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Improving grain yield is an essential long-term goal of maize breeding to meet continual and increasing food demands worldwide.We dissected the genetic architecture of maize ear traits using a set of 10 independent recombination inbred line (RIL) populations,termed the maize Random-Open-parents Association Mapping (ROAM) population.We found that dozens of minor-or moderate-effect loci influence ear traits,with little epistasis or environmental interactions,totally accounting for up to 82 %of phenotypic variation.Four novel quantitative trait loci (QTL) were validated and fine mapped by multiple approaches,including association analysis and analyses of expression-QTL and heterogeneous inbred family.Rare variants were found only in specific genetic backgrounds,but exhibiting extraordinary role on phenotypic variation.Different but complementary methodologies improved the systematic elucidation of the genetic bases of complex quantitative traits.