Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea

Vikash K Singh,Mohan Singh Rajkumar,Rohini Garg,Mukesh Jain

doi:10.1038/s41598-017-11327-5

Abstract

Auxin response factors (ARFs) are the transcription factors that regulate auxin responses in various aspects of plant growth and development. Although genome-wide analysis of ARF gene family has been done in some species, no information is available regarding ARF genes in chickpea. In this study, we identified 28 ARF genes (CaARF) in the chickpea genome. Phylogenetic analysis revealed that CaARFs can be divided into four different groups. Duplication analysis revealed that 50% of CaARF genes arose from duplication events. We analyzed expression pattern of CaARFs in various developmental stages. CaARF16.3, CaARF17.1 and CaARF17.2 showed highest expression at initial stages of flower bud development, while CaARF6.2 had higher expression at later stages of flower development. Further, CaARF4.2, CaARF9.2, CaARF16.2 and CaARF7.1 exhibited differential expression under different abiotic stress conditions, suggesting their role in abiotic stress responses. Co-expression network analysis among CaARF, CaIAA and CaGH3 genes enabled us to recognize components involved in the regulatory network associated with CaARFs. Further, we identified microRNAs that target CaARFs and TAS3 locus that trigger production of trans-acting siRNAs targeting CaARFs. The analyses presented here provide comprehensive information on ARF family members and will help in elucidating their exact function in chickpea.

Highlights

Auxin or indole-3-acetic acid (IAA), a crucial phytohormone, plays a vital function in regulation of numerous aspects of growth and development in plants
Auxin response factors (ARFs) proteins contain three domains, i.e. a N-terminal B3-like DNA binding domain (DBD), C-terminal PB1 (Phox and Bem1) domain contained within a region that was previously called motif III/IV, and a middle region (MR), which is responsible for gene activation/repression[8, 10,11,12,13,14,15]
To confirm the presence of ARF domain, protein sequences of putative ARF gene family members of chickpea were analyzed in Pfam and SMART databases

Summary

Introduction

Auxin or indole-3-acetic acid (IAA), a crucial phytohormone, plays a vital function in regulation of numerous aspects of growth and development in plants. To confirm the presence of ARF domain, protein sequences of putative ARF gene family members of chickpea were analyzed in Pfam and SMART databases. An unrooted phylogenetic tree was constructed using protein sequence alignment of ARF gene family members from Arabidopsis (23) and chickpea (28) for examining evolutionary relationship among them (Fig. 1).

Results

Conclusion