Spatial heterogeneity of disease infection attributable to neighbour genotypic identity in barley cultivars

Pest damage exhibits considerable spatial heterogeneity among individual plots in the field. Such spatial heterogeneity has often been treated as a nuisance in crop breeding trials; however, a part of among-plot variation may be explained by genetic factors such as neighbouring genotypes. To test whether neighbouring genotypes accounted for spatial variation in disease infection, we applied two methods, Spatial Analysis of Field Trials with Splines (SpATS) and Neighbor Genome-Wide Association Study (Neighbor GWAS), to barley cultivars. Having compiled the CIMMYT Australia ICARDA Germplasm Evaluation (CAIGE) data, we first applied SpATS to three disease phenotypes such as the net form net blotch, spot form net blotch, and scald damage. This SpATS analysis showed extraneous phenotypic variation unexplained by smooth spatial trends, thereby leading us to focus on neighbouring genotypes as an extraneous biological factor. We then applied the Neighbor GWAS model and found that neighbour genotypic identity explained 0.1–0.3 fractional variation in the three disease phenotypes. The Neighbor GWAS method also detected two significant variants on the barley 7H chromosome, which were associated with neighbour genotypic influence on the net form net blotch and scald damage. These variants were estimated to have beneficial effects that could reduce disease damage by their allelic mixtures. Our findings suggest that neighbour genotypic identity can account for spatial variation in disease infection and its genetic architecture may provide a key to multiline cultivation for pest management.