Genome-wide association analysis of seedling root development in maize (Zea mays L.)

Jordon Pace, Iowa State University
C. A. Gardner, United States Department of Agriculture
Cinta Tomay, Cornell University
Basker Ganapathysubramanian, Iowa State University
Thomas Lubberstedt, Iowa State University

This article is published as Pace, Jordon, Candice Gardner, Cinta Romay, Baskar Ganapathysubramanian, and Thomas Lübberstedt. "Genome-wide association analysis of seedling root development in maize (Zea mays L.)." BMC genomics 16, no. 1 (2015): 47. 10.1186/s12864-015-1226-9. Posted with permission.



Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped.


Utilizing both a general linear model and mixed linear model, a GWAS study was conducted identifying 268 marker trait associations (p ≤ 5.3×10-7). Analysis of significant SNP markers for multiple traits showed that several were located within gene models with some SNP markers localized within regions of previously identified root quantitative trait loci. Gene model GRMZM2G153722 located on chromosome 4 contained nine significant markers. This predicted gene is expressed in roots and shoots.


This study identifies putatively associated SNP markers associated with root traits at the seedling stage. Some SNPs were located within or near (<1>kb) gene models. These gene models identify possible candidate genes involved in root development at the seedling stage. These and respective linked or functional markers could be targets for breeders for marker assisted selection of seedling root traits.