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.