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.
Highlights
Auxin is the most important hormone involved in many plant organ development processes like root, flower, leaf and fruit, and regulates plant responses including phototropism, gravitropism, apical dominance and cell elongation [1, 2]
The resulted sequences were searched again using Pfam batch search and 55 B. rapa genes with confidant Auxin/indole-3-acetic acid (Aux/Indoleacetic acid (IAA)) domain were confirmed as representatives of B. rapa Aux/IAA (BrIAA) gene family after a manual curation
The Aux/IAA gene family was densely populated with 55 genes in B. rapa than the other plants like arabidopsis, rice, populus and maize
Summary
Auxin is the most important hormone involved in many plant organ development processes like root, flower, leaf and fruit, and regulates plant responses including phototropism, gravitropism, apical dominance and cell elongation [1, 2]. The Aux/IAA proteins are generally conserved with four characteristic motifs referred to as domain-I, -II, -III and -IV, proteins lacking one or two of these domains were included in this gene family [1]. Domain-II is highly conserved playing a major role in protein stability and it’s required for auxin-regulated signaling by interacting with a component of transport inhibitor response 1 (TIR1) [4]. Mutations occurring in this domain affect the interaction and results in low auxin response. Aux/ IAA proteins bind to the associate ARF proteins by the domains III/IV and repress the ARF activity. Studying the auxin regulator activity is highly complex due to the large number of Aux/IAA gene families, variations, expression patterns, auxin mediated transcriptional and posttranscriptional regulations
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