Abstract: Methods of identifying a single nucleotide polymorphism associated with a plant trait and methods of identifying a plant having an improved trait. The plant trait is correlated with at least one single nucleotide polymorphism in a microRNA region of a plant genome. Isolated nucleic acids, transgenic plants, and methods of producing the same are also disclosed.

Abstract: The presently disclosed subject matter relates to methods and compositions for identifying, selecting, and/or producing drought tolerant maize plants or germplasm. Maize plants or germplasm that have been identified, selected, and/or produced by any of the methods of the presently disclosed subject matter are also provided.

Abstract: Provided herein are methods for evaluating associations between candidate genes and a trait of interest in a population. The methods include a combination of genome-wide association analysis and one or more of nested association mapping (NAM), expression QTL analysis (eQTL), and allele epistastic analysis (AEA). Markers are selected or prioritized if they are shown to be positively-correlated with a trait of interest using GWA and a combination of one or both of NAM and eQTL. Also provided are models for evaluating the association between a candidate marker and a trait in a nested population of organisms. These methods include single marker regression and multiple marker regression models. Markers identified using the methods of the invention can be used in marker assisted breeding and selection, as genetic markers for constructing linkage maps, for gene discovery, for identifying genes contributing to a trait of interest, and for generating transgenic organisms having a desired trait.