The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis
Abstract Background 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. The zf_CCCH family have been reported involving in various processes of plant development and adaptation. Results In this study, the zf_CCC...
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doaj-25d92ac99be24f15a090162206065cc62021-07-11T11:32:29ZengBMCBMC Genomics1471-21642021-07-0122111910.1186/s12864-021-07787-9The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysisXin Hu0Jianfang Zuo1The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F UniversityCollege of Plant Science and Technology, Huazhong Agricultural UniversityAbstract Background 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. The zf_CCCH family have been reported involving in various processes of plant development and adaptation. Results In 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. Conclusions This 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.https://doi.org/10.1186/s12864-021-07787-9SoybeanCCCH zinc finger (zf_CCCH)ExpressionDomesticationHaplotype analysis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xin Hu Jianfang Zuo |
spellingShingle |
Xin Hu Jianfang Zuo The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis BMC Genomics Soybean CCCH zinc finger (zf_CCCH) Expression Domestication Haplotype analysis |
author_facet |
Xin Hu Jianfang Zuo |
author_sort |
Xin Hu |
title |
The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis |
title_short |
The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis |
title_full |
The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis |
title_fullStr |
The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis |
title_full_unstemmed |
The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis |
title_sort |
ccch zinc finger family of soybean (glycine max l.): genome-wide identification, expression, domestication, gwas and haplotype analysis |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2021-07-01 |
description |
Abstract Background 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. The zf_CCCH family have been reported involving in various processes of plant development and adaptation. Results In 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. Conclusions This 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. |
topic |
Soybean CCCH zinc finger (zf_CCCH) Expression Domestication Haplotype analysis |
url |
https://doi.org/10.1186/s12864-021-07787-9 |
work_keys_str_mv |
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