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

Abstract

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.

Fig 1. Chromosome positions of BrIAA genes.

From inner to outer ring A) Single Nucleotide Polymorphisms identified between the RcBr and Chiifu line. B) Physical positions of the Aux/IAA genes in the genome. C) GC % per 1Mb is illustrated in 3 different shades lesser GC% lighter the color. D) Shows the homologues crucifier building blocks of each gene and their clusters of the BrIAA genes. The colors representing the blocks are described as follows: green- A, B, C, D, E; red- G, H, I, J, K; pink- F, L, M, N; blue-O, P, T, U; brown- Q, R, S, V, W, X and white- nil.

Fig 2. Phylogenetics analysis of full length Aux/IAA protein sequences from A. thaliana, B. rapa, O. sativa and Z. mays using neighbor-joining method.

Motifs for each protein were predicted by MEME web server. Group (A, B and C) and their subgroups were distinguished by phylogeny conservation of Aux/IAA genes.

Fig 3. Response of BrIAA to Auxin treatment over a time course.

A) Expression pattern of BrIAA genes to auxin treatment at different time points. B) Relative fold changes of the BrIAA genes in form of heatmaps. C) Transcript level of the genes during auxin treatment.

Fig 4. Stress response of BrIAA genes to cold, salt and drought treatments at various time points.

Differentially expressed genes during A) cold B) drought C) salt treatments during various time. X axis represents the genes and Y axis represents the level of gene expression.

Fig 5. Expression of BrIAA genes in the different organs of ‘Chiifu’ and ‘RcBr’ lines were analyzed by semi qRT-PCR.

BrIAA32 showed no expression in the any organ of ‘Chiifu’ and ‘RcBr’. BraACTIN is used as control.