Genome-Wide Identification, Evolutionary Expansion, and Expression Analyses of Aux/IAA Gene Family in <i>Castanea mollissima</i> During Seed Kernel Development

Auxin/induced-3-acetic acid (Aux/IAA) serves as a key regulator in the auxin signaling pathway of plants, which exhibits crucial functions in the development of plants. However, the Aux/IAA gene family has not yet been characterized in the genome of <i>Castanea mollissima</i>, an important food source in the Northern Hemisphere. During this research, 23 <i>Aux</i>/<i>IAA</i> genes were identified in the <i>C. mollissima</i> genome, which were unevenly distributed across seven chromosomes. <i>CmAux</i>/<i>IAA</i> genes were assigned to four subfamilies by phylogenetic analysis, and members of the same subfamily exhibited similar molecular characteristics. Collinear analysis revealed that the expansion of <i>CmAux</i>/<i>IAA</i> genes was primarily driven by whole-genome duplication (WGD) and purifying selection. The promoter regions of <i>CmAux</i>/<i>IAA</i> genes were enriched with development-related and hormone-related <i>cis</i>-acting elements, suggesting their crucial functions in the growth and hormonal regulation of <i>C. mollissima</i>. Upon the maturation of the seed kernels, the size and starch content exhibited a significant increasing trend, alongside notable changes in hormone levels. Given the connections between expression levels and physiological indicators, as well as weighted gene co-expression network analysis (WGCNA) analysis, <i>CmIAA27a</i>, <i>CmIAA27b</i>, and <i>CmIAA27c</i> were identified as potential regulators involved in the development of <i>C. mollissima</i> seed kernels. Furthermore, the reliability of the transcriptomic data was further confirmed by RT-qPCR experiments. Overall, this study provides a theoretical basis for the evolutionary expansion of the Aux/IAA gene family in <i>C. mollissima</i>, alongside its potential functions in seed kernel development.