Genetic diversity created by transposable elements is an important source of functional variation upon which selection acts during evolution1–6. Transposable elements are associated with adaptation to temperate climates in Drosophila7, a SINE element is associated with the domestication of small dog breeds from the gray wolf8 and there is evidence that transposable elements were targets of selection during human evolution9. Although the list of examples of transposable elements associated with host gene function continues to grow, proof that transposable elements are causative and not just correlated with functional variation is limited. Here we show that a transposable element (Hopscotch) inserted in a regulatory region of the maize domestication gene, teosinte branched1 (tb1), acts as an enhancer of gene expression and partially explains the increased apical dominance in maize compared to its progenitor, teosinte. Molecular dating indicates that the Hopscotch insertion predates maize domestication by at least 10,000 years, indicating that selection acted on standing variation rather than new mutation.

The most critical step in maize domestication (Zea mays ssp. mays) was the liberation of the kernel from the hardened, protective casing that envelops the kernel in the maize progenitor, teosinte 1 . This evolutionary step exposed the kernel on the surface of the ear such that it could be readily utilized as a food source by humans. Here, we show that this key event in maize domestication is controlled by a single gene (teosinte glume architecture; tga1) belonging to the SBP-domain family 2 of transcriptional regulators. The factor controlling the phenotypic difference between maize and teosinte maps to a 1 kilobase region within which maize and teosinte show only six fixed differences in their DNA sequences. One of these differences encodes a non-conservative amino acid substitution and may affect protein function, while the other five differences potentially affect gene regulation. Molecular evolution analyses show that this region was the target of selection during maize domestication. Our results demonstrate that modest genetic changes in single genes can induce dramatic changes in phenotype during domestication and evolution.The origin of the maize ear has been considered one of the greatest mysteries in both crop domestication 3 and plant evolution 4 . While a wealth of botanical and genetic information has identified the wild Mexican grass, teosinte (Zea mays ssp. parviglumis), as the direct progenitor of maize, the profound differences in the structure of the maize and teosinte female inflorescences (ears) has posed a challenge to formulating a compelling model for the developmental and genetic steps involved in this evolutionary transition 3 . At the heart of the problem is the fact that teosinte kernels are tightly encased in structures called cupulate fruitcases, while maize kernels are borne uncovered on the surface of the ear (Figure 1a, b). The strength with which the fruitcase envelops the teosinte kernel and the stony nature of this casing far exceed the relatively flimsy and loosely bound chaff that surrounds the kernels of the ancestors of the other domesticated cereals. Indeed, the stony fruitcase of teosinte had been considered such an obstacle to the use of teosinte as a grain that teosinte was dismissed by some as a possible progenitor of maize 5 . It was argued that the genetic steps to free the grain from this casing and thereby convert teosinte into a useful crop were too complex to have arisen under domestication.Each of the 5 to 12 cupulate fruitcases in a teosinte ear is formed from an invaginated internode (cupule) within which the kernel sits, and a glume that covers the opening of the cupule such that the kernel is completely hidden from view (Figure 1b, d). When mature, the teosinte ear

Plant responses to ethylene are mediated by regulation of EBF1/2-dependent degradation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor. Here, we report that the level of EIL1 protein is upregulated by ethylene through an EBF1/2-dependent pathway. Genetic analysis revealed that EIL1 and EIN3 cooperatively but differentially regulate a wide array of ethylene responses, with EIL1 mainly inhibiting leaf expansion and stem elongation in adult plants and EIN3 largely regulating a multitude of ethylene responses in seedlings. When EBF1 and EBF2 are disrupted, EIL1 and EIN3 constitutively accumulate in the nucleus and remain unresponsive to exogenous ethylene application. Further study revealed that the levels of EBF1 and EBF2 proteins are downregulated by ethylene and upregulated by silver ion and MG132, suggesting that ethylene stabilizes EIN3/EIL1 by promoting EBF1 and EBF2 proteasomal degradation. Also, we found that EIN2 is indispensable for mediating ethylene-induced EIN3/EIL1 accumulation and EBF1/2 degradation, whereas MKK9 is not required for ethylene signal transduction, contrary to a previous report. Together, our studies demonstrate that ethylene similarly regulates EIN3 and EIL1, the two master transcription factors coordinating myriad ethylene responses, and clarify that EIN2 but not MKK9 is required for ethylene-induced EIN3/EIL1 stabilization. Our results also reveal that EBF1 and EBF2 act as essential ethylene signal transducers that by themselves are subject to proteasomal degradation.

The architecture of higher plants is established through the activity of lateral meristems--small groups of stem cells formed during vegetative and reproductive development. Lateral meristems generate branches and inflorescence structures, which define the overall form of a plant, and are largely responsible for the evolution of different plant architectures. Here, we report the isolation of the barren stalk1 gene, which encodes a non-canonical basic helix-loop-helix protein required for the initiation of all aerial lateral meristems in maize. barren stalk1 represents one of the earliest genes involved in the patterning of maize inflorescences, and, together with the teosinte branched1 gene, it regulates vegetative lateral meristem development. The architecture of maize has been a major target of selection for early agriculturalists and modern farmers, because it influences harvesting, breeding strategies and mechanization. By sampling nucleotide diversity in the barren stalk1 region, we show that two haplotypes entered the maize gene pool from its wild progenitor, teosinte, and that only one was incorporated throughout modern inbreds, suggesting that barren stalk1 was selected for agronomic purposes.

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