Genes associated with FAW damage ratings
When the GLM was used for association analysis, the observed -Log10(p values) were higher than the expected, as can be seen in the QQ plot in Supplemental Fig. 1a. The observed values were much closer to the expected when the MLM was used (Supplemental Fig. 1b), and thus the MLM results are presented here and were used in the subsequent pathway analysis. Because of missing data of some SNPs, several of the most significant SNPs ended up comparing only one or two individuals with one allele against one or more hundred with the other allele. To avoid this statistically risky analysis, the Minor Allele Frequency was increased to 0.09 and the GWAS run again with 940,585 remaining SNPs. Only results of this second analysis are presented here and were used in the pathway analysis. Setting a significance threshold of 1/n, there were 3 SNPs, corresponding to 2 linked loci, significantly associated at p < 1.06 x 10-6 with the data for FAW damage at 7 days after infestation, and 12 SNPs, corresponding to 5 linked loci, with the data at 14 days (Table 1). There was very good correspondence with the SNPs found to be associated in the 7-day and 14-day ratings. All 3 significantly associated SNPs in the 7-day rating analysis were associated in the 14-day analysis at the p < 10-5 or better, and all but one of the 12 SNPs significantly associated in the 14-day rating analysis were associated in the 7-day analysis at the p < 10-5 or better. The table of MLM association scores for p < 0.05 can be found in Supplemental Table 3. Associations that are better than the Bonferroni corrected threshold are highlighted in yellow.
Table 1: The 15 SNPs (listed by chromosome (Chr) and position along the chromosome) significantly (p < 1.06 x 10-6) associated with Fall Armyworm (FAW) damage levels measured at 7 and at 14 days after infestation were in or closely linked to 7 genes. Association values (degrees of freedom (df), F values, p values, and Error degrees of freedom (Error df) as well as correlations (Marker R2), gene identifications (“Linked gene”) and annotations (“Gene name or function”) are noted.