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

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 Plant Height in Winter Wheat (<i>Triticum aestivum</i> L.)

<div><p>The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the <i>Rht-D1b</i> mutant allele in 58% of the investigated varieties, while the <i>Rht-B1b</i> mutant was only present in 7% of the varieties. <i>Rht-D1</i> was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs) were observed for plant height and the SSR markers (−log₁₀ (P-value) ≥4.82) and 280 (−log₁₀ (P-value) ≥5.89) for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA) metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, <i>ent</i>-kaurenoic acid oxidase orthologous to wheat chromosome 7A, <i>ent</i>-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes <i>Rht-B1</i> and <i>Rht-D1</i> there is a wide spectrum of loci available that could be used for modulating plant height in variety development.</p></div

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