Identification, Characterization and Comparative Analysis of Aux/IAA Gene Family in Brassica rapa

Auxin is the most important multigene family involved in root development, leaf formation, phototropism, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) transcription factors are the key regulators of auxin responses in plants. A comprehensive genome-wide analysis was carried out to find all the auxin related genes in Brassica rapa. A total of 81 Aux/IAA genes were identified by HMMER search using Pfam Aux/IAA domain (PF02309). Comparative phylogenetic analysis of the identified genes discovered that several Aux/IAA genes differentially expanded between the two dicotyledonous plants, B. rapa and Arabidopsis thaliana. Computational comparative analysis rendered the complete information of the genome location, duplication and orthologs for the identified genes in A. thaliana.  Also we identified the expressed sequences for 63 genes from our 50K microarray data by comparing the identified B. rapa Aux/IAA genes. Furthermore, expression study of the selected Aux/IAA genes from the full length coding sequences and microarray data in different tissue revealed differential expressions of the genes.  In total, ~230 Single Nucleotide Polymorphisms (SNPs) were identified in the intronic and exonic regions from 51 Aux/IAA genes of the whole genome re-sequence data of the parental lines, Chiffu and RcBr, a few were validated also. Our study scrutinizes the conservation and divergence in the structure and evolution between B. rapa and A. thaliana Aux/IAA genes. Functional analysis, SNP annotation and expression study in the different tissues will pave the role of B. rapa Aux/IAA genes in the plant growth and development in the future.