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

Levels of Angiopoietin 2 Are Predictive for Mortality in Patients Infected With Yellow Fever Virus

In 2018 there was a large yellow fever outbreak in São Paulo, Brazil, with a high fatality rate. Yellow fever virus can cause, among other symptoms, hemorrhage and disseminated intravascular coagulation, indicating a role for endothelial cells in disease pathogenesis. Here, we conducted a case-control study and measured markers related to endothelial damage in plasma and its association with mortality. We found that angiopoietin 2 is strongly associated with a fatal outcome and could serve as a predictive marker for mortality. This could be used to monitor severe cases and provide care to improve disease outcome

Erosion of quantitative host resistance in the apple × Venturia inaequalis pathosystem

Theoretical approaches predict that host quantitative resistance selects for pathogens with a high level of pathogenicity, leading to erosion of the resistance. This process of erosion has, however, rarely been experimentally demonstrated. To investigate the erosion of apple quantitative resistance to scab disease, we surveyed scab incidence over time in a network of three orchards planted with susceptible and quantitatively resistant apple genotypes. We sampled Venturia inaequalis isolates from two of these orchards at the beginning of the experiment and we tested their quantitative components of pathogenicity (i.e., global disease severity, lesion density, lesion size, latent period) under controlled conditions. The disease severity produced by the isolates on the quantitatively resistant apple genotypes differed between the sites. Our study showed that quantitative resistance may be subject to erosion and even complete breakdown, depending on the site. We observed this evolution over time for apple genotypes that combine two broad-spectrum scab resistance QTLs, F11 and F17, showing a significant synergic effect of this combination in favour of resistance (i.e., favourable epistatic effect). We showed that isolates sampled in the orchard where the resistance was inefficient presented a similar level of pathogenicity on both apple genotypes with quantitative resistance and susceptible genotypes. As a consequence, our results revealed a case where the use of quantitative resistance may result in the emergence of a generalist pathogen population that has extended its pathogenicity range by performing similarly on susceptible and resistant genotypes. This emphasizes the need to develop quantitative resistances conducive to trade-offs within the pathogen populations concerned

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

A proposal for the nomenclature of Venturia inaequalis races.

The Venturia inaequalis-Malus pathosystem was one of the first for which gene-for-gene relationships were demonstrated following the discovery of such relationships between Melampsora lini and flax by Flor in the 1950s. An understanding of these relationships forms the basis for monitoring pathotypes of V. inaequalis at the population level and is employed to assess the usefulness of resistance genes for breeding durable resistance to scab. These pathotypes are difficult to accommodate in the current system of nomenclature for V. inaequalis races where each new combination of avirulence alleles is assigned a simple numerical descriptor as its name. We propose a system that is better suited to the increasing complexities of combinations of genes involved in both race-specific and race-nonspecific recognition by the host, while at the same time updating the name of scab resistance loci (Rvik) and QTL loci (Qvik) to international standards. For the race-specific interactions, the basic premise is that each Rvik-AvrRvik and Qvik-AvrQvik relationship should be represented by a differential host (k), abbreviated to h(k), carrying only the specific Rvik or (major) Qvik resistance allele and an isolate of the pathogen having lost only the complementary allele at the AvrRvik or AvrQvik locus, race (k), with k representing the number of the specific interaction. Races lacking more than one avirulence gene at different loci will be identified as race (k,l,m,\u2026) and apple hosts carrying multiple scab resistance genes as host (k,l,m,\u2026). The proposed system has some continuity with the current system, but should simplify the presentation and interpretation of studies on avirulence alleles in V. inaequalis at the population level. Gene-for-gene relationships reported to date for this pathosystem are reviewed, some inconsistencies clarified, and several new interactions added. The gene-for-gene relationships of European isolates collected in the last decade have been studied in order to establish a new set of reference isolates that represent various V. inaequalis races

A proposal for the nomenclature of Venturia inaequalis races

International audienceThe Venturia inaequalis-Malus pathosystem was one of the first for which gene-for-gene relationships were demonstrated following the discovery of such relationships between Melampsora lini and flax by Flor in the 1950s. An understanding of these relationships forms the basis for monitoring pathotypes of V. inaequalis at the population level and is employed to assess the usefulness of resistance genes for breeding durable resistance to scab. These pathotypes are difficult to accommodate in the current system of nomenclature for V. inaequalis races where each new combination of avirulence alleles is assigned a simple numerical descriptor as its name. We propose a system that is better suited to the increasing complexities of combinations of genes involved in both race-specific and race-nonspecific recognition by the host, while at the same time updating the name of scab resistance loci (Rvik) and QTL loci (Qvik) to international standards. For the race-specific interactions, the basic premise is that each Rvik-AvrRvik and Qvik-AvrQvik relationship should be represented by a differential host (k), abbreviated to h(k), carrying only the specific Rvik or (major) Qvik resistance allele and an isolate of the pathogen having lost only the complementary allele at the AvrRvik or AvrQvik locus, race (k), with k representing the number of the specific interaction. Races lacking more than one avirulence gene at different loci will be identified as race (k,l,m,...) and apple hosts carrying multiple scab resistance genes as host (k,l,m,...). The proposed system has some continuity with the current system, but should simplify the presentation and interpretation of studies on avirulence alleles in V. inaequalis at the population level. Gene-for-gene relationships reported to date for this pathosystem are reviewed, some inconsistencies clarified, and several new interactions added. The gene-for-gene relationships of European isolates collected in the last decade have been studied in order to establish a new set of reference isolates that represent various V.inaequalis races