RT Journal Article SR Electronic T1 Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of cotton JF bioRxiv FD Cold Spring Harbor Laboratory SP 062612 DO 10.1101/062612 A1 Ryan Andres A1 Viktoriya Coneva A1 Margaret H. Frank A1 John R. Tuttle A1 Sang-Won Han A1 Luis Fernando Samayoa A1 Baljinder Kaur A1 Linglong Zhu A1 Hui Fang A1 Daryl Bowman A1 Marcela Rojas-Pierce A1 Candace H. Haigler A1 Don C. Jones A1 James B. Holland A1 Daniel H. Chitwood A1 Vasu Kuraparthy YR 2016 UL http://biorxiv.org/content/early/2016/08/10/062612.abstract AB Leaf shape is spectacularly diverse. As the primary source of photo-assimilate in major crops, understanding the evolutionary and environmentally induced changes in leaf morphology are critical to improving agricultural productivity. The role of leaf shape in cotton domestication is unique, as breeders have purposefully selected for entire and lobed leaf morphs resulting from a single locus, okra (L-D1). The okra locus is not only of agricultural importance in cotton (Gossypium hirsutum L.), but through pioneering chimeric and morphometric studies it has contributed to fundamental knowledge about leaf development. Here we show that the major leaf shapes of cotton at the L-D1 locus are controlled by a HD-Zip transcription factor most similar to Late Meristem Identity1 (LMI1) gene. The classical okra leaf shape gene has133-bp tandem duplication in the promoter, correlated with elevated expression, while an 8-bp deletion in the third exon of the presumed wild-type normal leaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of this LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. An intermediate leaf shape allele, sub-okra, lacks both the promoter duplication and the exonic deletion. Our results indicate that sub-okra is the ancestral leaf shape of tetraploid cotton and normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton.