The MAGIC-WHEAT aims to develop new winter wheat cultivars with improved agronomic traits concerning yield, quality, pathogen resistance and nutrient efficiency. The WM-800 population, based on an eight-way-cross of modern German winter wheat cultivars, was cultivated in Germany at three and four locations in 2017 and 2018, respectively. The population of 800 MAGIC lines was examined for grain yield, yield components and grain protein content under two contrasting nitrogen levels (N0 low nitrogen treatment; N1 common practice nitrogen fertilization). Extensive variation for the traits grain yield (YLD), thousand kernel weight (TKW), grain number per ear (GNE), ears per square meter (EAR) and protein content (PC) were detected, as well as significant differences between the treatments. The ANOVA showed significant genotype effects, and also genotype x treatment interactions, which indicates that the WM-800 lines react differently to divergent nitrogen supply.

DNA marker data were collected based on the Illumina wheat 15k SNP chip and the Affymetrix wheat 135k SNP array (TraitGenetics, Gatersleben). After merging phenotype data of 800 MAGIC lines with 27,685 informative SNPs a Genome Wide Association Study was carried out (GWAS), assessed by a cross-validation approach. GWAS resulted in 67 highly significant QTLs with high detection rates for all traits (p  0.0001, cross validation detection rate minimum  20). The sum of all detected QTLs for every single trait explained between 11.7 and 47.2 % of the phenotypic variation, depending on the trait. Highly significant effects of the Rht-B1 and Rht-D1 genes were found for TKW and GNE. The semi-dwarf alleles of each Rht gene were associated with a decrease of TKW and an increase of GNE. Several additional SNPs were associated with more than one trait effect, often revealing opposite effect directions, which demonstrates the challenges of increasing grain yield. In addition, some N level-specific QTLs were associated with highly significant effects on YLD and EAR (up to 3,7 dt/ha and 31 ears/m2). The nitrogen use efficiency (NUE) and grain nitrogen uptake (GNU) were calculated to identify the genetic background of N stress tolerant lines. Further investigations are required to explain the genetic architecture of grain yield, particularly under low nitrogen conditions.