Wheat is the most widely grown crop worldwide and ranks 3rd behind maize and rice in production. P. neglectus is a rootlesion nematode causing severe yield losses in wheat. There are several methods to reduce negative effects of root lesion nematodes on yield. Out of these, growing of resistant or tolerant varieties is the most environmentally friendly and cost effective method to avoid yield losses by nematodes. Therefore, the aim of this study was to assess the reaction of diverse wheat genotypes to P. neglectus and to detect QTLs involved in resistance against P. neglectus by using genome wide association studies (GWAS). In order to achieve this, a diversity set of 314 wheat genotypes was inoculated with nematodes(1000 nematodes per pot) under greenhouse conditions in six replications. In parallel, genotypic data obtained by the Illumina iSelect 15K, 20K and 90K SNP chip, respectively was used for genome wide association studies (GWAS), i.e. 12,986 single nucleotide (SNP) markers. The flanking sequences of markers were mapped against the IWGSC reference genome of Chinese Spring (IWGSC, 2018) resulting in 9,839 mapped markers. After filtering for minor allele frequency (MAF)  5%, maximum percentage of missing values <10%, heterozygosity (12.5%), 9,253 high quality markers were used for GWAS. Based on LD prune by using PLINK (Purcellet al. 2007), a set of 2,343 markers was used to calculate kinship and population structure. The population structure was determined by principal coordinate analysis by using the Darwin software (Perrier and Jacquemoud-Collet. 2006). Subsequently, a compressed Mixed Linear Model approach corrected for Kinship (CMLM+K) was applied to conduct GWAS and to detect QTL associated with the number of nematodes per plant root.

In summary, phenotypic evaluation showed large variation between genotypes ranging from 105 to 8889 nematodes per plant. GWAS resulted in the detection of five QTLs on chromosome 1A, 2A, 2B, 3B and 7D significantly associated with resistance to P. neglectus explaining 4.6% to 6.5 % of the phenotypic variance. The results will be validated in bi-parental populations and based on the annotation available from the reference genome (Chinese spring) candidate genes may be identified which might play a role in nematode resistance in wheat.