Background: Root growth and development is not only critical for nitrogen acquisition in plants, but also to anchor the plant in the soil. Several genes involved in maize root development have been isolated. Identification of SNPs associated with root traits would enable the selection of maize lines with better root architecture that might help to improve N uptake, and consequently plant growth particularly under N deficient conditions.

Results: In the present study, an association study (AS) panel consisting of 74 maize inbred lines was screened for seedling root traits in 6, 10, and 14-day-old seedlings. Allele resequencing of candidate root genes Rtcl, Rth3, Rum1, and Rul1 was also carried out in the same AS panel lines. All four candidate genes displayed different levels of nucleotide diversity, haplotype diversity and linkage disequilibrium. Nucleotide diversity was highest in the Rtcl gene (π=0.021), intermediate in Rum1 (π=0.011), lowest in Rth3 (π=0.007) and Rul1 (π=0.005) gene. When coding and non-coding regions within the genes were compared, nucleotide diversity varied across the genes. Gene based association analyses were carried out between individual polymorphisms in candidate genes, and root traits measured in 6, 10, and 14-day-old maize seedlings. Association analyses revealed several polymorphisms within the Rtcl, Rth3, Rum1, and Rul1 genes associated with seedling root traits. These significantly associated SNPs also affected putative functional sequence motifs, mostly transcription factor binding sites, and major domains in the genes.

Conclusion: Several nucleotide polymorphisms in Rtcl, Rth3, Rum1, and Rul1 were significantly (P<0.05) associated with seedling root traits in maize suggesting that all four tested genes are involved in the maize root development. Thus considerable allelic variation present in these root genes can be exploited for improving maize root characteristics. Target nucleotide polymorphisms for functional marker development were identified which might find application in marker-based selection strategies in breeding programs.