Partial retention of ancient function increases genetic pleiotropy in grass evolution

Changes in form are driven by the differential, context-dependent regulation of pleiotropic genes. How genetic pleiotropy itself emerges, however, remains unclear. The maize genes GRASSY TILLERS1 (GT1) and RAMOSA3 (RA3) are required for axillary meristem suppression, a deeply conserved trait across angiosperms, and for floral organ suppression, a trait which evolved within the grass family. To determine how these pleiotropic functions are regulated, we first established a high-throughput method for quantitative phenotyping of grass flowers. Using this method, we show that distinct environmental mechanisms regulate axillary meristem versus floral organ suppression. In line with these differences, we find upstream regulation of GT1 and RA3 has diverged, consistent with their redeployment in flowers. Our results show that, rather than wholesale adoption of genetic networks, developmental genes can retain ancient functions and be recruited into other programs in the evolution of form, thereby increasing genetic pleiotropy.