Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm

Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13–0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.publishedVersio

A Haplotype-Based GWAS Identified Trait-Improving QTL Alleles Controlling Agronomic Traits under Contrasting Nitrogen Fertilization Treatments in the MAGIC Wheat Population WM-800

The multi-parent-advanced-generation-intercross (MAGIC) population WM-800 was developed by intercrossing eight modern winter wheat cultivars to enhance the genetic diversity present in breeding populations. We cultivated WM-800 during two seasons in seven environments under two contrasting nitrogen fertilization treatments. WM-800 lines exhibited highly significant differences between treatments, as well as high heritabilities among the seven agronomic traits studied. The highest-yielding WM-line achieved an average yield increase of 4.40 dt/ha (5.2%) compared to the best founder cultivar Tobak. The subsequent genome-wide-association-study (GWAS), which was based on haplotypes, located QTL for seven agronomic traits including grain yield. In total, 40, 51, and 46 QTL were detected under low, high, and across nitrogen treatments, respectively. For example, the effect of QYLD_3A could be associated with the haplotype allele of cultivar Julius increasing yield by an average of 4.47 dt/ha (5.2%). A novel QTL on chromosome 2B exhibited pleiotropic effects, acting simultaneously on three-grain yield components (ears-per-square-meter, grains-per-ear, and thousand-grain-weight) and plant-height. These effects may be explained by a member of the nitrate-transporter-1 (NRT1)/peptide-family, TaNPF5.34, located 1.05 Mb apart. The WM-800 lines and favorable QTL haplotypes, associated with yield improvements, are currently implemented in wheat breeding programs to develop advanced nitrogen-use efficient wheat cultivars

Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800

Abstract Background Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F4:6 lines derived from intercrossing eight recently released European winter wheat cultivars. Results Genotyping WM-800 with 7849 SNPs revealed a low mean genetic similarity of 59.7% between MAGIC lines. WM-800 harbours distinct genomic regions exposed to segregation distortion. These are mainly located on chromosomes 2 to 6 of the wheat B genome where founder specific DNA segments were positively or negatively selected. This suggests adaptive selection of individual founder alleles during population development. The application of a genome-wide association study identified 14 quantitative trait loci (QTL) controlling plant height in WM-800, including the known semi-dwarf genes Rht-B1 and Rht-D1 and a potentially novel QTL on chromosome 5A. Additionally, epistatic effects controlled plant height. For example, two loci on chromosomes 2B and 7B gave rise to an additive epistatic effect of 13.7 cm. Conclusion The present study demonstrates that plant height in the MAGIC-WHEAT population WM-800 is mainly determined by large-effect QTL and di-genic epistatic interactions. As a proof of concept, our study confirms that WM-800 is a valuable tool to dissect the genetic architecture of important agronomic traits

Additional file 1 of Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800

Table S1. SNP genotypes, plant height, QTL detection rate and genotype and allele frequencies for 910 MAGIC WHEAT lines and eight founders. Table S2. Plant height (cm) raw data for MAGIC WM-lines and founders for year 2015 and 2016. Table S3. Distribution of polymorphic SNPs within WM-800 according to genome positions of Wang et al.... [36]. Table S4. Mean, minimum, maximum and coefficient of variation (CV, in %) of linkage disequilibrium (r2) in WM-800, calculated per chromosome, subgenome and across the whole wheat genome. Table S5. Genetic similarity (GS) between founders and WM-800 lines based on 7849 polymorphic SNPs. Table S6. Principle Component Analysis (PCO) based on genetic similarities (GS) between founders and WM-800 lines. Table S7. Distribution of segregation distortion (SD) SNPs and segregation distortion regions (SDR) across the wheat genome and across allele frequency groups. Table S8. Selection of unique SNPs from AFG 1 and AFG 7 in WM-800. Major selection events, represented by > 10 SNPs, are indicated in bold. (XLSX 6618 kb

Additional file 2: of Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800

Figure S1. Linkage disequilibrium (r2) as a function of genetic distance (mean of whole genome) within WM-800. The horizontal line (0.02) indicates the 95th percentile of the LD distribution of unlinked pairs of loci, representing the population-specific critical r2 value. The curve (red line) was fitted with second-degree LOESS. (PNG 30 kb

Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat

The potential of big data to support businesses has been demonstrated in financial services, manufacturing, and telecommunications. Here, we report on efforts to enter a new data era in plant breeding by collecting genomic and phenotypic information from 12,858 wheat genotypes representing 6575 single-cross hybrids and 6283 inbred lines that were evaluated in six experimental series for yield in field trials encompassing ~125,000 plots. Integrating data resulted in twofold higher prediction ability compared with cases in which hybrid performance was predicted across individual experimental series. Our results suggest that combining data across breeding programs is a particularly appropriate strategy to exploit the potential of big data for predictive plant breeding. This paradigm shift can contribute to increasing yield and resilience, which is needed to feed the growing world population

Process Evaluation of a Medical Student-Delivered Smoking Prevention Program for Secondary Schools: Protocol for the Education Against Tobacco Cluster Randomized Trial

Background: Most smokers start smoking during their early adolescence under the impression that smoking entails positive attributes. Given the addictive nature of cigarettes, however, many of them might end up as long-term smokers and suffering from tobacco-related diseases. To prevent tobacco use among adolescents, the large international medical students' network Education Against Tobacco (EAT) educates more than 40,000 secondary school students per year in the classroom setting, using evidence-based self-developed apps and strategies. Objective: This study aimed to evaluate the long-term effectiveness of the school-based EAT intervention in reducing smoking prevalence among seventh-grade students in Germany. Additionally, we aimed to improve the intervention by drawing conclusions from our process evaluation. Methods: We conduct a cluster-randomized controlled trial with measurements at baseline and 9, 16, and 24 months postintervention via paper-and-pencil questionnaires administered by teachers. The study groups consist of randomized schools receiving the 2016 EAT curriculum and control schools with comparable baseline data (no intervention). The primary outcome is the difference of change in smoking prevalence between the intervention and control groups at the 24-month follow-up. Secondary outcomes are between-group differences of changes in smoking-related attitudes and the number of new smokers, quitters, and never-smokers. Results: A total of 11,268 students of both sexes, with an average age of 12.32 years, in seventh grade of 144 secondary schools in Germany were included at baseline. The prevalence of cigarette smoking in our sample was 2.6%. The process evaluation surveys were filled out by 324 medical student volunteers, 63 medical student supervisors, 4896 students, and 141 teachers. Conclusions: The EAT cluster randomized trial is the largest school-based tobacco-prevention study in Germany conducted to date. Its results will provide important insights with regards to the effectiveness of medical student-delivered smoking prevention programs at school