Genome‐wide dissection of the maize ear genetic architecture using multiple populations

Summary Improvement of grain yield is an essential long‐term goal of maize ( Zea mays ) breeding to meet continual and increasing food demands worldwide, but the genetic basis remains unclear. We used 10 different recombination inbred line ( RIL ) populations genotyped with high‐density markers and phenotyped in multiple environments to dissect the genetic architecture of maize ear traits. Three methods were used to map the quantitative trait loci ( QTL s) affecting ear traits. We found 17–34 minor‐ or moderate‐effect loci that influence ear traits, with little epistasis and environmental interactions, totally accounting for 55.4–82% of the phenotypic variation. Four novel QTL s were validated and fine mapped using candidate gene association analysis, expression QTL analysis and heterogeneous inbred family validation. The combination of multiple different populations is a flexible and manageable way to collaboratively integrate widely available genetic resources, thereby boosting the statistical power of QTL discovery for important traits in agricultural crops, ultimately facilitating breeding programs.