Genome-Wide Association Studies Combined with Genomic Selection as a Tool to Increase Fusarium Head Blight Resistance in Wheat

Abstract

Genomic selection (GS) has shown successful results as a tool to increase Fusarium Head Blight (FHB) resistance in wheat (Triticum aestivum L.). In this study we performed a genome-wide association study (GWAS) on regional FHB nurseries to select significant SNPs for deoxynivalenol (DON) and DSK, an index of DON, FHB rating and Fusarium damaged kernels (FDK). The objective was to determine whether a reduced number of markers could improve predictions of FHB traits compared to the full set of markers for three populations of 306, 281 and 198 lines that were evaluated in 2017, 2018, 2019 respectively at Lexington, Kentucky. Under a forward GS scheme, using regional nurseries as training populations (TP) of sizes 100 and 400, there was a substantial positive increase in prediction accuracy (PA) of 21% for DON (0.28 vs 0.22) and 12% for DSK (0.32 vs 0.28) using a reduced marker set at the smallest TP size. With cross validation, moderate PA was obtained consistently among populations and marker sets for both traits. While the full marker set showed the best performance, PA with reduced marker sets was only slightly lower, (0.55 vs 0.54) for DON and (0.60 vs 0.57) for DSK. Our results confirm first, that GWAS offers an excellent tool to select significant markers for traits like DON and DSK, which reduces the number of markers considerably. Secondly, under a forward GS scheme, using only SNPs significant at P < 0.1 was the most effective strategy in that PA was highest. With these results we move a step forward in selecting lines with good resistance to DON accumulation and other FHB traits before evaluating them in the field, reducing the costs of phenotyping and genotyping.