Long noncoding miRNA gene represses wheat β-diketone waxes

Significance

Higher plants have waxy surface layers that prevent uncontrolled water loss. Many wheat cultivars accumulate diketone epicuticular waxes in reproductive-age plants that produce a glaucous appearance. We identify INHIBITOR of WAX1 ( Iw1), a dominant glaucous repressor, as a young miRNA gene (MIRNA) that produces an miRNA, miRW1, which targets the transcript of the biosynthetic gene WAX1-CARBOXYLESTERASE ( W1-COE) for degradation. The high sequence similarity between the Iw1 hairpin sequence and W1-COE suggests that this MIRNA gene arose from an inverted duplication of its target. The cleavage specificity of miRW1 for its target gene defines the unique role of a young MIRNA gene in the regulation of an important agricultural trait related to stress tolerance.

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 WAX1 ( W1) locus and a dominant suppressor INHIBITOR of WAX1 ( Iw1) on chromosome 2B. The wheat D subgenome from progenitor Aegilops tauschii contains W2 and Iw2 paralogs on chromosome 2D. Here we identify the Iw1 gene from durum wheat and demonstrate the unique regulatory mechanism by which Iw1 acts to suppress a carboxylesterase-like protein gene, W1-COE, within the W1 multigene locus. Iw1 is a long noncoding RNA (lncRNA) containing an inverted repeat (IR) with >80% identity to W1-COE. The Iw1 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 Iw1 was introduced into glaucous bread wheat, miRW1 accumulated, W1-COE and its paralog W2-COE were down-regulated, and the phenotype was nonglaucous and β-diketone–depleted. The IR region of Iw1 has >94% identity to an IR region on chromosome 2 in Ae. tauschii that also produces miRW1 and lies within the marker-based location of Iw2. We propose the Iw loci arose from an inverted duplication of W1-COE and/or W2-COE in ancestral wheat to form evolutionarily young miRNA genes that act to repress the glaucous trait.