Genotypic Differences Research Articles

GWAS of adventitious root formation in roses identifies a putative phosphoinositide phosphatase (SAC9) for marker-assisted selection.

Rose propagation by cuttings is limited by substantial genotypic differences in adventitious root formation. To identify possible genetic factors causing these differences and to develop a marker for marker-assisted selection for high rooting ability, we phenotyped 95 cut and 95 garden rose genotypes in a hydroponic rooting system over 6 weeks. Data on rooting percentage after 3 to 6 weeks, root number, and root fresh mass were highly variable among genotypes and used in association mappings performed on genotypic information from the WagRhSNP 68 K Axiom SNP array for roses. GWAS analyses revealed only one significantly associated SNP for rooting percentage after 3 weeks. Nevertheless, prominent genomic regions/peaks were observed and further analysed for rooting percentage after 6 weeks, root number and root fresh mass. Some of the SNPs in these peak regions were associated with large effects on adventitious root formation traits. Very prominent were ten SNPs, which were all located in a putative phosphoinositide phosphatase SAC9 on chromosome 2 and showed very high effects on rooting percentage after 6 weeks of more than 40% difference between nulliplex and quadruplex genotypes. SAC9 was reported to be involved in the regulation of endocytosis and in combination with other members of the SAC gene family to regulate the translocation of auxin-efflux PIN proteins via the dephosphorylation of phosphoinositides. For one SNP within SAC9, a KASP marker was successfully derived and used to select genotypes with a homozygous allele configuration. Phenotyping these homozygous genotypes for adventitious root formation verified the SNP allele dosage effect on rooting. Hence, the presented KASP derived from a SNP located in SAC9 can be used for marker-assisted selection in breeding programs for high rooting ability in the future.

Chitinophaga pendula, sp. nov., from an air conditioner condensate drain line.

A Gram-negative, rod-shaped and filamentous bacterium designated MD30BT was isolated from a biofilm hanging in water flowing from an air conditioner condensate drain line in Honolulu, Hawai'i. Based on 1517 nucleotides of the strain's 16S rRNA gene, its nearest neighbours are Chitinophaga rhizosphaerae T16R-86T (96.7 %), Chitinophaga caseinilytica S-52T (96.6 %), Chitinophaga lutea ZY74T (96.6 %), Chitinophaga niabensis JS13-10T (96.6 %) and Chitinophaga ginsengisoli Gsoil 052T (96.5 %). MD30BT cells are non-motile, strictly aerobic, and catalase and oxidase positive. Growth occurs between 10 and 45 °C. Major fatty acids in whole cells of MD30BT are 13-methyl tetradecanoic acid (34.1 %), cis-11-hexadecenoic acid (30.3 %), and 3-hydroxy, 15-methyl hexadecanoic acid (13.3 %). The quinone system contains predominantly menaquinone MK-7. The polar lipid profile contains the major lipids phosphatidylethanolamine, one unidentified lipid lacking a functional group, and two unidentified aminolipids. sym-Homospermidine is the major polyamine. The G+C content of the genome is 47.58 mol%. Based on phenotypic and genotypic differences between MD30BT and extant species in the Chitinophaga, we propose that MD30BT represents a new Chitinophaga species, for which the name Chitinophaga pendula sp. nov. is proposed to accommodate strain MD30BT as the type strain (DSM 112477T=NCTC 14606T).

Association between Polymorphism eNOS4, tPA, Factor V Leiden, Prothrombin, and Methylenetetrahydrofolate Reductase and the Occurrence of Legg-Calvé-Perthes Disease.

Legg-Calvé-Perthes (LCPD) disease is a complex condition affecting the femoral head's epiphysis in children. It occurs with a prevalence ranging from 0.4 to 29.0 cases per 100,000 children under the age of 15. It involves various factors, including genes associated with coagulation and fibrinolysis, pro-inflammatory factors, and vasoactive substances. We investigated the relationship between genetic mutations associated with coagulation and vascular disorders and the occurrence of LCPD in Polish patients. We performed a study involving 25 patients with LCPD and 100 healthy controls. All subjects were genotyped for eNOS4, Factor V Leiden, prothrombin, tPA25, and MTHFR polymorphism. The analysis revealed that the frequencies of eNOS4 genotypes were significantly different in LCPD patients than in the control group (p = 0.018). The frequencies of 4a allele were significantly higher in patients with LCPD than in the healthy population (26% vs. 9%, p = 0.0012). There were no significant differences in genotype and allele frequencies for Factor V Leiden, prothrombin tPA 25, and MTHFR gene polymorphisms between patients with LCPD and the controls. Genotype and allele frequencies of eNOS4 were significantly higher in patients with LCPD. These findings suggest a potential association between the eNOS gene polymorphism and an increased risk of developing LCPD.

Epigenetic regulation in colorectal cancer: The susceptibility of microRNAs 145, 143 and 133b to DNA demethylation and histone deacetylase inhibitors.

Globally, colorectal cancer (CRC) is a major health concern. Despite improvements in CRC treatment, mortality rates remain high. Genetic instability and epigenetic dysregulation of gene expression are instigators of CRC development that result in genotypic differences, leading to often variable and unpredictable treatment responses. Three miRNAs, miR-143, -145 and -133b, are most commonly downregulated in CRC and are proposed here as potential tumour suppressors. Although the downregulation of these miRNAs in CRC is largely unexplained, epigenetic silencing has been postulated to be a causative regulatory mechanism. Potential epigenetic modulation of miRNA expression, by means of histone acetylation and DNA methylation, was assessed in this study by treating early (SW1116) and late stage (DLD1) CRC cells with the DNA demethylating agent 5-aza-2'-deoxycytidine (5-Aza-2'C) and the histone deacetylase (HDAC) inhibitor Trichostatin A (TSA), respectively. Subsequent quantification of miRNA expression revealed that while all the selected miRNAs were susceptible to DNA demethylation in early- and late-stage CRC cells, susceptibility to DNA demethylation was significantly pronounced in late-stage DLD1 cells. Conversely, although histone acetylation moderately affected miRNA expression in early-stage CRC, it had a marginal effect on the expression of miRNAs in late-stage CRC cells. Overall, this study provides further understanding of the contribution of epigenetics to the regulation of putative tumour suppressor miRNAs in CRC.

Salinity and sodicity stresses differentially influence growth and physiology in sapota (Achras zapota L.)

Salt stress adversely affects the growth and physiological relations in most tree fruit species. Little is known about genetic variation for salt tolerance, and the physiological mechanisms underlying salt tolerance in sapota (Achras zapota), an underutilized fruit crop valued for its nutritive and medicinal properties. Here, we examined the effects of saline (ECiw 4, 8, 12, and 16 dS/m) and sodic (RSC 2.5 and 5.0meq/l) water treatments on plant growth, physiology, and ion homeostasis in the different genotypes of Sapota. Although saline and sodic treatments appreciably reduced the plant growth (i.e., by 20–50%) compared to salt-free plants, genotypes ‘CSRS-13’ and ‘CSRS-15’ performed better than others. Salt-induced reductions in leaf area were indicative of the ability of sapota to better acclimatize to prolonged salinity stress by regulating the biomass production. Saline and sodic irrigation treatments increased the leaf Na+ and decreased the leaf K+; albeit with clear-cut genotypic differences. We observed better ion homeostasis in genotype ‘CSRS-17’ under salinity stress, and better physiological adaptations in genotypes ‘CSRS-11’ and ‘CSRS-17’ under sodicity stress. Principal Component Analysis revealed strikingly different responses of sapota genotypes to ‘low’ and ‘high’ salinity/sodicity treatments. Strong cultivar-specific responses to salinity and sodicity stresses evinced the existence of genetic variation for salt tolerance in sapota. Overall, our findings demonstrated the feasibility of sapota cultivation in areas with moderate sodicity (RSC ∼2.5 meq/l), and moderate-to-high salinity (∼8.0 dS/m).

Genotypic stability in root system architecture and aboveground biomass revealed diverse adaptability of peanut (Arachis hypogaea L.) to moderate water deficit

AbstractMany crop species, including cultivated peanut (Arachis hypogaea L.), modify their above‐ and below‐ground growth to cope with water deficit stress. This acclimation to water deficit often triggers a biomass partitioning shift—allocating more biomass to the roots, to increase the accessibility of roots to water resources. However, additional carbon partitioning to roots may not always translate into increased water use and maintenance of aboveground biomass (ABM) and yield. Therefore, selecting an efficient root system architecture (RSA) should aim to sustain a high ABM production under a water deficit scenario. To better understand the associations of above and belowground biomass partitioning under moderate water deficit, this study evaluated the genotypic stability of 40 peanut genotypes in ABM and RSA in greenhouse experiments and further assessed genotypic differences in 4 site‐year field experiments. Our results suggested that higher ABM‐producing genotypes generally had high plasticity when subjected to water deficit whereas the low ABM‐producing genotypes had relatively high stability. Hierarchical clustering analysis further revealed that genotypes with a high root‐to‐shoot ratio potentially had increased genotypic stability in ABM underwater deficit. Interestingly, genotypes that maintained the highest ABM underwater deficit did not have the highest total root biomass and length. Instead, these genotypes had the highest root length in the top layer of soil (0–0.3 m) and relatively fewer roots in the deeper layer of soil (0.3–1 m). Greenhouse‐screened stable genotypes exhibited minimal yield reduction when subjected to mid‐season water deficit in some of the field validation experiments, but it also happened to some plastic genotypes, indicating that further validation of controlled environment screenings for genotypic water‐deficit tolerance in the field is necessary.

Plant-insect interaction in underutilized horticultural crops for sustainable production

Plants and insects have been living together for more than 350 million years. In co-evolution, both have evolved strategies to avoid each other’s defense systems. This evolutionary arms race between plants and insects has resulted in the development of an elegant defense system in plants that can recognise the non-self-molecules or signals from damaged cells, much like animals. It activates the plant’s immune response against the herbivores. Differences in genotypes of plant characters may affect insect-plant herbivore interactions, and variations in genotype traits are responsible for modifying the bottom-up effects. Recent evidence shows that the simultaneous occurrence of abiotic and biotic stress can positively affect plant performance by reducing the susceptibility to biotic stress, a positive sign for pest management. Plant responses to these stresses are multifaceted and involve copious antibiosis, physiological, antixenotic, molecular, molecular and cellular adaptations. Plants with antibiosis characteristics such as flavonoids, phenols, tannins, alkaloids, etc., may cause reduced insect survival, prolonged development time, decreased size and reduced new generation fitness. Quality and quantity of constitutive secondary metabolites production is species as well as cultivar specific and can be expressed as the signature of a particular plant or species and leads to the phenomenon of host-plant resistance. Hence, such plant resistance mechanisms have been effectively and widely used for managing insect pests in fields of underutilized crops. Natural defences are mediated through plant characteristics that affect insect biology, such as mechanical protection on the surface of the plants (e.g., hairs, trichomes, thorns, spines and thicker leaves) that either kill or retard the development of the herbivores. These phenomena of host plant resistance to insects can be exploited for the development of resistance crop cultivars which readily produce the inducible response upon mild infestation and can perform as one of the integrated pest management for sustainable crop production.

Correlation of SV2C rs1423099 single nucleotide polymorphism with sporadic Parkinson's disease in Han population in Southern China

BackgroundThe synaptic vesicle glycoprotein 2 (SV2) has been implicated in synaptic function throughout the brain. Accumulating evidence investigated that SV2C contributed to dopamine release and the disrupted expression of SV2C was considered to be a unique feature of PD that may facilitate dopaminergic neuron dysfunction. ObjectiveThis study aimed to examine the relationship between the SV2C rs1423099 single nucleotide polymorphism and sporadic Parkinson's disease (PD) in the Chinese Han population. Materials and methodsThis study enrolled 351 patients with sporadic PD and 240 normal controls in Chinese Han population. Peripheral blood DNA was extracted by DNA extraction kits and the rs1423099 genotype was analyzed by Agena MassARRAY DNA mass spectrometry. The differences in genotype and allele distribution frequencies between PD patients and control groups were compared using chi-squared tests or Fisher's exact tests. ResultsNo statistical difference was revealed in age and sex distribution between the cases and control groups, and the distribution of genotype and allele frequencies was consistent with the Hardy-Weinberg equilibrium test. In SV2C rs1423099 dominant model, the frequency of the CC/CT genotype was significantly higher in the PD group compared to the control group (OR = 4.065,95% CI: 2.801–10.870, p = 0.002). Nevertheless, in the recessive model, CC or CT/TT genotypes have no statistical difference in the two groups (p = 0.09). Additionally, in allelic analysis, the C allele was investigated to increase the risk of PD (OR = 1.346, 95% CI: 1.036–1.745, p = 0.026); Furthermore, subgroup analysis suggested that those carrying the C allele in the male subgroup were at a higher risk to afflicted with PD (OR = 1.637, 95% CI: 1.147–2.336, p = 0.006). ConclusionSV2C rs1423099 single nucleotide polymorphism was associated with sporadic Parkinson's disease in the Chinese Han population, particularly in males.

Association of microRNA-146a rs57095329 Polymorphism with Susceptibility to Primary Gout in a Chinese Han Population.

MicroRNA-146a (miR-146a) plays a critical role in the regulation of autoinflammatory diseases, including gout. There is growing evidence that miR-146a gene single nucleotide polymorphisms (SNPs) are associated with different diseases, but no genetic relevance studies of miR-146a gene polymorphisms to gout have been reported by now. The purpose of this study was to examine the relationship between the miR-146a rs57095329 genetic polymorphism and the susceptibility to primary gout in the Chinese Han population. A case-control study was performed in this report to examine the potential association between gout and the functional rs57095329 SNP of miR-146a in a Chinese population consisting of 448 primary gout patients (containing 76 tophi patients) and 418 healthy controls. MiR-146a expression in peripheral blood mononuclear cells (PBMCs) was measured in 81 gout patients (including 32 tophi patients and 49 non-tophi patients) and 47 healthy subjects. There was no significant difference found in the distribution of miR-146a rs57095329 between 448 gout patients and 418 healthy subjects (P > 0.05). However, significant differences in genotypes and allele distributions were found between 76 gout with tophi patients and 418 healthy subjects, as well as between gout with tophi (76) and with no tophi patients (372) (P < 0.01, respectively). Gout patients with AG/GG genotypes had a 0.323-fold reduced risk for tophi than those with the AA genotype, and the G allele had a 0.362-fold reduced risk of tophi. Furthermore, in 32 tophi patients, the GG genotype was significantly associated with increased expression of miR- 146a. Our findings suggest that rs57095329 may play a protective role in tophi gout susceptibility, and rs57095329 A > G variant may modulate the expression of miR-146a in tophi patients.

Association of the Brain-Derived Neurotrophic Factor Gene (BDNF) Val66Met Polymorphism with Individual Alpha Peak Frequency and Alpha Power in Adults

—A single nucleotide polymorphism in the brain-derived neurotrophic factor (BDNF) gene (Val66Met) functions to regulate activity-dependent secretion of (BDNF), which plays an important role in neuroprotection and synaptic plasticity. In several studies, the Met allele was associated with lower electroencephalogram (EEG) α-power values, calculated in the standard frequency range, in young subjects. In addition to α-power, one of the inherited EEG correlates of brain functioning is individual alpha peak frequency (IAPF). Although IAPF has a separate functional role, its association with BDNF Val66Met polymorphism has not been studied. IAPF is also used to determine the boundaries of individual frequency ranges, which, unlike the standard ones, are more consistent with functional rhythm characteristics. Using a sample of 192 subjects aged 18–78 years, the association between parietal-occipital IAPF and BDNF polymorphism, as well as the genotype differences in α-power calculated in standard (8–12 Hz) and individual frequency ranges (from (IAPF –2) to (IAPF +2) Hz) were examined. A decrease of IAPF in Val/Met compared to Val/Val was observed. For power calculated in the individual frequency range, genetic differences in both eyes-closed (Val/Met > homozygous genotypes) and eyes-open (Val-carriers > Met/Met) conditions were revealed. Analysis within the standard frequency range showed differences only in the eyes-open condition, which could be due to a shift of power indicators calculated in the α-rhythm functional range to the low frequency region among Val/Met carriers, which showed a decrease in IAPF. The results suggest that the inclusion of Val/Met in the pooled group of Met carriers in the analysis of genetic differences in brain activity may level out the differences between the Val/Val and Val/Met genotypes and show the advantage of using individual frequency bands in the analysis of BDNF Val66Met-associated EEG features.

Differences in the Proportion of CYP2C19 Loss-of-Function Between Cerebral Infarction and Coronary Artery Disease Patients.

Cytochrome P450 2C19 (CYP2C19) genotypes and metabolic phenotypes (extensive metabolizer (EM), intermediate metabolizer (IM), and poor metabolizer (PM)) are related to the metabolism of therapeutic drugs for cardiovascular and cerebrovascular diseases. This study aimed to investigate the differences of CYP2C19 gene polymorphism distribution between coronary artery disease (CAD) patients and cerebral infarction (CI) patients. We identified 413 CI patients, 509 CAD patients, and 241 CI+CAD patients from 2016 to 2020 and studied genotypes of CYP2C19 rs4986893 (636G>A) and rs4244285 (681G>A) polymorphisms using PCR-gene chip detection method. Differences in CYP2C19 genotypes and metabolic phenotypes between the groups were compared. To analyze the efficacy of CYP2C19 metabolic phenotypes in discriminating between cerebral infarction and coronary artery disease, multiple logistic regression analysis was conducted after adjusting for gender, age, smoking history, drinking history, hypertension, and diabetes. There were significant differences in the distribution of CYP2C19 genotypes and metabolic phenotypes between CI and CAD patients. The results of multivariate logistic regression (adjusted for sex, age, smoking, drinking, hypertension, and diabetes) indicated that CYP2C19 IM phenotype (IM vs EM: OR 1.443, 95% CI: 1.086-1.918, P=0.011) and CYP2C19 IM+PM phenotype (IM or PM vs EM: OR 1.440, 95% CI: 1.100-1.885, P=0.008) may be indicators of CI from CAD. CYP2C19 EM metabolic phenotype was dominant in CAD patients, and CYP2C19 IM metabolic phenotype was dominant in CI patients. After adjusting for other confounding factors, patients with the CYP2C19 IM metabolic phenotype were more likely to develop CI than CAD.

Narrow root cone angle promotes deeper rooting, cooler canopy temperatures and higher grain yield in a rice (Oryza sativa L.) recombinant inbred line population grown under different water availabilities in aerobic production systems

Rice crops are one of the world’s major consumers of irrigation water. With water becoming more limited, water-saving aerobic production (AP) systems may provide an alternative to traditional flooded culture. Genotypes with narrow root cone angle (RCA) and subsequently deeper rooting systems are hypothesised as key for AP adaptation ensuring water uptake at depth. Using a recombinant inbred line (RIL) population and differential genotypes (narrow and wide RCA groups) derived from a Sherpa/IRAT109 cross, a glasshouse experiment and four field experiments with different water inputs in well-watered (WW, in two seasons), mild water deficit (MWD), and intermittent water deficit (IWD) conditions were carried out to characterise the relationship of RCA with grain yield (GY) and key physiological traits. Significant genotypic variation and group differences were found in root traits, canopy temperature and GY. Expression of genotypes with narrow RCA were found to be consistent across experiments and water availability conditions. Genotypes in the narrow RCA group produced a greater proportion of roots below 20 cm (7.4–17.7%), longer total root length (69.7%), cooler canopies (0.3–1.0 °C) and higher GY (14–62%) compared with wide RCA group. Two promising RILs were identified which expressed high GY in WW (12.0–13.4 t/ha) conditions while maintaining GY in IWD (up to 9.4 t/ha). Higher GY was obtained in genotypes with cooler canopies (r = −0.72) and narrow RCA (r = −0.39) in IWD. Narrower RCA was associated with higher total root length (r = −0.70) and higher stomatal conductance (r = −0.71) in the glasshouse and proportion of deep roots (r = −0.65) and cooler canopies (r = 0.66) in the field. To our knowledge, this was one of the foremost studies exploring and demonstrating such relationships in rice AP systems. Root traits determined in the field were congruent with the other root-related traits driving differences between RCA groups measured in the glasshouse providing confidence with the field phenotyping methods. This work demonstrated the advantage conferred by the development of narrow RCA in aerobic conditions, presented improved physiological understanding of RCA and with genomics assisted breeding, is considered valuable for the development of AP-adapted, sustainably produced rice.

Relationship between IL-17A gene polymorphism and susceptibility to Kawasaki disease.

Kawasaki disease (KD) is the most common autoimmune vasculitis syndrome in children, which supposed be a complex polygenic disorder. Interleukin-17 (IL-17) is a member of the pro-inflammatory cytokine family, which has a strong pro-inflammatory effect and can participate in various acute and chronic inflammatory responses. This study aims to investigate the relationship between the single-nucleotide polymorphism (SNP) locus rs3819025 in the IL-17A gene and the susceptibility to KD. A total of 120 patients with KD who met the diagnostic criteria (the KD group) and 120 healthy children (the control group) were enrolled retrospectively in this study. Polymerase chain reaction (PCR) and DNA direct sequencing were used to detect the SNPs of children in the 2 groups. The frequencies of GG, GA, and AA genotypes of rs3819025 locus in the IL-17A gene in the KD group were 82.5%, 17.5%, and 0, respectively, and the frequencies of GG, GA, and AA genotypes in the control group were 72.5%, 22.5%, and 5.0%, respectively. There were significant differences in both genotype (χ2=7.524, P=0.023). The allele frequencies G and A of rs3819025 locus in the KD group were 91.25% and 8.75%, respectively, while those in the control group were 83.75% and 16.25%, respectively. There was significant difference between the 2 groups (χ2=6.171, P=0.013). The distribution frequencies of GG or GA genotype and G or A allele were 88.46% or 11.54% and 94.23% or 5.77% in the KD group with coronary artery lesion, respectively. The distribution frequencies of GG or GA genotype and G or A allele were 78.72% or 21.28% and 89.36% or 10.64% in the KD group without coronary artery lesion, respectively. There were no significant differences in genotype and allele frequencies of rs3819025 between the KD with coronary artery lesion group and the KD group without coronary artery lesion (both P>0.05). Besides, children with the allele A had a 2.023 times higher risk of KD than those without the allele A (χ2=6.171, P=0.013; OR=2.023, 95% CI 1.151 to 3.557). The locus rs3819025 in the IL-17A gene is associated with the pathogenesis of KD. The allele A of the locus rs3819025 in the IL-17A gene may be a risk factor for KD.

Plant-insect interactions in different genotypes of ber (Ziziphus mauritiana L) against fruit borer (Meridarchis scyrodes Meyrick)

Differences in genotypes of ber plant characters may affect insect-plant herbivore interactions, and variation in genotype traits is responsible for modifying the bottom-up effects. We evaluated the performance of different genotypes of Z. mauritiana against fruit borer, Meridarchis scyrodes Meyrick, under field conditions in the semi-arid region of India. We found that: (i) four genotypes were resistant; 5 genotypes were moderately resistant; 7 genotypes were susceptible, and seven genotypes were highly susceptible to fruit borers infestation; (ii) per cent fruit infestation was highest in Sanur-5 (75.09 %) and lowest in Safeda (13.27 %) followed by Tikadi (14.01 %); (iii) phenols (0.96), Tannins (0.95), flavonoid (0.95) contents and pericarp thickness (0.88) had significant negative correlations with per cent fruit infestation of fruit borer, M. scyrodes; (iv) fruit length (0.50) and pulp: stone ratio (0.77) showed significant positive correlations with per cent fruit infestation of fruit borer, M. scyrodes and (v) flavonoid contents explained 91.40% of the total variation in fruit borer, M. scyrodes infestation. Two principal components (PCs) were extracted, explaining the cumulative variation of 88.48 %. PC1 explained 64.34 % of the variation, while PC2 explained 24.14 n. In conclusion, growers can adopt the potential resistant genotype (Safeda) of Z. mauritiana with minimal financial investment to obtain higher yields.

Optogenetic cortical spreading depolarization induces headache-related behaviour and neuroinflammatory responses some prolonged in familial hemiplegic migraine type 1 mice

BackgroundCortical spreading depolarization (CSD), the neurophysiological correlate of the migraine aura, can activate trigeminal pain pathways, but the neurobiological mechanisms and behavioural consequences remain unclear. Here we investigated effects of optogenetically-induced CSDs on headache-related behaviour and neuroinflammatory responses in transgenic mice carrying a familial hemiplegic migraine type 1 (FHM1) mutation.MethodsCSD events (3 in total) were evoked in a minimally invasive manner by optogenetic stimulation through the intact skull in freely behaving wildtype (WT) and FHM1 mutant mice. Related behaviours were analysed using mouse grimace scale (MGS) scoring, head grooming, and nest building behaviour. Neuroinflammatory changes were investigated by assessing HMGB1 release with immunohistochemistry and by pre-treating mice with a selective Pannexin-1 channel inhibitor.ResultsIn both WT and FHM1 mutant mice, CSDs induced headache-related behaviour, as evidenced by increased MGS scores and the occurrence of oculotemporal strokes, at 30 min. Mice of both genotypes also showed decreased nest building behaviour after CSD. Whereas in WT mice MGS scores had normalized at 24 h after CSD, in FHM1 mutant mice scores were normalized only at 48 h. Of note, oculotemporal stroke behaviour already normalized 5 h after CSD, whereas nest building behaviour remained impaired at 72 h; no genotype differences were observed for either readout. Nuclear HMGB1 release in the cortex of FHM1 mutant mice, at 30 min after CSD, was increased bilaterally in both WT and FHM1 mutant mice, albeit that contralateral release was more pronounced in the mutant mice. Only in FHM1 mutant mice, contralateral release remained higher at 24 h after CSD, but at 48 h had returned to abnormal, elevated, baseline values, when compared to WT mice. Blocking Panx1 channels by TAT-Panx308 inhibited CSD-induced headache related behaviour and HMGB1 release.ConclusionsCSDs, induced in a minimally invasive manner by optogenetics, investigated in freely behaving mice, cause various migraine relevant behavioural and neuroinflammatory phenotypes that are more pronounced and longer-lasting in FHM1 mutant compared to WT mice. Prevention of CSD-related neuroinflammatory changes may have therapeutic potential in the treatment of migraine.

Early postnatal development of the MDGA2+/- mouse model of synaptic dysfunction

Synaptic dysfunction underlies many neurodevelopmental disorders (NDDs). The membrane-associated mucin domain-containing glycosylphosphatidylinositol anchor proteins (MDGAs) regulate synaptic development by modulating neurexin–neuroligin complex formation. Since understanding the neurodevelopmental profile and the sex-based differences in the manifestation of the symptoms of NDDs is important for their early diagnosis, we tested a mouse model haploinsufficient for MDGA2 (MDGA2+/-) on a neurodevelopmental test battery, containing sensory, motor, and cognitive measures, as well as ultrasonic vocalizations. When male and female MDGA2+/- and wildtype (WT) C57BL/6 J mice were examined from 2 to 23 days of age using this test battery, genotype and sex differences in body weight, sensory-motor processes, and ultrasonic vocalizations were observed. The auditory startle reflex appeared earlier in the MDGA2+/- than in WT mice and the MDGA2+/- mice produced fewer ultrasonic vocalizations. The MDGA2+/- mice showed reduced locomotion and rearing than WT mice in the open field after 17 days of age and spent less time investigating a novel object than WT mice at 21 days of age. Female MDGA2+/- mice weighed less than WT females and showed lower grip strength, indicating a delay in sensory-motor development in MDGA2+/- mice, which appears to be more pronounced in females than males. The behavioural phenotypes resulting from MDGA2 haploinsufficiency suggests that it shows delayed development of motor behaviour, grip strength and exploratory behaviour, non-social phenotypes of NDDs.

The WUR0000125 PRRS resilience SNP had no apparent effect on pigs' infectivity and susceptibility in a novel transmission trial.

Porcine reproductive and respiratory syndrome (PRRS) remains one of the most important infectious diseases for the pig industry. A novel small-scale transmission experiment was designed to assess whether the WUR0000125 (WUR for Wageningen University and Research) PRRS resilience single nucleotide polymorphism (SNP) confers lower susceptibility and infectivity to pigs under natural porcine reproductive and respiratory syndrome virus (PRRSV-2) transmission. Commercial full- and half-sib piglets (n = 164) were assigned as either Inoculation, Shedder, or Contact pigs. Pigs were grouped according to their relatedness structure and WUR genotype, with R- and R+ referring to pigs with zero and one copy of the dominant WUR resilience allele, respectively. Barcoding of the PRRSV-2 strain (SD09-200) was applied to track pig genotype-specific transmission. Blood and nasal swab samples were collected and concentrations of PRRSV-2 were determined by quantitative (q)-PCR and cell culture and expressed in units of median tissue culture infectious dose (TCID50). The Log10TCID50 at each sampling event, derived infection status, and area under the curve (AUC) were response variables in linear and generalized linear mixed models to infer WUR genotype differences in Contact pig susceptibility and Shedder pig infectivity. All Shedder and Contact pigs, except one, became infected through natural transmission. There was no significant (p > 0.05) effect of Contact pig genotype on any virus measures that would indicate WUR genotype differences in susceptibility. Contact pigs tended to have higher serum AUC (p = 0.017) and log10TCID50 (p = 0.034) when infected by an R+ shedder, potentially due to more infectious R+ shedders at the early stages of the transmission trial. However, no significant Shedder genotype effect was found in serum (p = 0.274) or nasal secretion (p = 0.951) that would indicate genotype differences in infectivity. The novel design demonstrated that it is possible to estimate genotype effects on Shedder pig infectivity and Contact pig susceptibility that are not confounded by family effects. The study, however, provided no supportive evidence that genetic selection on WUR genotype would affect PRRSV-2 transmission. The results of this study need to be independently validated in a larger trial using different PRRSV strains before dismissing the effects of the WUR marker or the previously detected GBP5 gene on PRRSV transmission.

Genotypic difference of garlic (Allium sativum L.) cultivars for growth, bulb yield and yield related attributes at Tigray Province, Northern Ethiopia

The experiment was conducted at Ofla district from June to October of 2017 and 2018 cropping season to select high yielding and adaptable garlic cultivar(s). Six garlic cultivars namely Chefe, Tsedey, Holeta local, Kuriftu and Bora-4 and one Ofla Local were evaluated. The experiment was arranged in completely randomized block design (RCBD) with three replications. Different growth, phenology, yield and yield related data were collected. Leaf length, leaf width, bulb diameter and length were significantly (p&lt;0.05) influenced by garlic cultivars in both cropping seasons. Bulb weight and number of cloves per bulb were highly significantly (P&lt;0.01) influenced by cultivars in both cropping seasons. Also, marketable yield, unmarketable yield and total yield ha-1 were highly significantly (P&lt;0.01) influenced by cultivars in both seasons. During 2017 and 2018, the highest marketable bulb yield was observed from Ofla Local cultivar with an average value of (8.86 t/ha) and (9.06 t/ha) respectively. During the 2017 cropping year, the maximum and significantly higher total bulb yield of 10.21 t/ha was recorded on the Ofla Local cultivar. Moreover, in 2018, this cultivar provided the maximum total bulb yield of 9.80 t/ha. Therefore, the Ofla Local cultivar showed the greatest performance for growth, yield and yield related attributes. Thus, it is recommended for cultivation in areas having similar agro-ecology. To improve the productivity of garlic, it is important to study and identify the optimum fertilizer level and spacing in the study area.

Identification of Markers Associated with Wheat Dwarf Virus (WDV) Tolerance/Resistance in Barley (Hordeum vulgare ssp. vulgare) Using Genome-Wide Association Studies.

Wheat dwarf virus (WDV) causes an important vector transmitted virus disease, which leads to significant yield losses in barley production. Due to the fact that, at the moment, no plant protection products are approved to combat the vector Psammotettix alienus, and this disease cannot be controlled by chemical means, the use of WDV-resistant or -tolerant genotypes is the most efficient method to control and reduce the negative effects of WDV on barley growth and production. In this study, a set of 480 barley genotypes were screened to identify genotypic differences in response to WDV, and five traits were assessed under infected and noninfected conditions. In total, 32 genotypes showed resistance or tolerance to WDV. Subsequently, phenotypic data of 191 out of 480 genotypes combined with 34,408 single-nucleotide polymorphisms (SNPs) were used for a genome-wide association study to identify quantitative trait loci (QTLs) and markers linked to resistance/tolerance to WDV. Genomic regions significantly associated with WDV resistance/tolerance in barley were identified on chromosomes 3H, 4H, 5H, and 7H for traits such as relative virus titer, relative performance of total grain weight, plant height, number of ears per plant, and thousand grain weight.

Evaluation of the Roche MagNA Pure 96 nucleic acid extraction platform for the SPF10 line probe assay system.

To evaluate the MagNA Pure 96 (MP96) nucleic acid extraction system as an alternative for cervical specimen processing for human papillomavirus (HPV) genotyping detection by reverse hybridization line probe assay (LiPA-25), compared to the well-established extraction system MagNA Pure LC 2.0 (MPLC). A total of 200 cervical samples preserved in ThinPrepCyt® solution were extracted by MP96 and MPLC, respectively, and then purified nucleic acids were amplified using the SPF10 PCR primer set. Amplification products were subjected to SPF10-DNA enzyme immunoassay (DEIA) and LiPA-25. The concordance between different extraction methods in this study was reflected in the comparison of the results of the DEIA and LiPA-25. Agreement of HPV-positive results (DEIA) was 97.5% (Kappa=0.932). Pair-wise analyses of either HPV grouping (any HPV genotypes, any high-risk HPV genotypes, any low-risk HPV genotypes, any nonavalent vaccine-targeted HPV, and any non-vaccine-targeted oncogenic HPV genotypes) identified >95% agreement (all Kappa>0.900). For the two extraction methods, there was no statistical difference (chi-square test: P=0.690) for single versus multiple genotypes, and concordant, compatible, and discordant genotypes were observed in 87.0%, 9.5%, and 3.5% of 200 samples, respectively. HPV genotyping results of the MPLC system and the MP96 system showed a high degree of concordance. Combined with the advantages of high-throughput and anti-contamination of MP96, the MP96 extraction system could be more suitable for the testing of samples in future studies.