The effects of an allelic substitution at a gene often depend critically on genetic background, i.e., the genotypes at other genes in the genome. During the domestication of maize from its wild ancestor (teosinte), an allelic substitution at teosinte branched (tb1) caused changes in both plant and ear architecture. The effects of tb1 on phenotype were shown to depend on multiple background loci, including one called enhancer of tb1.2 (etb1.2). We mapped etb1.2 to a YABBY class transcription factor (ZmYAB2.1) and showed that the maize alleles of ZmYAB2.1 are either expressed at a lower level than teosinte alleles or disrupted by insertions in the sequences. tb1 and etb1.2 interact epistatically to control the length of internodes within the maize ear, which affects how densely the kernels are packed on the ear. The interaction effect is also observed at the level of gene expression, with tb1 acting as a repressor of ZmYAB2.1 expression. Curiously, ZmYAB2.1 was previously identified as a candidate gene for another domestication trait in maize, nonshattering ears. Consistent with this proposed role, ZmYAB2.1 is expressed in a narrow band of cells in immature ears that appears to represent a vestigial abscission (shattering) zone. Expression in this band of cells may also underlie the effect on internode elongation. The identification of ZmYAB2.1 as a background factor interacting with tb1 is a first step toward a gene-level understanding of how tb1 and the background within which it works evolved in concert during maize domestication. KEYWORDS domestication; epistasis; genetic-background; maize; teosinte-branched1 T HE effects of an allelic substitution at a gene can vary widely depending on the genetic background in which its effects are assayed (Chandler et al. 2013). In extreme cases, the effect of an allele may even exhibit a change in directionality across different genetic backgrounds (Wade et al. 2001). Often, genetic background is considered a "nuisance factor" and thus something that needs to be controlled by the usage of inbred lines in experiments involving model organisms such as maize, Arabidopsis, and mice, because the effect of an allele can change under different genetic backgrounds (Wade 2002;Chandler et al. 2013). However, in evolutionary biology, a knowledge of the extent and dynamics of genetic background is essential for a complete understanding of the evolutionary process.The teosinte branched (tb1) gene of maize (Zea mays ssp. mays) has been identified as one of the genes involved in the domestication of maize from its wild progenitor, teosinte (Z. mays ssp. parviglumis). tb1 acts pleiotropically to regulate both the architecture of the plant overall and the structure of the female inflorescence or ear (Doebley et al. 1997). Plants carrying the maize allele of tb1 have fewer, shorter branches than plants carrying teosinte alleles. The ears of plants with the maize allele have short internodes, such that the kernels are more tightly packed together as compared to plants with teosinte ...