Genome-wide association mapping and genomic prediction of Fusarium head blight resistance,heading stage and plant height in winter rye (Secale cereale)

Rye is a multi-purpose cereal crop grown in Central and Eastern Europe as well as in Western Canada. Fusarium head blight (FHB) is one of the diseases that have a severe negative impact on rye, but knowledge about FHB resistance at the genomic level is totally missing in rye. The objective of this study was to elucidate the genetic architecture of FHB resistance in winter rye using genome-wide association (GWA) mapping complemented by genomic prediction (GP) in comparison with marker-assisted selection (MAS). Additionally, plant height and heading stage were analysed. A panel of 465 S₁-inbred lines of winter rye was phenotyped in three environments (location–year combinations) for FHB resistance by inoculation with Fusarium culmorum and genotyped with a 15k SNP array. Significant genotypic variation and high heritabilities were found for FHB resistance, heading stage and plant height. FHB did not correlate with heading stage, but was moderately correlated with plant height (r = −.52, p < .001) caused by some susceptible short inbred lines. The GWA scan identified 15 QTL for FHB resistance that jointly explained 74% of the genotypic variance. In addition, we detected 11 QTL for heading stage and 8 QTL for plant height, explaining 26% and 14% of the genotypic variance, respectively. A genome-wide prediction approach resulted in 44% higher prediction abilities than marker-assisted selection for FHB resistance. In conclusion, genomic approaches appear promising to improve and accelerate breeding for complex traits in winter rye.