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.

Enhancing the output of Rubisco, an enzyme that converts atmospheric CO 2 into energy-rich molecules, could improve photo-synthetic efficiency, and therefore crop yield, in plants. Maize is a C4 grass, which uses four-carbon compounds to carry CO 2 into an interior compartment; subsequent release of CO 2 increases its local concentration and favors efficient activity of Rubisco. Rice, however, is a C3 grass and lacks this pathway. Wang et al. compared transcripts and metabolites in developing maize and rice plants as a step toward understanding the biochemical and anatomical bases of C4 photosynthesis. Furthermore, Lin et al. transplanted Rubisco from a cyanobacterium, which also relies on a CO 2-concentrating apparatus, into tobacco (a C3 plant) chloro-plasts.-GJC Nat.

Carbonic anhydrase (CA) catalyzes the first biochemical step of the carbon-concentrating mechanism of C4 plants, and in C4 monocots it has been suggested that CA activity is near limiting for photosynthesis. Here, we test this hypothesis through the characterization of transposon-induced mutant alleles of Ca1 and Ca2 in maize (Zea mays). These two isoforms account for more than 85% of the CA transcript pool. A significant change in isotopic discrimination is observed in mutant plants, which have as little as 3% of wild-type CA activity, but surprisingly, photosynthesis is not reduced under current or elevated CO2 partial pressure (pCO2). However, growth and rates of photosynthesis under subambient pCO2 are significantly impaired in the mutants. These findings suggest that, while CA is not limiting for C4 photosynthesis in maize at current pCO2, it likely maintains high rates of photosynthesis when CO2 availability is reduced. Current atmospheric CO2 levels now exceed 400 ppm (approximately 40.53 Pa) and contrast with the low-pCO2 conditions under which C4 plants expanded their range approximately 10 million years ago, when the global atmospheric CO2 was below 300 ppm (approximately 30.4 Pa). Thus, as CO2 levels continue to rise, selective pressures for high levels of CA may be limited to arid climates where stomatal closure reduces CO2 availability to the leaf.

Although hybrid crop varieties are among the most popular agricultural innovations, the rationale for hybrid crop breeding is sometimes misunderstood. Hybrid breeding is slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection and exploitation of heterosis simultaneously. Inbred parental lines can identically reproduce both themselves and their F1 progeny indefinitely, whereas outbred lines cannot, so uniform outbred lines must be bred indirectly through their inbred parents to harness heterosis. Heterosis is an expected consequence of whole-genome non-additive effects at the population level over evolutionary time. Understanding heterosis from the perspective of molecular genetic mechanisms alone may be elusive, because heterosis is likely an emergent property of populations. Hybrid breeding is a process of recurrent population improvement to maximize hybrid performance. Hybrid breeding is not maximization of heterosis per se, nor testing random combinations of individuals to find an exceptional hybrid, nor using heterosis in place of population improvement. Though there are methods to harness heterosis other than hybrid breeding, such as use of open-pollinated varieties or clonal propagation, they are not currently suitable for all crops or production environments. The use of genomic selection can decrease cycle time and costs in hybrid breeding, particularly by rapidly establishing heterotic pools, reducing testcrossing, and limiting the loss of genetic variance. Open questions in optimal use of genomic selection in hybrid crop breeding programs remain, such as how to choose founders of heterotic pools, the importance of dominance effects in genomic prediction, the necessary frequency of updating the training set with phenotypic information, and how to maintain genetic variance and prevent fixation of deleterious alleles.

Selection during evolution, whether natural or artificial, acts through the phenotype. For multifaceted phenotypes such as plant and inflorescence architecture, the underlying genetic architecture is comprised of a complex network of interacting genes rather than single genes that act independently to determine the trait. As such, selection acts on entire gene networks. Here, we begin to define the genetic regulatory network to which the maize domestication gene, (), belongs. Using a combination of molecular methods to uncover either direct or indirect regulatory interactions, we identified a set of genes that lie downstream of in a gene network regulating both plant and inflorescence architecture. Additional genes, known from the literature, also act in this network. We observed that regulates both core cell cycle genes and another maize domestication gene, (). We show that several members of the MADS-box gene family are either directly or indirectly regulated by and/or, and that sits atop a cascade of transcriptional regulators controlling both plant and inflorescence architecture. Multiple members of the network appear to have been the targets of selection during maize domestication. Knowledge of the regulatory hierarchies controlling traits is central to understanding how new morphologies evolve.