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Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in  Brassica rapa  ( B .  rapa ). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in  B .  rapa  using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the  B .  rapa  Aux/IAA ( BrIAA ) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of  BrIAA  with  Arabidopsis thaliana ,  Oryza sativa  and  Zea mays  identified 51 sister pairs including 15 same species ( BrIAA — BrIAA ) and 36 cross species ( BrIAA — AtIAA )  IAA  genes. Among the 55  BrIAA  genes, expression of 43 and 45 genes were verified using Genebank  B .  rapa  ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of  BrIAA  genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the  BrIAA  genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between  IAA  genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in  B .  rapa . Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of  Brassica  crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in  B .  rapa .

Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa