Supplementary file 2_Genome-wide association study and genomic prediction of root system architecture in a diverse field-grown maize panel.docx

However, the genetic basis of RSA at the mature stage under field conditions remains poorly characterized, primarily owing to the challenges of high-throughput phenotyping. In this study, RSA-related traits were evaluated in a diverse maize association panel across four field environments using Shovelomics combined with manual measurements.

Genome-wide association analysis (GWAS) was performed using the BLINK and 3VmrMLM models, identifying four main-effect loci consistently detected by both methods and three additional loci exhibiting significant QTN-by-environment interactions (QEIs).Notably, SNP AX-90556586 on chromosome 9 was consistently associated with nodal and crown root number across environments. Its candidate gene encodes a leucine-rich repeat receptor-like serine/threonine-protein kinase with similarity to BRI1/SOBIR1-like proteins, implicating hormone-mediated root development.