Modifications to a Late Meristem Identity 1-like Gene Are Responsible for the Major Leaf Shapes of Upland Cotton (Gossypium hirsutum L.).

Leaf shape in tetraploid Upland cotton (Gossypium hirsutum L.) is an important trait that influences yield, earliness, flowering rate, disease resistance, and the efficacy of foliar chemical application. Developmental aspects of classical leaf shapes of cotton have also been longstanding interest to plant biologists. In Upland cotton predominant leaf shapes normal, sub-okra, okra, and super-okra, with varying levels of lobe severity, are controlled by a multiple allelic series at the D-genome locus L-D₁. Using positional cloning approach we show that these major leaf shapes of cotton are controlled by the HD-Zip transcription factor Late Meristem Identity1-D1b (LMI1-D1b). A 133 bp tandem duplication in the promoter of okra leaf LMI1-D1b leads to elevated expression while an 8 bp deletion in the third exon of normal leaf LMI1-D1b causes a frameshift and truncated coding sequence. Virus-induced gene silencing (VIGS) of LMI1-D1b 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 mutant heavily selected for in agricultural production. Understanding the genetic mechanism controlling leaf shape could help its proper manipulation to develop a cotton ideotype that maximizes yield while minimizing inputs.