovitis. Micro-computed tomography was used to analyze trabecular bone parameters including subchondral bone plate thickness and synovial ectopic calcifications. Gene expression in the knees was assessed using a QuantiGene Plex assay. Broad-sense heritability ranged from 0.18 to 0.58, which suggested that the responses to surgery were moderately heritable. The LGXSM-33, LGXSM-5, LGXSM-46, and SM/J strains were highly susceptible to OA, while the LGXSM-131b, LGXSM-163, LGXSM-35, LGXSM-128a, LGXSM-6, and LG/J strains were relatively OA resistant. This study was the first to accomplish measurement of genetic correlations of phenotypes that are characteristic of posttraumatic OA. Cartilage degeneration was significantly positively associated with synovitis (r = 0.83-0.92), and subchondral bone plate thickness was negatively correlated with ectopic calcifications (r = -0.59). Moreover, we showed that 40 of the 78 genes tested were significantly correlated with various OA phenotypes. However, unlike the OA phenotypes, there was no evidence for genetic variation in differences in gene expression levels between DMM-operated and sham-operated knees. For these mouse strains, various characteristics of posttraumatic OA varied with genetic composition, which demonstrated a genetic basis for susceptibility to posttraumatic OA. The heritability of posttraumatic OA was established. Phenotypes exhibited various degrees of correlations; cartilage degeneration was positively correlated with synovitis, but not with the formation of ectopic calcifications. Further investigation of the genome regions that contain genes implicated in OA, as well as further investigation of gene expression data, will be useful for studying mechanisms of OA and identifying therapeutic targets.

Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infection

BackgroundHigh resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are resilient to infections. For Porcine Reproductive and Respiratory Syndrome (PRRS), one of the most devastating swine diseases worldwide, studies have identified substantial genetic variation in resistance of pigs, but evidence for genetic variation in tolerance has so far been inconclusive. Resistance and tolerance are usually considered as static traits. In this study, we used longitudinal viremia measurements of PRRS virus infected pigs to define discrete stages of infection based on viremia profile characteristics. These were used to investigate host genetic effects on viral load (VL) and growth at different stages of infection, to quantify genetic variation in tolerance at these stages and throughout the entire 42-day observation period, and to assess whether the single nucleotide polymorphism (SNP) WUR10000125 (WUR) with known large effects on resistance confers significant differences in tolerance.ResultsGenetic correlations between resistance and growth changed considerably over time. Individuals that expressed high genetic resistance early in infection tended to grow slower during that time-period, but were more likely to experience lower VL and recovery in growth by the later stage. The WUR genotype was most strongly associated with VL at early- to mid-stages of infection, and with growth at mid- to late-stages of infection. Both, single-stage and repeated measurements random regression models identified significant genetic variation in tolerance. The WUR SNP was significantly associated only with the overall tolerance slope fitted through all stages of infection, with the genetically more resistant AB pigs for the WUR SNP being also more tolerant to PRRS.ConclusionsThe results suggest that genetic selection for improved tolerance of pigs to PRRS is possible in principle, but may be feasible only with genomic selection, requiring intense recording schemes that involve repeated measurements to reliably estimate genetic effects. In the absence of such records, consideration of the WUR genotype in current selection schemes appears to be a promising strategy to improve simultaneously resistance and tolerance of growing pigs to PRRS.

136 Evidence of Genetic Variation for Recombination Events in Purebred Swine Populations.

136 Evidence of Genetic Variation for Recombination Events in Purebred Swine Populations.

Induction of novel mutants of Streptomyces lincolnensis with high Lincomycin production

Our research has revealed that an enhancement in lincomycin production by S. lincolnensis mutants after mutagenesis was obtained. Furthermore, the application of RAPD-PCR technique on some selected superior mutants in comparison with the wild type using three 15-mer random primers lead to detect of some differences in RAPD patterns which used as evidence of genetic variations of S. lincolnensis mutants.

Genetic Divergence for Physiological Response to Temperature between Populations of a C3-C4 Intermediate Annual

Premise of research. Local adaptation ultimately arises as a result of adaptive divergence in phenotypic characters. Within a species, a large portion of the phenotypic traits that confer local adaptation must be physiological characters. Yet few studies consider adaptive divergence in physiological characters or estimate genetic variation within populations for physiological traits that may confer local adaptation. Here I test the hypothesis that there is genetic variation within and between populations of a C3-C4 intermediate for the CO2 compensation point (Γ) and other photosynthetic traits. In addition to local adaptation, population-level variation in photosynthetic characters of C3-C4 intermediates reflects the potential for evolution of more C4-like photosynthesis.Methodology. I chose two populations of Mollugo verticillata, one from a relatively cool climate and one from a warm climate. I quantified variation within and between populations by measuring photosynthetic physiology at 24° and 35°C, temperatures that match the average maximums during the growing season at the populations’ native sites.Pivotal results. I detected little evidence of genetic variation within populations for Γ and carboxylation efficiency, but there was temperature-dependent population variation for Γ, where the population from the cool climate had a lower average Γ at 24°C. Apparent chlorophyll concentration was also greater in this population at both temperatures.Conclusions. The results demonstrate that there has been divergence among populations in Γ. Interestingly, the population from the cooler climate had lower Γ at 24°C. There is little evidence of adaptive evolutionary potential within populations; estimates of broad-sense heritability were not significant even when pooling samples from both populations to increase the overall sample size. Adaptation of more C4-like photosynthesis may proceed through the evolution of other physiological characters not directly related to concentrating carbon.

Further evidence for genetic variation at the serotonin transporter gene SLC6A4 contributing toward anxiety.

Social anxiety disorder (SAD) is a common and heritable psychiatric disorder. However, genetic studies in SAD are rare and only a few candidate genes have been implicated so far. In the present study, we investigated whether single-nucleotide polymorphisms (SNPs) associated with other psychiatric disorders also contribute toward the development of SAD and followed up variants associated with SAD on the phenotypic level. We genotyped a total of 24 SNPs in a German sample of 321 SAD patients and 804 controls. We carried out single-marker analyses as well as quantitative association analyses of SAD severity and harm avoidance. None of the variants investigated showed an association with SAD in our case-control sample after Bonferroni correction. Two SNPs reached nominal significance (rs818702, P=0.032; rs140701, P=0.048). Of these, only rs140701 showed an association in the same allelic direction as reported previously. This SNP is located within the serotonin transporter gene SLC6A4, which is the primary target of selective-serotonin reuptake inhibitors used for the treatment of depressive and anxiety disorders. The quantitative association analysis of all cases with available data on symptom severity showed four SNPs with a nominal significant association. Among these SNPs, rs10994359 showed the strongest association (P=0.001) and was located near the ANK3 gene. In addition, rs10994359 was nominally associated with harm avoidance scores (P=0.001). Our results provide further evidence for an involvement of the serotonin transporter gene SLC6A4 in the etiology of anxiety-related traits. Furthermore, our study implicates that genetic variation at the genome-wide associated bipolar disorder locus ANK3 might influence anxiety-related personality traits.

Evidence for genetic variation in Natterer\u2019s bats (Myotis nattereri) across three regions in Germany but no evidence for co-variation with their associated astroviruses

BackgroundAs bats have recently been described to harbor many different viruses, several studies have investigated the genetic co-variation between viruses and different bat species. However, little is known about the genetic co-variation of viruses and different populations of the same bat species, although such information is needed for an understanding of virus transmission dynamics within a given host species. We hypothesized that if virus transmission between host populations depends on events linked to gene flow in the bats, genetic co-variation should exist between host populations and astroviruses.ResultsWe used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer’s bat (Myotis nattereri) within and among populations at different geographical scales in Germany. Further, we correlated the observed bat population structure to that of partial astrovirus sequences (323–394 nt fragments of the RNA-dependent RNA polymerase gene) obtained from the same bat populations. Our analyses revealed that the studied bat colonies can be grouped into three distinct genetic clusters, corresponding to the three geographic regions sampled. Furthermore, we observed an overall isolation-by-distance pattern, while no significant pattern was observed within a geographic region. Moreover, we found no correlation between the genetic distances among the bat populations and the astrovirus sequences they harbored. Even though high genetic similarity of some of the astrovirus haplotypes found in several different regions was detected, identical astrovirus haplotypes were not shared between different sampled regions.ConclusionsThe genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. Identical astrovirus haplotypes were not shared between different sampled regions suggesting that astroviruses are mostly transmitted among host colonies at the local scale. Nevertheless, high genetic similarity of some of the astrovirus haplotypes found in several different regions implies that occasional transmission across regions with subsequent mutations of the virus haplotypes does occur.

Genetic resistance to infections in sheep

This paper considers genetic resistance to infectious disease in sheep, with appropriate comparison with goats, and explores how such variation may be used to assist in disease control. Many studies have attempted to quantify the extent to which host animals differ genetically in their resistance to infection or in the disease side-effects of infection, using either recorded animal pedigrees or information from genetic markers to quantify the genetic variation. Across all livestock species, whenever studies are sufficiently well powered, then genetic variation in disease resistance is usually seen and such evidence is presented here for three infections or diseases of importance to sheep, namely mastitis, foot rot and scrapie. A further class of diseases of importance in most small ruminant production systems, gastrointestinal nematode infections, is outside the scope of this review. Existence of genetic variation implies the opportunity, at least in principle, to select animals for increased resistance, with such selection ideally used as part of an integrated control strategy. For each of the diseases under consideration, evidence for genetic variation is presented, the role of selection as an aid to disease control is outlined and possible side effects of selection in terms of effects in performance, effects on resistance to other diseases and potential parasite/pathogen coevolution risks are considered. In all cases, the conclusion is drawn that selection should work and it should be beneficial, with the main challenge being to define cost effective selection protocols that are attractive to sheep farmers.

Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar).

Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one challenged with SAV as fry in freshwater (POP 1) and one challenged with SAV as post-smolts in sea water (POP 2). Analyses of the binary survival data revealed a moderate-to-high heritability for host resistance to PD in both populations (fry POP 1 h2~0.5; post-smolt POP 2 h2~0.4). Subsets of both populations were genotyped for single nucleotide polymorphism markers, and six putative resistance quantitative trait loci (QTL) were identified. One of these QTL was mapped to the same location on chromosome 3 in both populations, reaching chromosome-wide significance in both the sire- and dam-based analyses in POP 1, and genome-wide significance in a combined analysis in POP 2. This independently verified QTL explains a significant proportion of host genetic variation in resistance to PD in both populations, suggesting a common underlying mechanism for genetic resistance across lifecycle stages. Markers associated with this QTL are being incorporated into selective breeding programs to improve PD resistance.

Clonal fidelity of Iris sibirica plants regenerated by somatic embryogenesis and organogenesis in leaf-base culture — RAPD and flow cytometer analyses

Efficient protocols, safe from somaclonal variation, were developed for regeneration of Iris sibirica plants via organogenesis and somatic embryogenesis from leaf-base explants cultivated on Murashige and Skoog media supplemented with thidiazuron (TDZ, 1.0mg/l) or 2,4-dichlorophenoxyacetic acid (2,4-D, 1.0mg/l). The morphogenic response and callus formation efficiency differed significantly between 2,4-D (80.9%) and TDZ (67%) morphogenesis induction treatments. TDZ induced only organogenic calli, while calli obtained with 2,4-D were composed of three types differing in color and consistency: white, friable — embryogenic calli (4.5%, 3.8mg/explant), green, compact — organogenic calli (12.4%, 48.4mg/explants) and yellow — non-regenerative calli (77.3%, 254.4mg/explant). The cultivation of embryogenic calli on medium with 2,4-D and Kinetin resulted in further development of somatic embryos (54embryos/g of calli) which germinated with a frequency of 62% after being transferred to a medium without plant growth regulators. Stable shoot cultures were established by transferring organogenic calli with shoot primordia to media with 0.1mg/l α-naphthaleneacetic acid (NAA) and 1.0mg/l 6-benzylaminopurine (BA), while further cultivation on media of the same composition (TDZ or 2,4-D) resulted in the reduced growth and rhizogenesis, respectively. The TDZ induction treatment resulted in higher number of shoots per explant (7.9) than the 2,4-D treatment (4.3). After successful rooting and ex vitro acclimatization, plants were grown in the field and flowered to seed production. Flow cytometry, chromosome counting and random amplification of polymorphic DNA (RAPD) analysis indicated no evidence of genetic variation in plants regenerated via somatic embryogenesis or organogenesis. The results suggest that established protocols are safe for use in genetic transformation procedures or large-scale production of true-to-type I. sibirica plants.

No evidence of genetic variation in microsatellite and mitochondrial DNA markers among remaining populations of the Strange-tailed TyrantAlectrurus risora, an endangered grassland species

SummaryThe Strange-tailed TyrantAlectrurus risora(Aves: Tyrannidae) is an endemic species of southern South American grasslands that suffered a 90% reduction of its original distribution due to habitat transformation. This has led the species to be classified as globally Vulnerable. By the beginning of the last century, populations were partially migratory and moved south during the breeding season. Currently, the main breeding population inhabits the Iberá wetlands in the province of Corrientes, north-east Argentina, where it is resident all year round. There are two remaining small populations in the province of Formosa, north-east Argentina, and in southern Paraguay, which are separated from the main population by the Parana-Paraguay River and its continuous riverine forest habitat. The populations of Corrientes and Formosa are separated by 300 km and the grasslands between populations are non-continuous due to habitat transformation. We used mtDNA sequences and eight microsatellite loci to test if there were evidences of genetic isolation between Argentinean populations. We found no evidence of genetic structure between populations (ΦST= 0.004,P= 0.32;Fst = 0.01,P= 0.06), which can be explained by either retained ancestral polymorphism or by dispersal between populations. We found no evidence for a recent demographic bottleneck in nuclear loci. Our results indicate that these populations could be managed as a single conservation unit on a regional scale. Conservation actions should be focused on preserving the remaining network of areas with natural grasslands to guarantee reproduction, dispersal and prevent further decline of populations.

Prickly poppies can get pricklier: ontogenetic patterns in the induction of physical defense traits.

Plant ontogeny is a common source of variation in defense and herbivory. Yet, few studies have investigated how the induction of physical defense traits changes across plant ontogeny. Physical defense traits are costly to produce, and thus, it was predicted that induction as a cost-saving strategy would be particularly favorable for seedlings, leading to ontogenetic declines in the inducibility of these traits. We tested for induction of three different physical defense traits (prickles, latex and leaf toughness) in response to mechanical defoliation and jasmonic acid application using prickly poppies (Argemone glauca and A. mexicana, Papaveraceae) as a model system. Genetic variation in the induction of physical defenses was tested using maternal sib-ships sampled from multiple populations. Both species induced higher densities of laminar prickles, although the magnitude of induction was much higher in the endemic Hawaiian prickly poppy, A. glauca, than in the cosmopolitan A. mexicana. The magnitude of prickle induction was also higher in young compared to older juvenile plant stages in A. glauca, demonstrating a strong role of ontogeny. Neither latex exudation nor leaf toughness was induced in either species. Although significant genetic variation was detected within and among populations for constitutive expression of physical defense traits in Argemone, there was no evidence for genetic variation in the induction of these traits. This study provides the first evidence for the induction of physical defenses in prickly poppies, emphasizing how an ontogenetically explicit framework can reveal new insights into plant defense. Moreover, this study illustrates how sister species comparisons between island vs. continental plants can provide new insights into plant functional and evolutionary ecology, highlighting a fruitful area for future research on more species pairs.

Efficient plant regeneration, genetic fidelity and high-level accumulation of two pharmaceutical compounds in regenerated plants of Valeriana officinalis L.

An efficient regeneration system via adventitious shoot formation was developed in Valeriana officinalis, an important medicinal species. Regeneration response was significantly influenced by the type and concentrations of plant growth regulators as well as callus morphology. Optimum values for adventitious shoot–buds induction in both leaf and petiole explants were obtained when organogenic calli with compact, nodular and yellowish green phenotype was cultured in MS medium supplemented with 9.30μM Kn and 2.26μM 2,4-D. Well-developed shoots was achieved on a hormone-free half strength (1/2) MS basal medium. In vitro rooting of elongated shoots was tried on 1/2 MS medium supplemented with various concentrations of α-naphthalene acetic acid (NAA) or indole-3-butyric acid (IBA). IBA at a concentration of 2.46μM was found to be the best rooting treatment, which promoted the highest frequency of rooting (98%). Successful acclimatization of rooted plantlets was achieved in potting medium containing 5:1 mixture of peat and perlite with 95.34% survival rate. The contents of valtrate and valerenic acid in biomass extracts from petiole-derived plants were significantly (P<0.05) higher than leaf-derived plants as well as the seed-raised field-grown plants. Maximum valtrate (6.98mgg−1 DW) and valerenic acids (3.02mgg−1 DW) contents were quantified in root tissue of petiole-derived plants raised on medium with higher concentration of Kn (9.30μM) in combination with 2.26μM 2,4-D. Random amplified polymorphic DNA (RAPD) analysis indicated no evidence of genetic variation in the tissue culture-raised plants. The results suggest that the tissue culture-raised V. officinalis plants are capable of producing higher content of secondary metabolites under optimum in vitro conditions than that under natural wild growth conditions.

Evidence of genetic influence on the flowering pattern of Ficus microcarpa

Flowering patterns result from the interactions between genetic and environmental factors. While the genetic basis for flowering time variation in commercial plants is often well understood, few studies have been conducted to investigate these patterns in plants without economic importance. Ficus microcarpa is a commonly introduced horticultural fig tree. Asynchrony in syconium development and the initiation, frequency, and size of crops may affect its fitness as well as the success of mutualism with its pollinating wasps. In order to identify genetically determined patterns in the flowering traits in F. microcarpa, a 14-month census was taken on the flowering characteristics of 28 trees growing in close proximity along an urban street in Taipei, Taiwan. Weekly surveys were taken on 7 characteristics: crop number, syconia per branch, crop asynchrony, as well as flowering onset and seed development duration for both the spring and summer crops. Post-census genotyping at microsatellite loci distinguished 16 genetic groups (5 clonal groups and 11 non-clone trees). All crop characteristics presented higher variation across different genotype groups than within groups except for seed development duration. We found no evidence of adjacency effects or spatial auto-correlation of flowering traits. The study offers the first evidence of genetic variations in the flowering patterns in a species of Ficus. These findings lend insight into the adaptive characteristics that potentially facilitate the local establishment of F. microcarpa in new locations.

Analysis of the genetics of boar taint reveals both single SNPs and regional effects

BackgroundBoar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In most pig production systems, males, which are not required for breeding, are castrated shortly after birth to reduce the risk of boar taint. There is evidence for genetic variation in the predisposition to boar taint.A genome-wide association study (GWAS) was performed to identify loci with effects on boar taint. Five hundred Danish Landrace boars with high levels of skatole in fat (>0.3 μg/g), were each matched with a litter mate with low levels of skatole and measured for androstenone. DNA from these 1,000 non-castrated boars was genotyped using the Illumina PorcineSNP60 Beadchip. After quality control, tests for SNPs associated with boar taint were performed on 938 phenotyped individuals and 44,648 SNPs. Empirical significance thresholds were set by permutation (100,000). For androstenone, a ‘regional heritability approach’ combining information from multiple SNPs was used to estimate the genetic variation attributable to individual autosomes.ResultsA highly significant association was found between variation in skatole levels and SNPs within the CYP2E1 gene on chromosome 14 (SSC14), which encodes an enzyme involved in degradation of skatole. Nominal significance was found for effects on skatole associated with 4 other SNPs including a region of SSC6 reported previously. Genome-wide significance was found for an association between SNPs on SSC5 and androstenone levels and nominal significance for associations with SNPs on SSC13 and SSC17. The regional analyses confirmed large effects on SSC5 for androstenone and suggest that SSC5 explains 23% of the genetic variation in androstenone. The autosomal heritability analyses also suggest that there is a large effect associated with androstenone on SSC2, not detected using GWAS.ConclusionsSignificant SNP associations were found for skatole on SSC14 and for androstenone on SSC5 in Landrace pigs. The study agrees with evidence that the CYP2E1 gene has effects on skatole breakdown in the liver. Autosomal heritability estimates can uncover clusters of smaller genetic effects that individually do not exceed the threshold for GWAS significance.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-424) contains supplementary material, which is available to authorized users.

First Evidence of Genetic Intraspecific Variability and Occurrence of Entamoeba gingivalis in HIV(+)/AIDS

Entamoeba gingivalis is considered an oral commensal but demonstrates a pathogenic potential associated with periodontal disease in immunocompromised individuals. Therefore, this study evaluated the occurrence, opportunistic conditions, and intraspecific genetic variability of E. gingivalis in HIV(+)/AIDS patients. Entamoeba gingivalis was studied using fresh examination (FE), culture, and PCR from bacterial plaque samples collected from 82 HIV(+)/AIDS patients. Genetic characterization of the lower ribosomal subunit of region 18S (18S-SSU rRNA) was conducted in 9 positive samples using low-stringency single specific primer PCR (LSSP-PCR) and sequencing analysis. Entamoeba gingivalis was detected in 63.4% (52/82) of the samples. No association was detected between the presence of E. gingivalis and the CD4+ lymphocyte count (≤200 cells/mm3 (p = 0.912) or viral load (p = 0.429). The LSSP-PCR results helped group E. gingivalis populations into 2 polymorphic groups (68.3% similarity): group I, associated with 63.6% (7/11) of the samples, and group II, associated with 36.4% (4/11) of the samples, which shared 74% and 83.7% similarity and association with C and E isolates from HIV(−) individuals, respectively. Sequencing of 4 samples demonstrated 99% identity with the reference strain ATCC 30927 and also showed 2 divergent clusters, similar to those detected by LSSP-PCR. Opportunistic behavior of E. gingivalis was not detected, which may be related to the use of highly active antiretroviral therapy by all HIV(+)/AIDS patients. The high occurrence of E. gingivalis in these patients can be influenced by multifactorial components not directly related to the CD4+ lymphocyte counts, such as cholesterol and the oral microbiota host, which could mask the potential opportunistic ability of E. gingivalis. The identification of the 18S SSU-rRNA polymorphism by LSSP-PCR and sequencing analysis provides the first evidence of genetic variability in E. gingivalis isolated from HIV patients.