Identification and Characterization of Quantitative Trait Loci (QTL) for Resistance to the Cyst Nematode (Globodera pallida) in the Potato (Solanum tuberosum)

This work focused on the identification and characterization of the genetic basis of important agronomic traits in the potato with main interest centered on resistance to the potato cyst nematode, Globodera pallida. A high level of genetic resistance to nematodes is an important aspect in breeding new potato varieties. The first step towards that is the localization of genetic factors controlling resistance on the potato map. We made use of information obtained from experimental diploid mapping populations to evaluate tetraploid breeding material for the applied research. We explored the genetic resistances present in the crop, which show a continuous variation and are assumed to be controlled by several loci which act collectively on the expression of resistance. These loci are referred to as quantitative trait loci (QTL) (Meyer et al. 1998). The number of QTL for resistance was determined through an association mapping approach. Two tetraploid populations were genotyped with several markers either within or physically linked to candidate genes. Phenotypic data was supplied by the two breeding companies, Saka-Ragis and Böhm-Nordkartoffel. Significant associations with quantitative resistance were found for all marker types. Single nucleotide polymorphisms (SNPs) were shown to be the most efficient marker type to detect significant associations between markers and the resistance phenotype. Two of them served as basis for developing a PCR-based marker highly diagnostic for potato varieties with high resistance to Globodera pallida (Sattarzadeh et al. 2006). Based on an InDel in the sequence we designed an allele-specific CAPS marker for the quantitative detection of maturity corrected resistance to the oomycete Phytophthora infestans. Using this marker we provide solutions for the selection of superior potato genotypes through the development of easy-to-use DNA based molecular markers. Fine mapping of a QTL for resistance to the nematode located on chromosome V was done by a combination of association tests and physical mapping to gain more insight in the genomic organisation of a QTL. We were able to delimit the size to a genetic region of 2 cM. Fluorescent in situ hybridization (FISH) was applied to obtain valuable complementary information regarding size and chromosomal position of this QTL. The region was estimated to span less than 1 Mb and is located in the euchromatic region of the long arm of chromosome V. These findings will assist future map based cloning efforts in this region. The detection of numerous loci in tetraploid breeding material associated with important agronomic traits provides valuable data which can be used to design additional markers not just for resistance against G. pallida but also for other traits, such as resistance to Phytophthora infestans, maturity, yield, and starch content

Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

<p>Abstract</p> <p>Background</p> <p>Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (<it>Solanum tuberosum</it>). Potato species are tetraploid and highly heterozygous.</p> <p>Results</p> <p>Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes.</p> <p>Conclusion</p> <p>Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at <url>http://www.gabipd.org/projects/satlotyper/</url>. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.</p

Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.)

The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene

Lignan Derivatives from Krameria lappacea Roots Inhibit Acute Inflammation in Vivo and Pro-inflammatory Mediators in Vitro

The roots of Krameria lappacea are used traditionally against oropharyngeal inflammation. So far, the astringent and antimicrobial properties of its proanthocyanidin constituents are considered to account for the anti-inflammatory effect. The aim of the present study was to characterize pharmacologically a lipophilic extract of K. lappacea roots and several isolated lignan derivatives (111) in terms of their putative anti-inflammatory activity. The dichloromethane extract (ID50 77 \u3bcg/cm2) as well compounds 111 (ID50 0.310.60 \u3bcmol/cm2) exhibited topical antiedematous properties comparable to those of indomethacin (ID50 0.29 \u3bcmol/cm2) in a mouse ear in vivo model. Two of the most potent compounds, 2-(2-hydroxy-4-methoxyphenyl)-5-(3-hydroxypropyl)benzofuran (5) and (+)-conocarpan (7), were studied regarding their time-dependent edema development and leukocyte infiltration up to 48 h after croton oil-induced dermatitis induction, and they showed activity profiles similar to that of hydrocortisone. In vitro studies of the isolated lignan derivatives demonstrated the inhibition of NFkB, cyclooxygenase-1 and -2, 5-lipoxygenase, and microsomal prostaglandin E2 synthase-1 as well as antioxidant properties, as mechanisms possibly contributing to the observed in vivo effects. The present findings not only support the ethnopharmacological use of K. lappacea roots but also reveal that the isolated lignan derivatives contribute strongly to the anti-inflammatory activity of this herbal drug

Flex Your Muscles: EMG-Based Serious Game Controls

In recent years, non-traditional input devices for digital games and applications such as wearable sensors have become increasingly available and affordable. Electromyography (EMG) promises some unique advantages over traditional input devices such as keyboards or gamepads by collecting input data directly at a person’s muscle. As long as the corresponding muscle is intact, EMG can be used even when physical movement is not possible, for example when a person is injured or has an amputated limb. It also allows for unique wearable positioning on the body, potentially allowing for a larger freedom of movement. In this paper, we examine whether an EMG-based input device is feasible to control an in-game character in a digital game. In order to do so, we first assess different EMG-related technologies and available EMG devices. Based on this assessment, we develop an EMG-based input device that can be connected to a computer. We develop a side scrolling game which can be connected to the EMG-based input device and allows for the player to switch between keyboard- and EMG-based controls. Lastly, we evaluate our developed system empirically and discuss the feasibility of EMG-based game controllers based on observed practical and theoretical limitations of the technology

Characterisation and clinical outcomes in children and adolescents with diabetes according to newly defined subgroups: a cohort study from the DPV registryResearch in context

Summary: Background: Personalised therapy has emerged as a possibly more efficient approach taking disease heterogeneity into account. The aim of this study was to determine whether recently described subgroups of childhood diabetes have prognostic association with diabetes-specific complications and, therefore, might be a basis for personalised therapies. Methods: We applied a previously developed subgroup classification to pediatric patients (diabetes onset <18 years) from the prospective Diabetes Patient Follow-up (DPV) registry with documented data between January 1, 2000 and March 31, 2022, from diabetes centers in Germany, Austria, Switzerland, and Luxembourg. The classification required information on islet autoantibody status, age, haemoglobin A1c (HbA1c), and body-mass index (BMI-SDS) at disease manifestation, as well as follow up data after 2 and after 4 years, which was available in 22,719 patients. Patients without documented data on these parameters were excluded from the analysis. The cumulative risk of severe hypoglycemia, diabetic ketoacidosis (DKA), retinopathy, and nephropathy were analysed by Kaplan–Meier analyses over a median follow-up of 6.8 years (IQR 4.8–9.6). Findings: Patients were classified into 10 subgroups (P1–P7 islet autoantibody-positive, n = 19,811; N1–N3 islet autoantibody-negative, n = 2908). The groups varied markedly with respect to specific acute and chronic complications. Severe hypoglycemia was a characteristic feature in young islet autoantibody-positive subgroups P1, P3, P4 (10-year risk 46, 46 and 47%) and the islet autoantibody-negative groups N1, N2 (43 and 46%). Nephropathy was identified in patient groups P2 and P5 (10-year risk 16%), which had features of moderate disease such as preserved C-peptide, low HbA1c, and very low frequency of DKA at diabetes onset. Group P7, which was defined by a high BMI, was associated with poor metabolic control, DKA, and retinopathy. In contrast, islet autoantibody-negative patients with high BMI (N3) had a low risk for all four complications. Interpretation: Subgrouping of childhood diabetes at diabetes onset provided prognostic value for the development of acute and chronic diabetes-specific complications. Funding: The DPV initiative is supported by The German Ministry of Education and Research (BMBF) within the German Center for Diabetes Research, the diabetes surveillance of the Robert Koch Institute, the German Diabetes Association (DDG) and INNODIA

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

The oomycete Phytophthora infestans causes late blight, the most relevant disease of potato (Solanum tuberosum) worldwide. Field resistance to late blight is a complex trait. When potatoes are cultivated under long day conditions in temperate climates, this resistance is correlated with late plant maturity, an undesirable characteristic. Identification of natural gene variation underlying late blight resistance not compromised by late maturity will facilitate the selection of resistant cultivars and give new insight in the mechanisms controlling quantitative pathogen resistance. We tested 24 candidate loci for association with field resistance to late blight and plant maturity in a population of 184 tetraploid potato individuals. The individuals were genotyped for 230 single nucleotide polymorphisms (SNPs) and 166 microsatellite alleles. For association analysis we used a mixed model, taking into account population structure, kinship, allele substitution and interaction effects of the marker alleles at a locus with four allele doses. Nine SNPs were associated with maturity corrected resistance (P < 0.001), which collectively explained 50% of the genetic variance of this trait. A major association was found at the StAOS2 locus encoding allene oxide synthase 2, a key enzyme in the biosynthesis of jasmonates, plant hormones that function in defense signaling. This finding supports StAOS2 as being one of the factors controlling natural variation of pathogen resistance