SNPs significantly associated with HR-related traits (LES, HTR, SWR and DTAR), and closest predicted maize genes (more details can be found in File S5).

1chromosome; 2physical map position based on B73 maize reference genome v2; 3−log10 of average p value from GWA analysis based on 100 resampling method; 4resampling model inclusion probability (RMIP); 5positive and negative allelic effects relative to B73 imply enhancing and suppressing effect on the HR phenotype, respectively; 6Number of HR-related trait QTL colocalizing with associated SNP hits (maximum is 4); 7mutations of these candidate genes induce lesion phenotypes; 8differentially expressed genes (DEG), expression level ratios of candidate genes between mutant and wild type F1 plants from the cross B73×Rp1-D21-H95 and Mo17: Rp1-D21-H95. 9Associated SNPs/candidate genes colocalized within QTL that were detected in more than 12 of the 24 NAM populations. Key: Lignification: LIG; Programed cell death: PCD,; Autophagy, AUT; monoubiquitination, mUBQ; Calcium signaling, Ca2+Sig; defense response, DFR; redox homeostasis, RxH; ubiquitination, UBQ; CWM: cell wall modification; TF, transcription factor; STR: stress response; CHP: molecular chaperone; RNAp, RNA processing. SNPs significantly associated with HR-related traits (LES, HTR, SWR and DTAR), and closest predicted maize genes (more details can be found in File S5).