The Maize (<i>Zea mays</i> L.) <i>AUXIN/INDOLE-3-ACETIC ACID</i> Gene Family: Phylogeny, Synteny, and Unique Root-Type and Tissue-Specific Expression Patterns during Development

<div><p>The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. <i>AUXIN/INDOLE-3-ACETIC ACID</i> (<i>Aux/IAA</i>) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize <i>Aux/IAA</i> gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (<i>ZmIAA23</i>) tested maize <i>Aux/IAA</i> genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential <i>Aux</i>/<i>IAA</i> expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of <i>Aux/IAA</i> transcript abundance. In summary, the detailed analysis of the maize <i>Aux/IAA</i> gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.</p>