A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis.

Chromosome substitution lines (CSLs) are tentatively supreme resources to investigate non-allelic genetic interactions. However, the difficulty of generating such lines in most species largely yielded imperfect CSL panels, prohibiting a systematic dissection of epistasis. Here, we present the development and use of a unique and complete panel of CSLs in Arabidopsis thaliana, allowing the full factorial analysis of epistatic interactions. A first comparison of reciprocal single chromosome substitutions revealed a dependency of QTL detection on different genetic backgrounds. The subsequent analysis of the complete panel of CSLs enabled the mapping of the genetic interactors and identified multiple two- and three-way interactions for different traits. Some of the detected epistatic effects were as large as any observed main effect, illustrating the impact of epistasis on quantitative trait variation. We, therefore, have demonstrated the high power of detection and mapping of genome-wide epistasis, confirming the assumed supremacy of comprehensive CSL sets.

Genotype-Phenotype Correlations in Chronic Granulomatous Disease: Insights From a Large National Cohort.

Neutrophils are the first line of defense against invading pathogens. Neutrophils execute and modulate immune responses by generating reactive oxygen species (ROS). Chronic Granulomatous Disease (CGD) is a primary immune deficiency disorder of phagocytes, caused by inherited mutations in the genes of the NADPH oxidase enzyme. These mutations lead to failure of ROS generation followed by recurrent bacterial and fungal infections, frequently associated with hyper-inflammatory manifestations. We report a multi-center cumulative experience in diagnosing and treating patients with CGD. From 1986 to 2021, 2,918 patients suffering from frequent infections were referred for neutrophil evaluation. Among them, 110 patients were diagnosed with CGD, 56 of Jewish ancestry, 48 of Arabic ancestry and 6 non-Jewish/non-Arabic. As opposed to other Western countries, the autosomal recessive (AR) CGD subtypes were predominant in Israel (71/110 patients). Thirty-nine patients had X-linked CGD, in most patients associated with severe infections (clinical severity score ≥3) and poor outcomes, presenting at a significantly earlier age than AR-CGD subtypes. The full spectrum of infections and hyper-inflammatory manifestations are described. Six patients had hypomorphic mutations with significantly milder phenotype, clinical severity score ≤2, and better outcomes. Hematopoietic stem cell transplantation was implemented in 39/110 patients (35.5%). Successful engraftment was achieved in 92%, with 82% long-term survival and 71% full clinical recovery. CGD is a complex disorder requiring a multi-professional team. Early identification of the genetic mutation is essential for prompt diagnosis, suitable management and prevention.

Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea.

Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013-14 and 2014-15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high-density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome-wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity-by-descent (IBD)-based mixed model approach was used to map quantitative trait loci (QTLs). The IBD-based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker-trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas.

A conceptual framework for the dynamic modeling of time-resolved phenotypes for sets of genotype-environment-management combinations: a model library.

Introduction: Dynamic crop growth models are an important tool to predict complex traits, like crop yield, for modern and future genotypes in their current and evolving environments, as those occurring under climate change. Phenotypic traits are the result of interactions between genetic, environmental, and management factors, and dynamic models are designed to generate the interactions producing phenotypic changes over the growing season. Crop phenotype data are becoming increasingly available at various levels of granularity, both spatially (landscape) and temporally (longitudinal, time-series) from proximal and remote sensing technologies. Methods: Here we propose four phenomenological process models of limited complexity based on differential equations for a coarse description of focal crop traits and environmental conditions during the growing season. Each of these models defines interactions between environmental drivers and crop growth (logistic growth, with implicit growth restriction, or explicit restriction by irradiance, temperature, or water availability) as a minimal set of constraints without resorting to strongly mechanistic interpretations of the parameters. Differences between individual genotypes are conceptualized as differences in crop growth parameter values. Results: We demonstrate the utility of such low-complexity models with few parameters by fitting them to longitudinal datasets from the simulation platform APSIM-Wheat involving in silico biomass development of 199 genotypes and data of environmental variables over the course of the growing season at four Australian locations over 31 years. While each of the four models fits well to particular combinations of genotype and trial, none of them provides the best fit across the full set of genotypes by trials because different environmental drivers will limit crop growth in different trials and genotypes in any specific trial will not necessarily experience the same environmental limitation. Discussion: A combination of low-complexity phenomenological models covering a small set of major limiting environmental factors may be a useful forecasting tool for crop growth under genotypic and environmental variation.

Genetic Mapping of Genotype-by-Ploidy Effects in Arabidopsis thaliana.

Plants can express different phenotypic responses following polyploidization, but ploidy-dependent phenotypic variation has so far not been assigned to specific genetic factors. To map such effects, segregating populations at different ploidy levels are required. The availability of an efficient haploid inducer line in Arabidopsis thaliana allows for the rapid development of large populations of segregating haploid offspring. Because Arabidopsis haploids can be self-fertilised to give rise to homozygous doubled haploids, the same genotypes can be phenotyped at both the haploid and diploid ploidy level. Here, we compared the phenotypes of recombinant haploid and diploid offspring derived from a cross between two late flowering accessions to map genotype × ploidy (G × P) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels. This implies that mapping power will increase when phenotypic measurements of monoploids are included in QTL analyses. A multi-trait analysis further revealed pleiotropic effects for a number of the ploidy-specific QTLs as well as opposite effects at different ploidy levels for general QTLs. Taken together, we provide evidence of genetic variation between different Arabidopsis accessions being causal for dissimilarities in phenotypic responses to altered ploidy levels, revealing a G × P effect. Additionally, by investigating a population derived from late flowering accessions, we revealed a major vernalisation-specific QTL for variation in flowering time, countering the historical bias of research in early flowering accessions.

Hematologically important mutations: Leukocyte adhesion deficiency (second update).

Leukocyte adhesion deficiency (LAD) is an immunodeficiency caused by defects in the adhesion of leukocytes (especially neutrophils) to the blood vessel wall. As a result, patients with LAD suffer from severe bacterial infections and impaired wound healing, accompanied by neutrophilia. In LAD-I, characterized directly after birth by delayed separation of the umbilical cord, mutations are found in ITGB2, the gene that encodes the ß subunit (CD18) of the ß2 integrins. In the rare LAD-II disease, the fucosylation of selectin ligands is disturbed, caused by mutations in SLC35C1, the gene that encodes a GDP-fucose transporter of the Golgi system. LAD-II patients lack the H and Lewis Lea and Leb blood group antigens. Finally, in LAD-III, the conformational activation of the hematopoietically expressed ß integrins is disturbed, leading to leukocyte and platelet dysfunction. This last syndrome is caused by mutations in FERMT3, encoding the kindlin-3 protein in all blood cells, involved in the regulation of ß integrin conformation. This article contains an update of the mutations that we consider to be relevant for the various forms of LAD.

statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations.

MOTIVATION: Multi-parent populations (MPPs) are popular for QTL mapping because they combine wide genetic diversity in parents with easy control of population structure, but a limited number of software tools for QTL mapping are specifically developed for general MPP designs. RESULTS: We developed an R package called statgenMPP, adopting a unified identity-by-descent (IBD)-based mixed model approach for QTL analysis in MPPs. The package offers easy-to-use functionalities of IBD calculations, mixed model solutions and visualizations for QTL mapping in a wide range of MPP designs, including diallele, nested-association mapping populations, multi-parent advanced genetic inter-cross populations and other complicated MPPs with known crossing schemes. AVAILABILITY AND IMPLEMENTATION: The R package statgenMPP is open-source and freely available on CRAN at https://CRAN.R-project.org/package=statgenMPP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Two-dimensional P-spline smoothing for spatial analysis of plant breeding trials.

Large agricultural field trials may display irregular spatial trends that cannot be fully captured by a purely randomization-based analysis. For this reason, paralleling the development of analysis-of-variance procedures for randomized field trials, there is a long history of spatial modeling for field trials, starting with the early work of Papadakis on nearest neighbor analysis, which can be cast in terms of first or second differences among neighboring plot values. This kind of spatial modeling is amenable to a natural extension using splines, as has been demonstrated in recent publications in the field. Here, we consider the P-spline framework, focusing on model options that are easy to implement in linear mixed model packages. Two examples serve to illustrate and evaluate the methods. A key conclusion is that first differences are rather competitive with second differences. A further key observation is that second differences require special attention regarding the representation of the null space of the smooth terms for spatial interaction, and that an unstructured variance-covariance structure is required to ensure invariance to translation and rotation of eigenvectors associated with that null space. We develop a strategy that permits fitting this model with ease, but the approach is more demanding than that needed for fitting models using first differences. Hence, even though in other areas, second differences are very commonly used in the application of P-splines, our conclusion is that with field trials, first differences have advantages for routine use.

Identification of environment types and adaptation zones with self-organizing maps; applications to sunflower multi-environment data in Europe.

KEY MESSAGE: We evaluate self-organizing maps (SOM) to identify adaptation zones and visualize multi-environment genotypic responses. We apply SOM to multiple traits and crop growth model output of large-scale European sunflower data. Genotype-by-environment interactions (G × E) complicate the selection of well-adapted varieties. A possible solution is to group trial locations into adaptation zones with G × E occurring mainly between zones. By selecting for good performance inside those zones, response to selection is increased. In this paper, we present a two-step procedure to identify adaptation zones that starts from a self-organizing map (SOM). In the SOM, trials across locations and years are assigned to groups, called units, that are organized on a two-dimensional grid. Units that are further apart contain more distinct trials. In an iterative process of reweighting trial contributions to units, the grid configuration is learnt simultaneously with the trial assignment to units. An aggregation of the units in the SOM by hierarchical clustering then produces environment types, i.e. trials with similar growing conditions. Adaptation zones can subsequently be identified by grouping trial locations with similar distributions of environment types across years. For the construction of SOMs, multiple data types can be combined. We compared environment types and adaptation zones obtained for European sunflower from quantitative traits like yield, oil content, phenology and disease scores with those obtained from environmental indices calculated with the crop growth model Sunflo. We also show how results are affected by input data organization and user-defined weights for genotypes and traits. Adaptation zones for European sunflower as identified by our SOM-based strategy captured substantial genotype-by-location interaction and pointed to trials in Spain, Turkey and South Bulgaria as inducing different genotypic responses.

A two-stage approach for the spatio-temporal analysis of high-throughput phenotyping data.

High throughput phenotyping (HTP) platforms and devices are increasingly used for the characterization of growth and developmental processes for large sets of plant genotypes. Such HTP data require challenging statistical analyses in which longitudinal genetic signals need to be estimated against a background of spatio-temporal noise processes. We propose a two-stage approach for the analysis of such longitudinal HTP data. In a first stage, we correct for design features and spatial trends per time point. In a second stage, we focus on the longitudinal modelling of the spatially corrected data, thereby taking advantage of shared longitudinal features between genotypes and plants within genotypes. We propose a flexible hierarchical three-level P-spline growth curve model, with plants/plots nested in genotypes, and genotypes nested in populations. For selection of genotypes in a plant breeding context, we show how to extract new phenotypes, like growth rates, from the estimated genotypic growth curves and their first-order derivatives. We illustrate our approach on HTP data from the PhenoArch greenhouse platform at INRAE Montpellier and the outdoor Field Phenotyping platform at ETH Zürich.

Hematologically important mutations: The autosomal forms of chronic granulomatous disease (third update).

Chronic granulomatous disease (CGD) is an immunodeficiency disorder affecting about 1 in 250,000 individuals. CGD patients suffer from severe, recurrent bacterial and fungal infections. The disease is caused by mutations in the genes encoding the components of the leukocyte NADPH oxidase. This enzyme produces superoxide, which is subsequently metabolized to hydrogen peroxide and other reactive oxygen species (ROS). These products are essential for intracellular killing of pathogens by phagocytic leukocytes (neutrophils, eosinophils, monocytes and macrophages). The leukocyte NADPH oxidase is composed of five subunits, four of which are encoded by autosomal genes. These are CYBA, encoding p22phox, NCF1, encoding p47phox, NCF2, encoding p67phox and NCF4, encoding p40phox. This article lists all mutations identified in these genes in CGD patients. In addition, cytochrome b558 chaperone-1 (CYBC1), recently recognized as an essential chaperone protein for the expression of the X-linked NADPH oxidase component gp91phox (also called Nox2), is encoded by the autosomal gene CYBC1. Mutations in this gene also lead to CGD. Finally, RAC2, a small GTPase of the Rho family, is needed for activation of the NADPH oxidase, and mutations in the RAC2 gene therefore also induce CGD-like symptoms. Mutations in these last two genes are also listed in this article.

An IBD-based mixed model approach for QTL mapping in multiparental populations.

KEY MESSAGE: The identity-by-descent (IBD)-based mixed model approach introduced in this study can detect quantitative trait loci (QTLs) referring to the parental origin and simultaneously account for multilevel relatedness of individuals within and across families. This unified approach is proved to be a powerful approach for all kinds of multiparental population (MPP) designs. Multiparental populations (MPPs) have become popular for quantitative trait loci (QTL) detection. Tools for QTL mapping in MPPs are mostly developed for specific MPPs and do not generalize well to other MPPs. We present an IBD-based mixed model approach for QTL mapping in all kinds of MPP designs, e.g., diallel, Nested Association Mapping (NAM), and Multiparental Advanced Generation Intercross (MAGIC) designs. The first step is to compute identity-by-descent (IBD) probabilities using a general Hidden Markov model framework, called reconstructing ancestry blocks bit by bit (RABBIT). Next, functions of IBD information are used as design matrices, or genetic predictors, in a mixed model approach to estimate variance components for multiallelic genetic effects associated with parents. Family-specific residual genetic effects are added, and a polygenic effect is structured by kinship relations between individuals. Case studies of simulated diallel, NAM, and MAGIC designs proved that the advanced IBD-based multi-QTL mixed model approach incorporating both kinship relations and family-specific residual variances (IBD.MQMkin_F) is robust across a variety of MPP designs and allele segregation patterns in comparison to a widely used benchmark association mapping method, and in most cases, outperformed or behaved at least as well as other tools developed for specific MPP designs in terms of mapping power and resolution. Successful analyses of real data cases confirmed the wide applicability of our IBD-based mixed model methodology.

Hematologically important mutations: X-linked chronic granulomatous disease (fourth update).

Chronic granulomatous disease (CGD) is an immunodeficiency disorder affecting about 1 in 250,000 individuals. CGD patients suffer from severe bacterial and fungal infections. The disease is caused by a lack of superoxide production by the leukocyte enzyme NADPH oxidase. Superoxide and subsequently formed other reactive oxygen species (ROS) are instrumental in killing phagocytosed micro-organisms in neutrophils, eosinophils, monocytes and macrophages. The leukocyte NADPH oxidase is composed of five subunits, of which the enzymatic component is gp91phox, also called Nox2. This protein is encoded by the CYBB gene on the X chromosome. Mutations in this gene are found in about 70% of all CGD patients in Europe and in about 20% in countries with a high ratio of parental consanguinity. This article lists all mutations identified in CYBB and should therefore help in genetic counseling of X-CGD patients' families. Moreover, apparently benign polymorphisms in CYBB are also given, which should facilitate the recognition of disease-causing mutations. In addition, we also include some mutations in G6PD, the gene on the X chromosome that encodes glucose-6-phosphate dehydrogenase, because inactivity of this enzyme may lead to shortage of NADPH and thus to insufficient activity of NADPH oxidase. Severe G6PD deficiency can induce CGD-like symptoms.

Mutations in cis that affect mRNA synthesis, processing and translation.

Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.

Clinical, Immunological, and Molecular Profile of Chronic Granulomatous Disease: A Multi-Centric Study of 236 Patients From India.

Background: Chronic granulomatous disease (CGD) is an inherited defect in phagocytic respiratory burst that results in severe and life-threatening infections in affected children. Single center studies from India have shown that proportion of autosomal recessive (AR) CGD is more than that reported from the West. Further, affected patients have high mortality rates due to late referrals and difficulties in accessing appropriate treatment. However, there is lack of multicentric collaborative data on CGD from India. Objective: To describe infection patterns, immunological, and molecular features of CGD from multiple centers in India. Methods: A detailed proforma that included clinical and laboratory details was prepared and sent to multiple centers in India that are involved in the care and management of patients with inborn errors of immunity. Twelve centers have provided data which were later pooled together and analyzed. Results: Of the 236 patients analyzed in our study, X-linked and AR-CGD was seen in 77 and 97, respectively. Male female ratio was 172:64. Median age at onset of symptoms and diagnosis was 8 and 24 months, respectively. Common infections documented include pneumonia (71.6%), lymphadenitis (31.6%), skin and subcutaneous abscess (23.7%), blood-stream infection (13.6%), osteomyelitis (8.6%), liver abscess (7.2%), lung abscess (2.9%), meningoencephalitis (2.5%), splenic abscess (1.7%), and brain abscess (0.9%). Forty-four patients (18.6%) had evidence of mycobacterial infection. Results of molecular assay were available for 141 patients (59.7%)-CYBB (44.7%) gene defect was most common, followed by NCF1 (31.9%), NCF2 (14.9%), and CYBA (8.5%). While CYBA variants were documented only in Southern and Western parts of India, a common dinucleotide deletion in NCF2 (c.835_836delAC) was noted only in North Indian population. Of the 174 patients with available outcome data, 67 (38.5%) had expired. Hematopoietic stem cell transplantation was carried out in 23 patients, and 12 are doing well on follow-up. Conclusions: In India, proportion of patients with AR-CGD is higher as compared to Western cohorts, though regional differences in types of AR-CGD exist. Clinical profile and mortality rates are similar in both X-linked and AR-CGD. However, this may be a reflection of the fact that milder forms of AR-CGD are probably being missed.

Clinical and Immunological Characteristics of 63 Patients with Chronic Granulomatous Disease: Hacettepe Experience.

BACKGROUND: Chronic granulomatous disease (CGD), one of the phagocytic system defects, is the primary immunodeficiency caused by dysfunction of the NADPH oxidase complex which generates reactive oxygen species (ROS), which are essential for killing pathogenic microorganisms, especially catalase-positive bacteria and fungi. OBJECTIVE: The objective of our study was to assess the clinical and laboratory characteristics, treatment modalities, and prognosis of patients with CGD. METHODS: We retrospectively reviewed 63 patients with CGD who have been diagnosed, treated, and/or followed-up between 1984 and 2018 in Hacettepe University, Ankara, in Turkey, as a developing country. RESULTS: The number of female and male patients was 26/37. The median age at diagnosis was 3.8 (IQR: 1.0-9.6) years. The rate of consanguinity was 63.5%. The most common physical examination finding was lymphadenopathy (44/63), growth retardation (33/63), and hepatomegaly (27/63). One adult patient had squamous cell carcinoma of the lung. The most common infections were lung infection (53/63), skin abscess (43/63), and lymphadenitis (19/63). Of the 63 patients with CGD, 6 patients had inflammatory bowel disease (IBD). Twelve of the 63 patients died during follow-up. CYBA, NCF1, CYBB, and NCF2 mutations were detected in 35%, 27.5%, 25%, and 12.5% of the patients, respectively. CONCLUSION: We identified 63 patients with CGD from a single center in Turkey. Unlike other cohort studies in Turkey, due to the high consanguineous marriage rate in our study group, AR form of CGD was more frequent, and gastrointestinal involvement were found at relatively lower rates. The rate of patients who treated with HSCT was lower in our research than in the literature. A majority of the patients in this study received conventional prophylactic therapies, which highlight on the outcome of individuals who have not undergone HSCT.

Temperature response of wheat affects final height and the timing of stem elongation under field conditions.

In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.

Genetic Characteristics, Infectious, and Noninfectious Manifestations of 32 Patients with Chronic Granulomatous Disease.

BACKGROUND: Chronic granulomatous disease (CGD) is a rare genetic disorder characterized by failure of phagocytic leukocytes to destroy certain microbes. We present a study on CGD patients enrolled at a single medical center concerning the infectious and noninfectious complications and genetic properties of the disease. METHODS: Icotinamide adenine dinucleotide phosphate oxidase activity and the expression of flavocytochrome b558 were measured by flow cytometry, and clinical outcomes of the patients were listed in relation to the genetic results. RESULTS: The clinical and genetic findings of 32 pediatric cases with CGD from 23 families were enrolled. Pneumonia and anemia were the most common infectious and noninfectious symptoms. Genetic analysis showed that 10 families (43.5%) carried CYBB variants and 13 families (56.5%) have autosomal recessive (AR) CGD, in which 6 families (26%) carried NCF1 variants, 4 (17.4%) carried CYBA variants, and 3 (13%) carried NCF2 variants. The median age of clinical onset was 3.3 and 48 months for patients with X-linked CGD (X-CGD) and AR-CGD, respectively. The onset of symptoms before age 1 year was 94% in X-CGD, 28.5% in AR-CGD, and 12.5% in patients with oxidase residual activity. Moreover, a de novo germline mutation at c.1415delG in CYBB (OMIM#300481) and a novel c.251_263del13bp in CYBA (OMIM#608508) were also investigated. CONCLUSIONS: Ihydrorhodamine-1,2,3 assay could not detect carrier mother in de novo case with CYBB variant. Most X-CGD patients have the onset of symptoms before age 1 year. Additionally, residual oxidase activity in AR-CGD causes a delay in onset, diagnosis, and prophylaxis. The protective role of residual activity is limited while the infection is ongoing and becoming serious.

MKL1 deficiency results in a severe neutrophil motility defect due to impaired actin polymerization.

Megakaryoblastic leukemia 1 (MKL1) promotes the regulation of essential cell processes, including actin cytoskeletal dynamics, by coactivating serum response factor. Recently, the first human with MKL1 deficiency, leading to a novel primary immunodeficiency, was identified. We report a second family with 2 siblings with a homozygous frameshift mutation in MKL1. The index case died as an infant from progressive and severe pneumonia caused by Pseudomonas aeruginosa and poor wound healing. The younger sibling was preemptively transplanted shortly after birth. The immunodeficiency was marked by a pronounced actin polymerization defect and a strongly reduced motility and chemotactic response by MKL1-deficient neutrophils. In addition to the lack of MKL1, subsequent proteomic and transcriptomic analyses of patient neutrophils revealed actin and several actin-related proteins to be downregulated, confirming a role for MKL1 as a transcriptional coregulator. Degranulation was enhanced upon suboptimal neutrophil activation, whereas production of reactive oxygen species was normal. Neutrophil adhesion was intact but without proper spreading. The latter could explain the observed failure in firm adherence and transendothelial migration under flow conditions. No apparent defect in phagocytosis or bacterial killing was found. Also, monocyte-derived macrophages showed intact phagocytosis, and lymphocyte counts and proliferative capacity were normal. Nonhematopoietic primary fibroblasts demonstrated defective differentiation into myofibroblasts but normal migration and F-actin content, most likely as a result of compensatory mechanisms of MKL2, which is not expressed in neutrophils. Our findings extend current insight into the severe immune dysfunction in MKL1 deficiency, with cytoskeletal dysfunction and defective extravasation of neutrophils as the most prominent features.

Assessment of Multi-Image Unmanned Aerial Vehicle Based High-Throughput Field Phenotyping of Canopy Temperature.

Canopy temperature (CT) has been related to water-use and yield formation in crops. However, constantly (e.g., sun illumination angle, ambient temperature) as well as rapidly (e.g., clouds) changing environmental conditions make it difficult to compare measurements taken even at short time intervals. This poses a great challenge for high-throughput field phenotyping (HTFP). The aim of this study was to i) set up a workflow for unmanned aerial vehicles (UAV) based HTFP of CT, ii) investigate different data processing procedures to combine information from multiple images into orthomosaics, iii) investigate the repeatability of the resulting CT by means of heritability, and iv) investigate the optimal timing for thermography measurements. Additionally, the approach was v) compared with other methods for HTFP of CT. The study was carried out in a winter wheat field trial with 354 genotypes planted in two replications in a temperate climate, where a UAV captured CT in a time series of 24 flights during 6 weeks of the grain-filling phase. Custom-made thermal ground control points enabled accurate georeferencing of the data. The generated thermal orthomosaics had a high spatial accuracy (mean ground sampling distance of 5.03 cm/pixel) and position accuracy [mean root-mean-square deviation (RMSE) = 4.79 cm] over all time points. An analysis on the impact of the measurement geometry revealed a gradient of apparent CT in parallel to the principle plane of the sun and a hotspot around nadir. Averaging information from all available images (and all measurement geometries) for an area of interest provided the best results by means of heritability. Correcting for spatial in-field heterogeneity as well as slight environmental changes during the measurements were performed with the R package SpATS. CT heritability ranged from 0.36 to 0.74. Highest heritability values were found in the early afternoon. Since senescence was found to influence the results, it is recommended to measure CT in wheat after flowering and before the onset of senescence. Overall, low-altitude and high-resolution remote sensing proved suitable to assess the CT of crop genotypes in a large number of small field plots as is required in crop breeding and variety testing experiments.