Maize (Zea mays L.) is a complex crop. Governed by the universal processes of evolution that dictate the differential reproduction of all life, maize germplasm has been gradually adapted to better suit societal needs through domestication and breeding. However, these modifications were largely accomplished with little knowledge of the genetic architecture or molecular mechanics of its traits. Investigating the reaches of the rhizosphere to the top of the tassel, the following studies analyze the natural variation of complex maize traits to better understand both their means and degree of inheritance. First, the heritability and environmental specificity of maize-microbe interactions were estimated by pyrosequence profiling 16s rRNA gene amplicons from rhizosphere bacterial populations of diverse inbreds grown in multiple maize field environments. We found substantial variation in bacterial diversity was attributable to environment. Nonetheless, a small but significant proportion of variation was heritable. While kinship inferred from a simple additive model assuming contributions from all polymorphisms did not explain this heritable variation, its discovery is a step toward identifying those genes responsible for novel plantmicrobe interactions in natural environments. Second, maize stalk strength variation was analyzed to delineate the accuracy of genomic prediction in a low heritability trait. While few robust loci were associated with stalk strength, a significant proportion of heritable variation was captured by kinship among the inbreds. This revealed the efficacy of genomic prediction and suggested the potential to accurately predict other low heritability phenotypes such as yield. These and similar efforts to facilitate the selection of genotyped seed with desirable qualities before planting will enhance breeding efficiency. Finally, variation in the most classic and heritable of complex traits, maize height was partitioned to reveal its genetic architecture and pleiotropy with other traits such as flowering time and node counts. As anticipated height was highly polygenic and well captured by kinship; however, an interesting finding was the lacking concordance between mapped loci and those established through previous cloning efforts. Equally intriguing was the paucity of pleiotropic loci identified for height and flowering time. These findings reveal the potential for independent evolvability of these traits during maize breeding.