Linear regressions of the most PH reducing (“best”) and the most PH promoting (“worst”) SNP-alleles with PH-BLUEs.

<p>Linear regression resulted in a relationship between PH-BLUEs and the 20, 10 or 5 “best” or “worst” SNP-alleles from different loci in 372 varieties.</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

Linear regressions of the most PH reducing (“best”) and the most PH promoting (“worst”) SSR-alleles with PH-BLUEs.

<p>Linear regression resulted in a relationship between PH-BLUEs and the 20, 10 or 5 “best” or “worst” SSR-alleles in 372 varieties.</p

Keyword search in rice for PH candidate genes.

<p>Keyword search in rice for PH candidate genes.</p

List of orthologous loci in rice with genes of the GA metabolism or related to dwarfing phenotypes.

<p>*Nomenclature according to Sakamoto et al. 2004 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113287#pone.0113287-Sakamoto1" target="_blank">[58]</a></p><p>List of orthologous loci in rice with genes of the GA metabolism or related to dwarfing phenotypes.</p

Coincidences of significant MTAs in our study with QTL or meta-QTL regions described by Griffiths et al. 2012 [54].

<p>Coincidences of significant MTAs in our study with QTL or meta-QTL regions described by Griffiths et al. 2012 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113287#pone.0113287-Griffiths1" target="_blank">[54]</a>.</p

Number of MTAs per environment for the SSR markers and the SNPs of the 90K iSelect chip.

<p>Number of MTAs per environment for the SSR markers and the SNPs of the 90K iSelect chip.</p

List of the most PH reducing (“best”) and most PH enhancing (“worst”) SNP-alleles.

<p>*Nomenclature according to Sakamoto et al. 2004 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113287#pone.0113287-Sakamoto1" target="_blank">[58]</a>.</p><p>List of the most PH reducing (“best”) and most PH enhancing (“worst”) SNP-alleles.</p

Boxplots for plant height.

<p>Boxplots for eight field environments are depicted in green, the untreated control in a nursery is shown in red. Asterisks mark outlier varieties.</p

Manhattan plots of SSR or SNP marker alleles associated with plant height.

<p>The plot presents significant MTAs at a threshold of –log₁₀ (P-value) ≥4.0 for BLUEs sorted according to their chromosomal location. The red line indicates the threshold for Bonferroni correction, –log₁₀ (P-value) ≥4.82 (SSR) and ≥5.89 (SNP).</p