Long noncoding miRNA gene represses wheat β-diketone waxes

Abstract

The cuticle of terrestrial plants functions as a protective barrier against many biotic and abiotic stresses. In wheat and other Triticeae, β-diketone waxes are major components of the epicuticular layer leading to the bluish-white glaucous trait in reproductive-age plants. Glaucousness in durum wheat is controlled by a metabolic gene cluster at the <i>WAX1</i> (<i>W1</i>) locus and a dominant suppressor <i>INHIBITOR of WAX1</i> (<i>Iw1</i>) on chromosome 2B. The wheat D subgenome from progenitor <i>Aegilops tauschii</i> contains <i>W2</i> and <i>Iw2</i> paralogs on chromosome 2D. Here we identify the <i>Iw1</i> gene from durum wheat and demonstrate the unique regulatory mechanism by which <i>Iw1</i> acts to suppress a carboxylesterase-like protein gene, <i>W1-COE</i>, within the <i>W1</i> multigene locus. <i>Iw1</i> is a long noncoding RNA (lncRNA) containing an inverted repeat (IR) with >80% identity to <i>W1-COE</i> The <i>Iw1</i> transcript forms a miRNA precursor-like long hairpin producing a 21-nt predominant miRNA, miRW1, and smaller numbers of related sRNAs associated with the nonglaucous phenotype. When <i>Iw1</i> was introduced into glaucous bread wheat, miRW1 accumulated, <i>W1-COE</i> and its paralog <i>W2-COE</i> were down-regulated, and the phenotype was nonglaucous and β-diketone-depleted. The IR region of <i>Iw1</i> has >94% identity to an IR region on chromosome 2 in <i>Ae. tauschii</i> that also produces miRW1 and lies within the marker-based location of <i>Iw2</i> We propose the <i>Iw</i> loci arose from an inverted duplication of <i>W1-COE</i> and/or <i>W2-COE</i> in ancestral wheat to form evolutionarily young miRNA genes that act to repress the glaucous trait.