Fig. 6

Novel trait-SNP associations for inflorescence architecture traits revealed using MNase-seq guided GWAS. Results from GWAS for inflorescence architecture traits, Ear Row Number (ERN) and Tassel Branch Number (TBN), comparing two sets of SNP markers, all HapMap v3 SNPs and the subset residing in MNase HS regions, revealed common and novel trait-SNP associations with candidate genes. a Significant SNP associations for ERN and TBN that were included in stepwise GWAS models using both marker sets displayed as a Z-browse view across the genome. Novel marker associations were found using the SNPs within MNase HS only for each trait. These include (b} ramosa enhancer locus 2 (rel2), which was adjacent to a SNP associated with ERN and (c) sbp3, an SBP TF in immediate proximity of a SNP association for TBN and just up-stream of co-expressed lncRNA21521. The gray track beneath the GWAS SNPs defines the MNase HS portion of the genome (tassel and ear combined), which was used to subset the SNP set