Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids

BACKGROUND: Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. RESULTS: Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. CONCLUSIONS: The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Spring air temperature accounts for the bimodal temporal distribution of Septoria tritici epidemics in the winter wheat stands of Luxembourg

Septoria tritici is the causal agent of leaf blotch in wheat and among the most damaging fungal cereal pathogens in the humid regions of central Europe. The percentage of the leaf area colonized by S. tritici was recorded weekly between April and July every season between 2004 and 2010. A total of 11 cultivars with moderate susceptibility [ratings of 4e6 on a 1 (resistant) to 9 (susceptible) scale] were included. The disease level was assessed on the upper three leaf layers at 2 locations between 2004 and 2006 and at 3 locations between 2007 and 2010. The period between sowing and the point of time, when 50% of the leaf area was necrotized due to colonization by S. tritici (T50) was estimated for each year, site, cultivar and leaf layer by non-linear regression. T50 values followed a bimodal distribution with one maximum at 245 days after sowing (DAS; early epidemics) and one maximum at 270 DAS (late epidemics). Early epidemics were preceded by almost constant daily average temperatures of 13.2 0.8 C between 181 and 210 DAS. Late epidemics were preceded by an approximately linear increase in temperature from 8.7 0.9 to 12.1 0.9 C during the same period of time. Based on these differences, it seems possible to predict whether an early or a late epidemic can be expected at least 35 days before the epidemic outbreak. Temperature sums calculated with a base temperature of 6.6 C starting at sowing and ending when T50 was reached were not significantly different between early and late epidemics (P ¼ 0.73) and averaged 1721 49 days. Fungicide applications, which resulted into a delay of the epidemic development similar to the difference between early and late epidemics, resulted in a yield increase between 11.7 and 12.6%.Septoria tritici is the causal agent of leaf blotch in wheat and among the most damaging fungal cereal pathogens in the humid regions of central Europe. The percentage of the leaf area colonized by S. tritici was recorded weekly between April and July every season between 2004 and 2010. A total of 11 cultivars with moderate susceptibility [ratings of 4e6 on a 1 (resistant) to 9 (susceptible) scale] were included. The disease level was assessed on the upper three leaf layers at 2 locations between 2004 and 2006 and at 3 locations between 2007 and 2010. The period between sowing and the point of time, when 50% of the leaf area was necrotized due to colonization by S. tritici (T50) was estimated for each year, site, cultivar and leaf layer by non-linear regression. T50 values followed a bimodal distribution with one maximum at 245 days after sowing (DAS; early epidemics) and one maximum at 270 DAS (late epidemics). Early epidemics were preceded by almost constant daily average temperatures of 13.2 0.8 C between 181 and 210 DAS. Late epidemics were preceded by an approximately linear increase in temperature from 8.7 0.9 to 12.1 0.9 C during the same period of time. Based on these differences, it seems possible to predict whether an early or a late epidemic can be expected at least 35 days before the epidemic outbreak. Temperature sums calculated with a base temperature of 6.6 C starting at sowing and ending when T50 was reached were not significantly different between early and late epidemics (P ¼ 0.73) and averaged 1721 49 days. Fungicide applications, which resulted into a delay of the epidemic development similar to the difference between early and late epidemics, resulted in a yield increase between 11.7 and 12.6%

Azoxystrobin and epoximazole sensitivity profiles of Mycosphaerella graminicola populations from the Grand-Duchy of Luxemburg in 2007 and 2008

Mycosphaerella graminicola strains were isolated from symptomatic winter wheat (Triticum aestivum) and spelt (Triticum spelta) leaves sampled across the Grand-Duchy of Luxembourg. In total, 484 strains were isolated from winter wheat, and 31 from spelt leaves. The sensitivity profiles of these strains towards azoxystrobin (Amistar®, Syngenta Agro GmbH, Germany) and against epoxiconazole (Opus®, BASF Belgium NV/S A, Brussels, Belgium) were assessed in microplates, allowing to test 10 different concentrations for each active substance (0, 0.00316, 0.01, 0.0316, 0.1, 0.316, 1, 3.16, 10 and 31.6μg/mL). 100μ g/mL of salicylhydroxamic acid (SHAM) was also added to the medium, in order to prevent the strains from using alternative respiration. Results of the sensitivity tests for azoxystrobin showed a dose-dependent decrease of in vitro growth for all the strains. During both years, strains could be divided into two distinct sub-populations in relation to their azoxystrobin sensitivity, thus forming a bimodal distribution commonly reported to be associated with a single gene-mediated resistance. For wheat, the dominant sub-population was the one showing full resistance to azoxystrobin. The results of the sensitivity tests to epoxiconazole in liquid media showed a dose-dependent decrease of fungal growth for all the strains tested. The EC50 values followed an unimodal distribution. When the sensitivity distribution of the strains collected in 2008 (n=379) was compared to that observed in 2007, although the populations have remained unimodal, a minor shift towards less sensitive populations was observed. Compared to strains originating from wheat, the spelt strains were more sensitive towards both fungicides (p ≤ 0.001)

Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids

Abstract Background Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. Results Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. Conclusions The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids.</p

The plastidial Arabidopsis thaliana NFU1 protein binds and delivers [4Fe-4S] clusters to specific client proteins

The plastidial Arabidopsis thaliana NFU1 protein binds and delivers [4Fe-4S] clusters to specific client protein

Iron–sulfur protein NFU2 is required for branched-chain amino acid synthesis in Arabidopsis roots

International audienceNumerous proteins require a metallic co-factor for their function. In plastids, the maturation of iron-sulfur (Fe-S) proteins necessitates a complex assembly machinery. In this study, we focused on Arabidopsis thaliana NFU1, NFU2, and NFU3, which participate in the final steps of the maturation process. According to the strong photosynthetic defects observed in high chlorophyll fluorescence 101 (hcf101), nfu2, and nfu3 plants, we determined that NFU2 and NFU3, but not NFU1, act immediately upstream of HCF101 for the maturation of [Fe4S4]-containing photosystem I subunits. An additional function of NFU2 in the maturation of the [Fe2S2] cluster of a dihydroxyacid dehydratase was obvious from the accumulation of precursors of the branched-chain amino acid synthesis pathway in roots of nfu2 plants and from the rescue of the primary root growth defect by supplying branched-chain amino acids. The absence of NFU3 in roots precluded any compensation. Overall, unlike their eukaryotic and prokaryotic counterparts, which are specific to [Fe4S4] proteins, NFU2 and NFU3 contribute to the maturation of both [Fe2S2] and [Fe4S4] proteins, either as a relay in conjunction with other proteins such as HCF101 or by directly delivering Fe-S clusters to client proteins. Considering the low number of Fe-S cluster transfer proteins relative to final acceptors, additional targets probably await identification