Maize association population: a high‐resolution platform for quantitative trait locus dissection

TLDR

Crop improvement relies on germplasm diversity, yet most maize studies use a limited set of inbred lines, making inclusion of population structure essential for meaningful analyses. The study characterizes the population structure of 302 maize lines and examines its relationship with phenotypic and breeding value measures. The authors employed statistical models that correct for population structure to analyze the 302‑line association population and assess its relationship with phenotypic and breeding value. The 302‑line population captures most cultivated maize alleles, explains up to 35 % of phenotypic variation, and can identify small‑effect QTL, aiding complex trait dissection.

Abstract

Crop improvement and the dissection of complex genetic traits require germplasm diversity. Although this necessary phenotypic variability exists in diverse maize, most research is conducted using a small subset of inbred lines. An association population of 302 lines is now available--a valuable research tool that captures a large proportion of the alleles in cultivated maize. Provided that appropriate statistical models correcting for population structure are included, this tool can be used in association analyses to provide high-resolution evaluation of multiple alleles. This study describes the population structure of the 302 lines, and investigates the relationship between population structure and various measures of phenotypic and breeding value. On average, our estimates of population structure account for 9.3% of phenotypic variation, roughly equivalent to a major quantitative trait locus (QTL), with a high of 35%. Inclusion of population structure in association models is critical to meaningful analyses. This new association population has the potential to identify QTL with small effects, which will aid in dissecting complex traits and in planning future projects to exploit the rich diversity present in maize.