Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean.

Vikash K Singh,Mukesh Jain

doi:10.3389/fpls.2015.00918

Vikash K Singh, Mukesh Jain

Open Access

https://doi.org/10.3389/fpls.2015.00918

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Abstract

Auxin plays a central role in many aspects of plant growth and development. Auxin/Indole-3-Acetic Acid (Aux/IAA) genes cooperate with several other components in the perception and signaling of plant hormone auxin. An investigation of chickpea and soybean genomes revealed 22 and 63 putative Aux/IAA genes, respectively. These genes were classified into six subfamilies on the basis of phylogenetic analysis. Among 63 soybean Aux/IAA genes, 57 (90.5%) were found to be duplicated via whole genome duplication (WGD)/segmental events. Transposed duplication played a significant role in tandem arrangements between the members of different subfamilies. Analysis of Ka/Ks ratio of duplicated Aux/IAA genes revealed purifying selection pressure with restricted functional divergence. Promoter sequence analysis revealed several cis-regulatory elements related to auxin, abscisic acid, desiccation, salt, seed, and endosperm, indicating their role in development and stress responses. Expression analysis of chickpea and soybean Aux/IAA genes in various tissues and stages of development demonstrated tissue/stage specific differential expression. In soybean, at least 16 paralog pairs, duplicated via WGD/segmental events, showed almost indistinguishable expression pattern, but eight pairs exhibited significantly diverse expression patterns. Under abiotic stress conditions, such as desiccation, salinity and/or cold, many Aux/IAA genes of chickpea and soybean revealed differential expression. qRT-PCR analysis confirmed the differential expression patterns of selected Aux/IAA genes in chickpea. The analyses presented here provide insights on putative roles of chickpea and soybean Aux/IAA genes and will facilitate elucidation of their precise functions during development and abiotic stress responses.

Highlights

Auxin regulates cell division and elongation to drive plant growth and development (Woodward and Bartel, 2005)
In order to identify the members of Auxin/Indole-3-Acetic Acid (Aux/IAA) gene family in chickpea and soybean genome, BLASTP and HMM profile searches were performed against their respective proteomes
The Aux/IAA gene family members identified via these two searches were combined and a non-redundant list was obtained for chickpea and soybean

Summary

Introduction

Auxin regulates cell division and elongation to drive plant growth and development (Woodward and Bartel, 2005). Perception of auxin and control of auxin-regulated gene expression is mediated by proteins belonging to three families including, receptors (F-box proteins), repressors [Auxin/Indole-3-Acetic Acids (Aux/IAAs)] and transcription activators auxin response factors (ARFs). The F-box protein, being a component of a Skp1–Cullin–F-box (SCF) E3 ubiquitin ligase (Gray et al, 2001; Kepinski and Leyser, 2005), polyubiquitinylates and targets the Aux/IAA proteins for degradation (Maraschin et al, 2009). This degradation event relieves ARF transcription factor repression, allowing auxin-regulated gene transcription (Reed, 2001; Tiwari et al, 2001)

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