Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas.

Yuehui Tang,Shen Li,Yingying He,Yiru Niu,Ying Li,Wei Cheng,Xiang Wang,Xinxin Bao,Qian Wu,Yaoyu Wang,Jiatong Xie,Baohong Zhang

doi:10.1371/journal.pone.0254711

Abstract

GRF genes have been confirmed to have important regulatory functions in plant growth, development and response to abiotic stress. Although the genome of Jatropha curcas is sequenced, knowledge about the identification of the species' GRF genes and their expression patterns is still lacking. In this study, we characterized the 10 JcGRF genes. A detailed investigation into the physic nut GRF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under both normal growth and abiotic stress conditions. Phylogenetic analysis indicated that the 10 JcGRF genes were classified into five groups corresponding to group I, II, III, IV and V. The analysis of conserved domains showed that the motifs of JcGRF genes were highly conserved in Jatropha curcas. Expression analysis based on RNA-seq and qRT-PCR showed that almost all JcGRF genes had the highest expression in seeds, but very low expression was detected in the non-seed tissues tested, and four JcGRF genes responded to at least one abiotic stress at at least one treatment point. Our research will provide an important scientific basis for further research on the potential functions of JcGRF genes in Jatropha curcas growth and development, and response to abiotic stress, and will eventually provide candidate genes for the breeding of Jatropha curcas.

Highlights

Growth-regulating factors (GRFs) are plant-specific transcription factors with important regulatory functions in plant development and adaptation to environmental stress, which are characterized by two highly conserved domains, namely QLQ and WRC [1]
Among the 10 JcGRF, the amino acid sequences of these proteins ranged from 204 amino acid (JcGRF08) to 613 aa (JcGRF05), and the length of their corresponding coding sequence (CDS) ranged from 615 bp to 1842 bp
The results showed that the JcGRF genes expression results detected by qRT-PCR had a similar change trend compared with the RNA-Seq results (Fig 7B), indicating that our expression profile data was reliable and could provide candidate genes for the cultivation of stress-tolerant varieties of Jatropha curcas

Summary

Introduction

Growth-regulating factors (GRFs) are plant-specific transcription factors with important regulatory functions in plant development and adaptation to environmental stress, which are characterized by two highly conserved domains, namely QLQ and WRC [1]. QLQ domain is an important protein-protein interaction domain, whereas WRC domain is a kind of plant-specific motif, which is mainly responsible for the interaction between transcription factors and DNA [2]. Since the first GRF family gene, namely OsGRF1, is isolated and functionally studied in rice [3], many GRF genes have been identified and characterized in a variety of plant species such as tomato, soybean, rice, cotton, streptophyta and Arabidopsis [2, 4,5,6,7].

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Conclusion