Genome-wide association study identifies elite germplasm for improving lodging-related morphologic traits in maize

Abstract Maize lodging is an important cause of grain yield loss and difficulties with mechanized harvesting. Here, we have evaluated maize lodging-related morphologic traits, including stem height (SH), ear height (EH), stem node number (SN), ear node (EN), and two derived traits (ear height coefficient (EHc) and ear node coefficient (ENc) in 213 maize inbred lines among which 13 elite lines were repeatedly identified across different environments. Using 4000 SNPs evenly scattered across the 10 maize chromosomes, the 213 lines clustered into five subgroups, including Reid, PB, Lan, SPT (Si-ping-tou), and LRC (Lvda Reb Cob), across which significant phenotypic variance was observed. For example, germplasm in the LAN subgroup has fewer stem nodes and lower ear nodes than do those in the SPT and LRC subgroups. Using FarmCPU and MLM in TASSEL, 44 significant SNPs were significantly associated with lodging-related morphological traits. Three of these significant SNPs were repeatedly associated with the same trait in different environments. In addition, based on the superior genotypic combination of the significant SNPs on chromosome 5.02 and 5.03 associated with SN and EN across all environments, we identified four lines from the LAN subgroup, including Ji419, Si419, 416, and SiF1 as elite germplasm that could be used for breeding and improvement of lodging resistance in domestic local germplasm in maize.