Genome wide association analysis reveals multiple QTLs controlling root development in maize

Maize root system plays a crucial role in the development of the aboveground plant and determines the yield via the uptake of water and nutrients in the field. However, the genetic architecture of the maize root system is largely unknown mainly due to the complexity of maize root system and the interaction between genotype and environment. Using a high-throughput semi-automatic hydroponic platform with stable conditions, we comprehensively characterized the root system in a core population of 518 diverse inbred lines of maize. Population structure analysis revealed that the panel has a stratification and linkage disequilibrium decay distance was less than 50 Kb. Based on the genotyping with the high density of 600 K SNPs, we conducted a genome wide association analysis (GWAS) and identified nine SNPs and seven candidate genes significantly associated with 24 traits. A candidate gene GRMZM2G400533 located at the upstream 5 Kb region from the leading SNP (AX-91771718) was significantly associated with primary root length and preferentially expressed in primary root and crown root. The expression of GRMZM2G400533 increased as the primary root developed but negatively correlated with primary root elongation. We also identified three functional variants and eight allelic haplotypes based on candidate gene analysis of GRMZM2G400533. The present study will broaden our understanding of maize root development and provide a theoretical basis for maize improvement through optimizing root system.