The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis

Xin Hu,Jianfang Zuo

doi:10.1186/s12864-021-07787-9

Abstract

BackgroundThe CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes of plant development and adaptation.ResultsIn this study, the zf_CCCH genes were identified via a genome-wide search and were systematically analyzed. 116 Gmzf_CCCHs were obtained and classified into seventeen subfamilies. Gene duplication and expansion analysis showed that tandem and segmental duplications contributed to the expansion of the Gmzf_CCCH gene family, and that segmental duplication play the main role. The expression patterns of Gmzf_CCCH genes were tissue-specific. Eleven domesticated genes were detected involved in the regulation of seed oil and protein synthesis as well as growth and development of soybean through GWAS and haplotype analysis for Gmzf_CCCH genes among the 164 of 302 soybeans resequencing data. Among which, 8 genes play an important role in the synthesis of seed oil or fatty acid, and the frequency of their elite haplotypes changes significantly among wild, landrace and improved cultivars, indicating that they have been strongly selected in the process of soybean domestication.ConclusionsThis study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, meanwhile, it was also helpful for the improvement of soybean with high oil content.

Highlights

The CCCH zinc finger is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues
This study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, it was helpful for the improvement of soybean with high oil content
Identification of Gmzf_CCCH genes in soybean In soybean, 116 Gmzf_CCCHs were identified via genome-wide search using HMM profiles and confirmed by the conserved domain of CCCH- zinc finger detected in Pfam databases and SMART domain search database

Summary

Introduction

The CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. Most of the Zf subfamilies have been identified as DNA-binding proteins or protein-binding proteins [11], while more and more evidence demonstrates that CCCH zinc finger (zf_CCCH) may be RNA-binding proteins functions in RNA processing [12,13,14]. It has been reported the zf_CCCH family plays a key role involving in various processes of plant development and adaptation. It is reported that salt stress-inducible Zf protein 1 (AtSZF1) and AtSZF2 negatively regulate the expression of many salt-responsive genes, improving the salt tolerance of Arabidopsis [19]. OsDOS (a CCCH gene in rice) was detected involved in the negative regulation of the jasmonic acid (JA) pathway, and its overexpression significantly delayed the leaf senescence [21]

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