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

Allelic effects of dwarfing gene <i>Rht-D1</i> in a population of 372 European wheat varieties.

<p>Varieties carrying the mutant allele <i>Rht-D1b</i> (dwarfing type) showed an increased FHB score resulting in decreased resistance in four different environments.</p

Manhattan plots of marker-trait associations for FHB resistance.

<p>The plot represents the individual significant −log₁₀(p)>3.0 marker-trait associations of four environments plus BLUEs sorted according to their chromosomal location. The dotted line indicates the threshold of −log₁₀(p) = 4.82 for Bonferoni correction. All markers which were not associated or associated with a −log₁₀(p) below 3.0 were set to 0. Green dots represent the MTA of a single environment, red dots represent the MTA of a BLUE value.</p

Whole Genome Association Mapping of <em>Fusarium</em> Head Blight Resistance in European Winter Wheat (<em>Triticum aestivum</em> L.)

<div><p>A total of 358 recent European winter wheat varieties plus 14 spring wheat varieties were evaluated for resistance to <i>Fusarium</i> head blight (FHB) caused by <i>Fusarium graminearum</i> and <i>Fusarium culmorum</i> in four separate environments. The FHB scores based on FHB incidence (Type I resistance)×FHB severity (Type II resistance) indicated a wide phenotypic variation of the varieties with BLUE (best linear unbiased estimation) values ranging from 0.07 to 33.67. Genotyping with 732 microsatellite markers resulted in 782 loci of which 620 were placed on the ITMI map. The resulting average marker distance of 6.8 cM allowed genome wide association mapping employing a mixed model. Though no clear population structure was discovered, a kinship matrix was used for stratification. A total of 794 significant (−log₁₀(p)-value≥3.0) associations between SSR-loci and environment-specific FHB scores or BLUE values were detected, which included 323 SSR alleles. For FHB incidence and FHB severity a total of 861 and 877 individual marker-trait associations (MTA) were detected, respectively. Associations for both traits co-located with FHB score in most cases. Consistent associations detected in three or more environments were found on all chromosomes except chromosome 6B, and with the highest number of MTA on chromosome 5B. The dependence of the number of favourable and unfavourable alleles within a variety to the respective FHB scores indicated an additive effect of favourable and unfavourable alleles, i.e. genotypes with more favourable or less unfavourable alleles tended to show greater resistance to FHB. Assessment of a marker specific for the dwarfing gene <i>Rht-D1</i> resulted in strong effects. The results provide a prerequisite for designing genome wide breeding strategies for FHB resistance.</p> </div

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

Frequency of (A) favourable FHB alleles and (B) unfavourable FHB alleles in individual varieties.

<p>Most varieties carried between 20 to 40 alleles increasing or decreasing the resistance to FHB.</p

Linkage disequilibrium represented as r² of marker pairs versus genetic distance in centiMorgan over all chromosomes.

<p>The horizontal line marks the threshold above which LD is likely due to genetic linkage.</p

Genomic and Phenotypic data

The excel sheet contains the genomic data and the phenotypic dat

Phenotypic distribution of FHB score BLUEs in 372 varieties.

<p>The BLUEs of the FHB score (FHB incidence×FHB severity) were based on resistance tests in four environments. A low FHB score indicates high resistance.</p

Effect of (A) favourable and (B) unfavourable FHB alleles.

<p>Linear regression resulted in a relationship of FHB-BLUEs score and number of favourable and number of unfavourable alleles in 372 wheat varieties.</p