Evaluation of maize root growth and genome-wide association studies of root traits in response to low nitrogen supply at seedling emergence

Nitrogen (N) deficiency is one of the main factors limiting maize (Zea mays L.) productivity. Genetic improvement of root traits could improve nitrogen use efficiency. An association panel of 461 maize inbred lines was assayed for root growth at seedling emergence under high-nitrate (HN, 5 mmol L⁻¹) and low-nitrate (LN, 0.05 mmol L⁻¹) conditions. Twenty-one root traits and three shoot traits were measured. Under LN conditions, the root-to-shoot ratio, root dry weight, total root length, axial root length, and lateral root length on the primary root were all increased. Under LN conditions, the heritability of the plant traits ranged from 0.43 to 0.82, a range much wider than that of 0.27 to 0.55 observed under HN conditions. The panel was genotyped with 542,796 high-density single-nucleotide polymorphism (SNP) markers. Totally 328 significant SNP markers were identified using either mixed linear model (MLM) or general linear model analysis, with 34 detected by both methods. In the 100-kb intervals flanking these SNP markers, four candidate genes were identified. Under LN conditions, the protoporphyrinogen IX oxidase 2 gene was associated with total root surface area and the DELLA protein-encoding gene was associated with the length of the visible lateral root zone of the primary root. Under HN conditions, a histone deacetylase gene was associated with plant height. Under both LN and HN conditions, the gene encoding MA3 domain-containing protein was associated with the first whorl crown root number. The phenotypic and genetic information from this study may be exploited for genetic improvement of root traits aimed at increasing NUE in maize.