Genome-Wide Identification of the Early Flowering 4 (ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance.

Miaomiao Tian,Xu Yang,Jianhua Lu,Xiaokang Fu,Meng Zhang,Aimin Wu,Hantao Wang,Jingjing Zhang,Shuxun Yu,Hengling Wei,Liang Ma

doi:10.3389/fgene.2021.686852

Abstract

The early flowering 4 (ELF4) family members play multiple roles in the physiological development of plants. ELF4s participated in the plant biological clock’s regulation process, photoperiod, hypocotyl elongation, and flowering time. However, the function in the ELF4s gene is barely known. In this study, 11, 12, 21, and 22 ELF4 genes were identified from the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. There ELF4s genes were classified into four subfamilies, and members from the same subfamily show relatively conservative gene structures. The results of gene chromosome location and gene duplication revealed that segmental duplication promotes gene expansion, and the Ka/Ks indicated that the ELF4 gene family has undergone purification selection during long-term evolution. Spatio-temporal expression patterns and qRT-PCR showed that GhELF4 genes were mainly related to flower, leaf, and fiber development. Cis-acting elements analysis and qRT-PCR showed that GhELF4 genes might be involved in the regulation of abscisic acid (ABA) or light pathways. Silencing of GhELF4-1 and GhEFL3-6 significantly affected the height of cotton seedlings and reduced the resistance of cotton. The identification and functional analysis of ELF4 genes in upland cotton provide more candidate genes for genetic modification.

Highlights

The early flowering 4 (ELF4) family belongs to a small and highly conserved gene family, discovered and named by Doyle (Doyle et al, 2002)
Based on the HMM model of the ELF4 specific conserved domain constructed by the DUF1313 (Pfam07011) protein sequence, a total of 11, 12, 21, and 22 ELF4 genes were identified from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively (Supplementary Table 1)
Using the online tool WebLogo to construct sequence logos from the predicted ELF4s of the G. arboreum, G. raimondii, G. hirsutum, G. barbadense, A. thaliana, and Populus trichocarpa domain (Supplementary Figure 2), the results show that the DUF1313 domain of ELF4s was conserved in multiple species

Summary

Introduction

The early flowering 4 (ELF4) family belongs to a small and highly conserved gene family, discovered and named by Doyle (Doyle et al, 2002). The conserved domain of the ELF4 gene family is DUF1313, which is a highly conserved domain At present, it belongs to the domain of unknown function, and few researches have been reported in this area. Studies have shown that ELF4 is a central gene in the circadian clock, which is involved in photoperiod perception, circadian regulation, signal transmission in the early flowering of Arabidopsis, promotion of seedling de-etiolation, and hypocotyl growth of Arabidopsis (Doyle et al, 2002; Khanna et al, 2003; Harriet et al, 2007; Kolmos and Davis, 2007; Nusinow et al, 2011). In Arabidopsis, deletion of the AtELF4 gene leads to an impaired photoperiod response, and circadian dysfunction (imprecision and arrhythmicity), and very low amplitude of the light-induced clock gene CCA1 (Doyle et al, 2002)

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Discussion

Conclusion