Genetic and physical mapping of anther extrusion in elite European winter wheat

<div><p>The production and cultivation of hybrid wheat is a possible strategy to close the yield gap in wheat. Efficient hybrid wheat seed production largely depends on high rates of cross-pollination which can be ensured through high anther extrusion (AE) by male parental lines. Here, we report the AE capacity and elucidate its genetics in 514 elite European winter wheat varieties via genome-wide association studies (GWAS). We observed a wide range of variation among genotypes and a high heritability (0.80) for AE. The whole panel was genotyped with the 35k Affymetrix and 90k iSELECT single nucleotide polymorphism (SNP) arrays plus <i>Ppd-D1</i>, <i>Rht-B1 and Rht-D1</i> candidate markers. GWAS revealed 51 marker-trait associations (MTAs) on chromosomes 1A, 1B, 2A, 4D and 5B, with <i>Rht-D1</i> (4D) being the most significant marker. Division of whole panel according to the <i>Rht-D1</i> genotype resulted in 212 and 294 varieties harboring <i>Rht-D1a</i> and <i>Rht-D1b</i> allele, respectively. The presence of <i>Rht-D1a</i> compared to <i>Rht-D1b</i> (mutant) allele had a large phenotypic influence on AE resulting in its ~17% increase. GWAS performed on the sub-panels detected novel MTAs on chromosomes 2D, 3B and 6A with increased phenotypic variance imparted by individual markers. Our study shows that AE is a highly quantitative trait and wild type <i>Rht-D1a</i> allele greatly improves AE. Moreover, demarcating the quantitative trait loci regions based on intra-chromosomal linkage disequilibrium revealed AE’s candidate genes/genomic regions. Understanding the genetics of AE in elite European wheat and utilizing the linked markers in breeding programs can help to enhance cross-pollination for better exploitation of heterosis.</p></div

Summary of genome-wide association studies (GWAS) for anther extrusion in different wheat panels.

<p><b>(A)</b> Manhattan plot based on linear mixed model using kinship matrix for correction of population stratification. <b>(B)</b> Quantile-quantile plot depicting expected <i>versus</i> observed <i>P</i> values at −log₁₀ scale. Full-set represents the GWAS results of varieties harboring both <i>Rht-D1a</i> and <i>Rht-D1b</i> alleles. <i>Rht-D1a</i> and <i>Rht-D1b</i> set represent the GWAS results in individual panels harboring either of the alleles. <i>n</i> denotes the total number of varieties used in GWAS panels.</p

Distribution of the best linear unbiased estimates (BLUEs) of the trait anther extrusion.

<p>Distribution of the best linear unbiased estimates (BLUEs) of the trait anther extrusion.</p

Principal component analysis (PCA) of wheat varieties based on SNP genotype explains the absence of pronounced population structure.

<p>Full-set means that the varieties harbored both <i>Rht-D1a</i> and <i>Rht-D1b</i> alleles and <i>n</i> denotes the total number of varieties used.</p

Influence of the most significant SNPs (SNPs with the largest additive effect) on AE phenotype based on GWAS conducted on panels harboring full-set of varieties and varieties harboring only <i>Rht-D1a</i> and <i>Rht-D1b</i> alleles.

<p>Horizontal dotted line marks the mean of AE BLUEs. R and V denote the varieties harboring reference (major) and variant (minor) alleles, respectively.</p

Distribution of anther extrusion in wheat panels harboring both <i>Rht-D1a</i> and <i>Rht</i>-<i>D1b</i> alleles (full-set) and panels harboring only one of the alleles.

<p><i>n</i> denotes the number of varieties in individual panels.</p

List of most significant SNPs (MS-SNPs) representing QTLs on individual chromosomes.

<p>List of most significant SNPs (MS-SNPs) representing QTLs on individual chromosomes.</p

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

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

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