Genome-wide association study and genomic selection of brace root traits related to lodging resistance in maize

Brace roots are the primary organs for water and nutrient absorption, and play an important role in lodging resistance. Dissecting the genetic basis of brace root traits will facilitate breeding new varieties with lodging resistance and high yield. In present study, genome-wide association study (GWAS) and genomic selection (GS) for brace root penetrometer resistance (PR), root number (RN), and tier number (TN) were conducted in a multi-parent doubled haploid (DH) population. Although the three brace root traits were significantly influenced by genotype-by-environment interactions, relatively high heritabilities were observed for RN (79.25%), TN (81.00%), and PR (74.28%). At the threshold of P-value < 7.42 × 10^{- 6}, 22 SNPs distributed on all 10 chromosomes, except for chromosome 7, and 50 candidate genes were identified using the FarmCPU model. Zm00001d028733, Zm00001d002350, Zm00001d002349, and Zm00001d043694 may be involved in brace root growth. The prediction accuracies of RN, TN, and PR estimated by five-fold cross-validation method with genome-wide SNPs were 0.39, 0.36, and 0.51, respectively, which can be greatly improved by using 100-300 significant SNPs. This study provides new insights into the genetic architecture of brace root traits and genomic selection for breeding lodging resistance maize varieties.