The EIL transcription factor family in soybean: Genome-wide identification, expression profiling and genetic diversity analysis

Abstract

The ETHYLENE INSENSITIVE3-LIKE (EIL) transcription factor family plays a critical role in the ethylene signaling pathway, which regulates a broad spectrum of plant growth and developmental processes, as well as defenses to myriad stresses. Although genome-wide analysis of this family has been carried out for several plant species, no comprehensive analysis of the EIL gene family in soybean has been reported so far. Furthermore, there are few studies on the functions of EIL genes in soybean. In this study, we identified 12 soybean (Gm) EIL genes, which we divided into three groups based on their phylogenetic relationships. We then detected their duplication status and found that most of the GmEIL genes have duplicated copies derived from two whole-genome duplication events. These duplicated genes underwent strong negative selection during evolution. We further analyzed the transcript profiles of GmEIL genes using the transcriptome data and found that their spatio-temporal and stress expression patterns varied considerably. For example, GmEIL1-GmEIL5 were found to be strongly expressed in almost every sample, while GmEIL8-GmEIL12 exhibited low expression, or were not expressed at all. Additionally, these genes showed different responses to dehydration, salinity and phosphate starvation. Finally, we surveyed genetic variations of these genes in 302 resequenced wild soybeans, landraces and improved soybean cultivars. Our data showed that most GmEIL genes are well conserved, and are not modified in domesticated or improved cultivars. Together, these findings provide a potentially valuable resource for characterizing the GmEIL gene family and lay the basis for further elucidation of their molecular mechanisms.

Keywords: EIL gene family; ethylene; ethylene signaling; soybean.

Figure 1

Summary of the EIL TF family in soybean and 18 representative species.

Figure 2

Phylogenetic relationships, gene structures and motif compositions of EIL genes from Arabidopsis and soybean. (A) The phylogenetic tree of EILs. A neighbor‐joining tree was constructed with mega 6.0 software using protein sequences. The Marchantia polymorpha EIL (Mapoly0088s0024.1) protein was used as an outgroup. (B) The exon–intron structures of EILs. Gene structural features were drawn using gsds 2.0 software. (C) The motif distribution of EILs. The conserved motifs were identified using the meme program. Different motifs are represented by different colored boxes numbered M1–M10.

Figure 3

The collinear relationships of homologous blocks containing GmEIL genes. The green and red colored rainbows represent the collinear relationships that arose from the Glycine WGD event and legume WGD event, respectively. The black lines within these blocks display the location of GmEIL genes. The positions of GmEIL2 and GmEIL5 were hard to separate since they are adjacent in the same chromosome.

Figure 4

The spatio‐temporal expression profiles of GmEIL genes in soybean. The gene expression values (FPKM values) were log2 transformed and displayed in the form of heat maps. Black indicates an FPKM value of 0. The numbers near the same tissue/organ represent earlier to later developmental stages.

Figure 5

The expression patterns of GmEIL genes against abiotic stresses. Gradient colors represent log2 FC in gene expression of different samples compared with control.