Genome-wide survey and expression analysis of F-box genes in chickpea.

Shefali Gupta,Vanika Garg,Sabhyata Bhatia,Chandra Kant

doi:10.1186/s12864-015-1293-y

Abstract

BackgroundThe F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.ResultsA total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.ConclusionsThe genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1293-y) contains supplementary material, which is available to authorized users.

Highlights

The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins
The presence of F-box genes in such large numbers implies that diverse SCF complexes are possible which can recognize a wide array of substrates and have the ability to regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence [2]
The roles of several F-box genes such as MAX2 [69], FBP7 [70], DOR [71] and MAIF1 [67] have been well established during abiotic stress conditions. Their chickpea homolog such as Ca_19880 (60% homology with MAX2) exhibited comparatively higher expression during salinity stress in root [69] thereby indicating a putatively similar role in chickpea. These findings indicate that the F-box genes might be mediating specific responses to various stress conditions such as desiccation, salinity and cold

Summary

Introduction

The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. F-box proteins form a subunit of SCF complex (one of the best characterized E3 ligases) and confer specificity for a target substrate to be degraded [1]. The presence of F-box genes in such large numbers implies that diverse SCF complexes are possible which can recognize a wide array of substrates and have the ability to regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence [2]. A great deal of experimental work is required in order to determine the specific biological function of each of these genes comprising the F-box family

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Discussion

Conclusion