The MRZ reaction in primary progressive multiple sclerosis

BACKGROUND: The MRZ reaction (MRZR), composed of the three antibody indices (AI) against measles, rubella and varicella zoster virus and found positive in the majority of relapsing-remitting multiple sclerosis (RRMS) patients, is absent in other inflammatory neurological diseases (OIND). So far, it has been uncertain whether its differential diagnostic promise extends to patients with primary-progressive multiple sclerosis (PPMS). OBJECTIVE: To investigate the prevalence of MRZR in PPMS compared to RRMS and OIND patients. METHODS: MRZR was assessed in patients with PPMS (n = 103), RRMS (n = 100) and OIND (n = 48). Both stringency levels for MRZR testing, MRZR-1 (≥1 AI positive) and MRZR-2 (≥2 AI positive), were applied. RESULTS: Prevalence of positive MRZR-1 was 83.5% in PPMS and 67.8% in RRMS (p < 0.05). A positive MRZR-2 was found in 54.4% of PPMS and in 43.0% of RRMS patients (not significant). Compared to both MS subgroups, OIND patients exhibit lower frequencies of positive MRZR (MRZR-1: 22.9%, MRZR-2: 8.3%; p < 0.0001 each). CONCLUSION: Positive MRZR was at least as frequent in PPMS as in RRMS and much less frequent in OIND, confirming its promise as a potentially useful diagnostic tool for distinguishing both MS course types from OIND

Transient spurious intrathecal immunoglobulin synthesis in neurological patients after therapeutic apheresis

Background The analysis of cerebrospinal fluid (CSF) is usually done under steady-state conditions, when proteins (e.g., immunoglobulins) reach diffusion equilibrium between blood and CSF. However, little data has been published on CSF analysis under non-steady-state conditions after therapeutic apheresis. By reducing serum proteins (e.g., immunoglobulins), while leaving CSF unchanged, therapeutic apheresis might cause spuriously altered intrathecal immunoglobulin fractions. Methods Based on the incidental finding of plasma exchange-induced increased intrathecal immunoglobulin fractions in a cohort of 12 unsystematically selected patients with various neurological disorders, we retrospectively investigated CSF results that had been raised during routine diagnostic work-up from 41 consecutive neurological patients (predominantly Guillain-Barré syndrome and autoimmune encephalitis) treated with plasmapheresis or immunoadsorption in a tertiary care university hospital in whom lumbar puncture (LP) was performed after a varying number of treatments of therapeutic apheresis. Results Only when LP was performed 1 day after therapeutic apheresis, spurious quantitative intrathecal immunoglobulin (Ig) synthesis of at least one subclass (IgG, IgA and/or IgM) was found in 68.4 % of the patients, irrespective of the number of treatments, in all age groups and independent of other previous immunotherapies (e.g., steroids). This phenomenon occurred only transiently and was almost always accompanied by an elevation of the IgG index. In one patient, an elevated IgG index was noticed even 2 days after plasmapheresis. Neither quantitative Ig synthesis, nor elevated IgG index was observed when the LP was performed three or more days after therapeutic apheresis. Conclusions Spurious quantitative intrathecal Ig synthesis and increased IgG index are common findings shortly after plasmapheresis or immunoadsorption due to altered serum immunoglobulin levels. Knowledge of this phenomenon is needed for clinicians to prevent false interpretations leading to unnecessary diagnostic and therapeutic procedures. Misdiagnoses can be avoided by considering the characteristic CSF constellation including absence of oligoclonal bands and the close temporal relation to therapeutic apheresi

Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis

<p>Abstract</p> <p>Background</p> <p>In recent years, several attempts have been made in plant genetics to detect QTL by using association mapping methods. The objectives of this study were to (i) evaluate various methods for association mapping in five plant species and (ii) for three traits in each of the plant species compare the <it>T</it>_<it>opt</it>, the restricted maximum likelihood (REML) estimate of the conditional probability that two genotypes carry at the same locus alleles that are identical in state but not identical by descent. In order to compare the association mapping methods based on scenarios with realistic estimates of population structure and familial relatedness, we analyzed phenotypic and genotypic data of rapeseed, potato, sugar beet, maize, and Arabidopsis. For the same reason, QTL effects were simulated on top of the observed phenotypic values when examining the adjusted power for QTL detection.</p> <p>Results</p> <p>The correlation between the <it>T</it>_{<it>opt </it>}values identified using REML deviance profiles and profiles of the mean of squared difference between observed and expected <it>P </it>values was 0.83.</p> <p>Conclusion</p> <p>The mixed-model association mapping approaches using a kinship matrix, which was based on <it>T</it>_<it>opt</it>, were more appropriate for association mapping than the recently proposed QK method with respect to the adherence to the nominal <it>α </it>level and the adjusted power for QTL detection. Furthermore, we showed that <it>T</it>_{<it>opt </it>}differs considerably among the five plant species but only marginally among different traits.</p

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de. This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research

Co-Variation between Seed Dormancy, Growth Rate and Flowering Time Changes with Latitude in Arabidopsis thaliana

Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis.<br

Linkage disequilibrium and association mapping in elite germplasm of European maize

In der Pflanzengenetik ist die Kopplungsanalyse das Standardwerkzeug um Genloci zu identifizieren, die für quantitative Merkmale kodieren (QTL). Ein alternativer und vielversprechender Ansatz, der in der Humangenetik bereits erfolgreich dazu eingesetzt wurde, um QTL für Mukoviszidose und Alzheimer-Krankheit aufzufinden, ist die Assoziationskartierung. In der vorliegenden Arbeit werden die Anwendbarkeit von Assoziationskartierungsmethoden zum Auffinden von QTL in Maiselitezüchtungsmaterial untersucht sowie für diesen Zweck geeignete biometrische Methoden entwickelt. Ob Assoziationskartierungsansätze auch in Pflanzenzüchtungspopulationen zum Auffinden von QTL eingesetzt werden können, hängt vom Ausmaß des Gametenphasenungleichgewichtes (GPU) in der interessierenden Population ab. Des weiteren wird die Anwendbarkeit von Assoziationskartierungsmethoden von den Kräften beeinflußt, die in der betreffenden Population GPU verursachen und aufrechterhalten. Die Ziele unserer Studien waren (i) die Erfassung des Ausmaßes und der genomweiten Verteilung des GPU zwischen Mikrosatelliten (SSR) Markern, (ii) der Vergleich dieser Ergebnisse mit denjenigen für Amplifizierte-Fragment-Längen-Polymorphismus (AFLP) Markern sowie (iii) die Untersuchung von Kraften, die in Maiselitezüchtungsmaterial GPU verursachen und aufrechterhalten. Unsere Studien basierten sowohl auf experimentellen Daten von europäischen Maiseliteinzuchtlinien als auch auf Computersimulationen. Unsere Ergebnisse legen nahe, dass in europäischem Maiselitezüchtungsmaterial das Ausmaß an GPU sowohl zwischen SSR Markern als auch zwischen AFLP Markern ausreichend ist, um mit Hilfe der Assoziationskartierung genomweit QTL auffinden zu können. Da die Güte von SSR Markern GPU aufzufinden höher ist als diejenige von AFLP Markern, sind in Populationen mit kurzer Rekombinationsgeschichte SSR Marker geeigneter für Assoziationskartierungen als AFLP Marker. In Populationen mit langer Rekombinationsgeschichte, für die kein signifikantes GPU zwischen SSR Markern zu erwarten ist, sind AFLP Marker geeigneter für Assoziationskartierungen, da in diesem Fall ihre mit gleichem finanziellem Aufwand erzeugte höhere Markerdichte genutzt werden kann. Die Ergebnisse unserer experimentellen Untersuchungen und Simulationsstudien deuten darauf hin, dass in Pflanzenzüchtungspopulationen nicht nur physikalische Kopplung eine Ursache für GPU ist, sondern auch Verwandschaft, Populationsstratifizierung, genetische Drift und Selektion. Der Assoziationstest, der bislang in der Pflanzengenetik eingesetzt wurde, ist der ?logistic regression ratio test? (LRRT). Dieser Test korrigiert allerdings nur für GPU, das durch Populationsstratifizierung verursacht wird. Aus diesem Grund wird erwartet, dass der LRRT das alpha-Niveau nicht einhält, wenn er zur Assoziationskartierung in Populationen eingesetzt wird, in denen GPU vorhanden ist, das durch Verwandschaft, genetische Drift oder Selektion verursacht wird. Die Ziele unserer Studie waren (i) den ?quantitative pedigree disequilibrium test? so zu modifizieren, dass er zur Assoziationskartierung in Pflanzenzüchtungspopulationen eingesetzt werden kann und (ii) den neuentwickelten Test (QIPDT) hinsichtlich seiner Güte und Typ I Fehlerrate bei der Detektion von QTL zu untersuchen und mit dem bislang eingesetzten LRRT zu vergleichen. Diese Studie basierte auf Computersimulationen. Wir beobachteten für den QIPDT eine höhere Güte, QTL aufzufinden, als für den LRRT, wenn Daten verwendet wurden, die routinemäßig in Pflanzenzüchtungsprogrammen erhoben wurden. Im Gegensatz zum LRRT hielt der QIPDT stets das alpha-Niveau ein. Diese Ergebnisse belegen, dass der QIPDT zur genomweiten Assoziationskartierung mit Daten, die routinemäßig in Pflanzenzüchtungsprogrammen erhoben werden, geeigneter ist als der LRRT. Epistatische Interaktionen zwischen QTL tragen wesentlich zur genetischen Variation komplexer Merkmale bei. Die Ziele unserer Studie waren (i) Populationen rekombinanter Inzuchtlinien (RIL), die von einem geschachtelten Kreuzungsschema abgeleitet wurden, hinsichtlich ihrer Güte und Rate an falsch Positiven beim Auffinden epistatischer Interaktionen zwischen drei Loci, zu untersuchen und (ii) diese Ergebnisse mit jenen zu vergleichen, die beobachtet werden, wenn RIL von vollständigen oder unvollständigen Kreuzungsdiallelen abgeleitet wurden. Die Computersimulationen dieser Studie basierten auf Haplotypdaten von 26 Maisinzuchtlinien. Sowohl die Güte als auch die Rate an falsch Positiven beim Auffinden von epistatischen Interaktionen zwischen drei Loci waren für 5000 RIL, die von einem geschachtelten Kreuzungsschema abgeleitet wurden, auf einem Niveau, das vielversprechend für deren Detektion ist. Für RIL, die von optimal allozierten distanz-basierten Kreuzungsschemata abgeleitet wurden, wurde eine höhere Güte, epistatische Interaktionen zwischen drei Loci aufzufinden, beobachtet, als für die gleiche Anzahl an RIL, die von einem geschachtelten Kreuzungsschema oder Kreuzungsdiallelen abgeleitet wurden. Unsere Ergebnisse belegen, dass Assoziationskartierungsmethoden, die an die Besonderheiten von Pflanzenzüchtungspopulationen angepasst sind, in diesen erfolgreich zum Auffinden von QTL eingesetzt werden können.Linkage mapping has become a routine tool for the identification of quantitative trait loci (QTL) in plants. An alternative, promising approach is association mapping, which has been successfully applied in human genetics to detect QTL coding for diseases. The objectives of this research were to examine the feasibility of association mapping in elite maize breeding populations and develop for this purpose appropriate biometric methods. The feasibility of association mapping depends on the extent of linkage disequilibrium (LD) as well as on the forces generating and conserving LD in the population under consideration. The objectives of our studies were to (i) examine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) marker loci, (ii) compare these results with those obtained with amplified fragment length polymorphism (AFLP) markers, and (iii) investigate the forces generating and conserving LD in plant breeding populations. Our studies were based on experimental data of European elite maize inbreds as well as on computer simulations modeling the breeding history of the European flint heterotic group. The experimental results on European elite maize germplasm suggested that the extent of LD between SSR markers as well as AFLP markers are encouraging for the detection of marker-phenotype associations in genomewide scans. In populations with a short history of recombination, SSRs are advantageous over AFLPs in that they have a higher power to detect LD. In contrast, in populations with a long history of recombination, for which no LD is expected between pairs of SSR markers, AFLP markers should be favored over SSRs because then their higher marker density that is generated with a fixed budget can be used. Furthermore, the results of our experimental and simulation studies indicated that not only physical linkage is a cause of LD in plant breeding populations, but also relatedness, population stratification, genetic drift, and selection. So far, in plant genetics the logistic regression ratio test (LRRT) has been applied as a population-based association mapping approach. However, this test does only correct for LD caused by population stratification. The objectives of the presented study were to (i) adapt the quantitative pedigree disequilibrium test to typical pedigrees of inbred lines produced in plant breeding programs and (ii) compare the newly developed quantitative inbred pedigree disequilibrium test (QIPDT) and the commonly employed LRRT with respect to the power and type I error rate of QTL detection. This study was based on computer simulations modeling the breeding history of the European maize heterotic groups. In QIPDT the power of QTL detection was higher with 75 extended pedigrees than in LRRT with 75 independent inbreds. Furthermore, while the type I error rate of LRRT surpassed the nominal ® level, the QIPDT adhered to it. These results suggested that the QIPDT is superior to the LRRT for genome-wide association mapping if data collected routinely in plant breeding programs are available. Epistatic interactions among QTL contribute substantially to the genetic variation in complex traits. The main objectives of our study were to (i) investigate by computer simulations the power and proportion of false positives for detecting three-way interactions among QTL involved in a metabolic pathway in populations of recombinant inbred lines (RILs) derived from a nested design and (ii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The computer simulations of this study were based on single nucleotide polymorphism haplotype data of 26 diverse maize inbreds. The power and proportion of false positives to detect three-way interactions with 5000 RILs derived from a nested design was relatively high for both the 4 QTL and the 12 QTL scenario. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distancebased designs than for RILs derived from a nested or diallel design. Our results suggested that association mapping methods adapted to the special features of plant breeding populations have the potential to overcome the limitations of classical linkage mapping methods

Affordable, accurate and unbiased RNA sequencing by manual library miniaturization: A case study in barley

We present an easy-to-reproduce manual miniaturized full-length RNA sequencing (RNAseq) library preparation workflow that does not require the upfront investment in expensive lab equipment or long setup times. With minimal adjustments to an established commercial protocol, we were able to manually miniaturize the RNAseq library preparation by a factor of up to 1:8. This led to cost savings for miniaturized library preparation of up to 86.1% compared to the gold standard. The resulting data were the basis of a rigorous quality control analysis that inspected: sequencing quality metrics, gene body coverage, raw read duplications, alignment statistics, read pair duplications, detected transcripts and sequence variants. We also included a deep dive data analysis identifying rRNA contamination and suggested ways to circumvent these. In the end, we could not find any indication of biases or inaccuracies caused by the RNAseq library miniaturization. The variance in detected transcripts was minimal and not influenced by the miniaturization level. Our results suggest that the workflow is highly reproducible and the sequence data suitable for downstream analyses such as differential gene expression analysis or variant calling

Genome-wide distribution of genetic diversity and linkage disequilibrium in elite sugar beet germplasm

<p>Abstract</p> <p>Background</p> <p>Characterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore the patterns of population structure in the pollen parent heterotic pool using different methods, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in elite sugar beet germplasm.</p> <p>Results</p> <p>A total of 264 and 238 inbred lines from the yield type and sugar type inbreds of the pollen parent heterotic gene pools, respectively, which had been genotyped with 328 SNP markers, were used in this study. Two distinct subgroups were detected based on different statistical methods within the elite sugar beet germplasm set, which was in accordance with its breeding history. MCLUST based on principal components, principal coordinates, or lapvectors had high correspondence with the germplasm type information as well as the assignment by STRUCTURE, which indicated that these methods might be alternatives to STRUCTURE for population structure analysis. Gene diversity and modified Roger's distance between the examined germplasm types varied considerably across the genome, which might be due to artificial selection. This observation indicates that population genetic approaches could be used to identify candidate genes for the traits under selection. Due to the fact that <it>r</it>²<it>></it>0.8 is required to detect marker-phenotype association explaining less than 1% of the phenotypic variance, our observation of a low proportion of SNP loci pairs showing such levels of LD suggests that the number of markers has to be dramatically increased for powerful genome-wide association mapping.</p> <p>Conclusions</p> <p>We provided a genome-wide distribution map of genetic diversity and linkage disequilibrium for the elite sugar beet germplasm, which is useful for the application of genome-wide association mapping in sugar beet as well as the efficient organization of germplasm.</p

Using drone-retrieved multispectral data for phenomic selection in potato breeding

Predictive breeding approaches, like phenomic or genomic selection, have the potential to increase the selection gain for potato breeding programs which are characterized by very large numbers of entries in early stages and the availability of very few tubers per entry in these stages. The objectives of this study were to (i) explore the capabilities of phenomic prediction based on drone-derived multispectral reflectance data in potato breeding by testing different prediction scenarios on a diverse panel of tetraploid potato material from all market segments and considering a broad range of traits, (ii) compare the performance of phenomic and genomic predictions, and (iii) assess the predictive power of mixed relationship matrices utilizing weighted SNP array and multispectral reflectance data. Predictive abilities of phenomic prediction scenarios varied greatly within a range of − 0.15 and 0.88 and were strongly dependent on the environment, predicted trait, and considered prediction scenario. We observed high predictive abilities with phenomic prediction for yield (0.45), maturity (0.88), foliage development (0.73), and emergence (0.73), while all other traits achieved higher predictive ability with genomic compared to phenomic prediction. When a mixed relationship matrix was used for prediction, higher predictive abilities were observed for 20 out of 22 traits, showcasing that phenomic and genomic data contained complementary information. We see the main application of phenomic selection in potato breeding programs to allow for the use of the principle of predictive breeding in the pot seedling or single hill stage where genotyping is not recommended due to high costs

Characterization of the resistance mechanism against BYDV-PAV in maize

Arthropods threaten crop production by feeding on plants and, most importantly, by transmitting viruses. BYDV-PAV is the most prevalent virus species that causes barley yellow dwarf disease, one of the most economically important viral diseases affecting cereals worldwide. Maize plays a central role in BYDV-PAV epidemiology, serving as a “green bridge” for BYDV-PAV and its vector Rhopalosiphum padi in summer. Some studies have reported that the incidence of persistently transmitted viruses may be reduced in plants that are resistant to their insect vectors. In contrast, the choice test applied in our study revealed that R. padi is not repelled by the included BYDV-PAV-resistant maize inbreds. Significant differences in phloem architecture observed among the inbreds suggested that aphids feeding on BYDV-PAV-resistant maize may have difficulties reaching the phloem or establishing a stable feeding site. However, monitoring of aphid feeding behavior using the electrical penetration graph technique on maize inbreds that differed in their BYDV-PAV susceptibility revealed no correlation between R. padi feeding and BYDV-PAV resistance. Furthermore, we could not confirm the generation of reactive oxygen species (ROS), a typical reaction of plants during aphid infestation and infection of some viruses. In summary, we conclude that the BYDV-PAV resistance mechanisms in maize act directly on the virus and not on its vector, R. padi