Genome-Wide Association Study of Plant and Ear Height in Maize

Abstract

Both plant height (PH) and ear height (EH) are key agronomic traits in maize that are associated with plant lodging resistance and population density. To explore the genetic basis for PH and EH in maize, we conducted a genome-wide association study (GWAS) based upon 1.49 × 106 single nucleotide polymorphisms (SNPs) identified following the sequencing of 80 backbone inbred maize lines in Jilin Province. By comparing genotypic data and these two traits of interest, we identified 27 total SNPs significantly associated with PH and EH (P < 0.000001). Of these SNPs, 12 were significantly associated with PH and were found on chromosomes 1, 3, 4, 6, 7, and 9, accounting for 25.8% of the phenotypic variability for this trait. The remaining 15 SNPs were significantly linked with EH and were located on chromosomes 1, 2, 4, 6, 7, 8, 9, and 10, accounting for 30% of the phenotypic variability for this trait. Within a mean linkage disequilibrium (LD) distance of 9.7 kb from these SNP loci, we identified 5 candidate genes associated with PH, with one of these candidate genes harboring a significant SNP. Similarly, we identified 12 candidate genes associated with EH, of which 3 harbored significant SNPs. We then isolated RNA from 8 different inbred maize lines from this GWAS study cohort and assessed the expression of these candidate genes of interest via quantitative real-time PCR (qRT-PCR). Through this analysis, we were able to verify that there were significant differences in the expression of these four SNP-harboring candidate genes in plants with a range of EH and PH phenotypes.