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 through the uptake of water and nutrients in the field. However, the genetic architecture of the maize root system is largely unknown mainly due to its complexity and the interactions 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 stratification and a linkage disequilibrium decay distance of less than 50 kb. Based on genotyping with the high-density 600 K SNPs, we conducted a genome wide association analysis (GWAS) and identified nine SNPs and seven candidate genes significantly associated with 24 traits. One candidate gene, GRMZM2G400533, is located at the upstream 5 kb region from the leading SNP (AX-91771718) and was significantly associated with primary root length and preferentially expressed in the primary root and crown root. Expression of GRMZM2G400533 increased as the primary root developed but was negatively correlated with primary root elongation. An analysis of candidate gene GRMZM2G400533 identified three functional variants and eight allelic haplotypes. This study will broaden our understanding of maize root development and provide a theoretical basis for maize improvement through optimization of the root system.