Genome-wide identification and analysis of the Q-type C2H2 gene family in potato (Solanum tuberosum L.)

Zhen Liu; Jeffrey A. Coulter; Yuanming Li; Xiaojing Zhang; Jiangang Meng; Junlian Zhang; Yuhui Liu

doi:10.1016/j.ijbiomac.2020.03.022

Genome-wide identification and analysis of the Q-type C2H2 gene family in potato (Solanum tuberosum L.)

Zhen Liu, Jeffrey A. Coulter, Yuanming Li, Xiaojing Zhang, Jiangang Meng, Junlian Zhang, Yuhui Liu

Agronomy and Plant Genetics

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

Abstract

Plant Q-type C2H2 zinc finger proteins play an important role in plant tolerance to abiotic stresses. Although the Q-type C2H2 gene family has been identified in many plants, little is known about it in potato (Solanum tuberosum). In the present study, a total of 79 Q-type C2H2 proteins in potato (StZFPs) were identified and their distribution on chromosomes, gene structure, and conserved motifs was assessed. According to their protein structural and phylogenetic features, these 79 StZFPs were classified into 12 distinct subclasses. Collinearity analysis showed that tandem and segmental duplication events played a crucial role in expansion of the StZFP gene family. Synteny analysis indicated that 11 and 21 StZFP genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively. RNA-seq data were used to analyze the tissue-specific expression and abiotic stress responses of the StZFP genes. Furthermore, we analyzed the expression of StZFP genes in drought-sensitive and drought-tolerant potato cultivars under drought stress. Subsequently, we used qPCR (Quantitative real-time-PCR) to calculate the relative expression of candidate genes in potato plantlets treated with NaCl (100 mM) and PEG 6000 (10% w/v) for 24 h. Such candidate genes could provide valuable information for abiotic stress resistance research in potato.

Original language	English (US)
Pages (from-to)	327-340
Number of pages	14
Journal	International Journal of Biological Macromolecules
Volume	153
DOIs	https://doi.org/10.1016/j.ijbiomac.2020.03.022
State	Published - Jun 15 2020

Bibliographical note

Funding Information:
This research was funded by the Gansu Science Foundation for Distinguished Young Scholars ( 17JR5RA138 ), the National Natural Science Foundation of China ( 31601356 and 31860398 ), the China Agriculture Potato Research System ( CARS-09-P14 ), the Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University (No. GSCS-2017-2 ), the Program for Longyuan Innovation Teams of Gansu Province, the Fuxi Talent Project of Gansu Agricultural University ( Gaufx-02Y04 ), and Special Funds for Discipline Construction of Gansu Agricultural University ( GSAU-XKJS-2018-218 ).

Publisher Copyright:
© 2020 Elsevier B.V.

Keywords

Drought stress
Expression profiles
Potato (Solanum tuberosum)
Q-type C2H2 zinc finger proteins

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title = "Genome-wide identification and analysis of the Q-type C2H2 gene family in potato (Solanum tuberosum L.)",

abstract = "Plant Q-type C2H2 zinc finger proteins play an important role in plant tolerance to abiotic stresses. Although the Q-type C2H2 gene family has been identified in many plants, little is known about it in potato (Solanum tuberosum). In the present study, a total of 79 Q-type C2H2 proteins in potato (StZFPs) were identified and their distribution on chromosomes, gene structure, and conserved motifs was assessed. According to their protein structural and phylogenetic features, these 79 StZFPs were classified into 12 distinct subclasses. Collinearity analysis showed that tandem and segmental duplication events played a crucial role in expansion of the StZFP gene family. Synteny analysis indicated that 11 and 21 StZFP genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively. RNA-seq data were used to analyze the tissue-specific expression and abiotic stress responses of the StZFP genes. Furthermore, we analyzed the expression of StZFP genes in drought-sensitive and drought-tolerant potato cultivars under drought stress. Subsequently, we used qPCR (Quantitative real-time-PCR) to calculate the relative expression of candidate genes in potato plantlets treated with NaCl (100 mM) and PEG 6000 (10% w/v) for 24 h. Such candidate genes could provide valuable information for abiotic stress resistance research in potato.",

keywords = "Drought stress, Expression profiles, Potato (Solanum tuberosum), Q-type C2H2 zinc finger proteins",

author = "Zhen Liu and Coulter, {Jeffrey A.} and Yuanming Li and Xiaojing Zhang and Jiangang Meng and Junlian Zhang and Yuhui Liu",

note = "Funding Information: This research was funded by the Gansu Science Foundation for Distinguished Young Scholars ( 17JR5RA138 ), the National Natural Science Foundation of China ( 31601356 and 31860398 ), the China Agriculture Potato Research System ( CARS-09-P14 ), the Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University (No. GSCS-2017-2 ), the Program for Longyuan Innovation Teams of Gansu Province, the Fuxi Talent Project of Gansu Agricultural University ( Gaufx-02Y04 ), and Special Funds for Discipline Construction of Gansu Agricultural University ( GSAU-XKJS-2018-218 ). Publisher Copyright: {\textcopyright} 2020 Elsevier B.V.",

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AU - Meng, Jiangang

AU - Zhang, Junlian

AU - Liu, Yuhui

N1 - Funding Information: This research was funded by the Gansu Science Foundation for Distinguished Young Scholars ( 17JR5RA138 ), the National Natural Science Foundation of China ( 31601356 and 31860398 ), the China Agriculture Potato Research System ( CARS-09-P14 ), the Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University (No. GSCS-2017-2 ), the Program for Longyuan Innovation Teams of Gansu Province, the Fuxi Talent Project of Gansu Agricultural University ( Gaufx-02Y04 ), and Special Funds for Discipline Construction of Gansu Agricultural University ( GSAU-XKJS-2018-218 ). Publisher Copyright: © 2020 Elsevier B.V.

PY - 2020/6/15

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N2 - Plant Q-type C2H2 zinc finger proteins play an important role in plant tolerance to abiotic stresses. Although the Q-type C2H2 gene family has been identified in many plants, little is known about it in potato (Solanum tuberosum). In the present study, a total of 79 Q-type C2H2 proteins in potato (StZFPs) were identified and their distribution on chromosomes, gene structure, and conserved motifs was assessed. According to their protein structural and phylogenetic features, these 79 StZFPs were classified into 12 distinct subclasses. Collinearity analysis showed that tandem and segmental duplication events played a crucial role in expansion of the StZFP gene family. Synteny analysis indicated that 11 and 21 StZFP genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively. RNA-seq data were used to analyze the tissue-specific expression and abiotic stress responses of the StZFP genes. Furthermore, we analyzed the expression of StZFP genes in drought-sensitive and drought-tolerant potato cultivars under drought stress. Subsequently, we used qPCR (Quantitative real-time-PCR) to calculate the relative expression of candidate genes in potato plantlets treated with NaCl (100 mM) and PEG 6000 (10% w/v) for 24 h. Such candidate genes could provide valuable information for abiotic stress resistance research in potato.

AB - Plant Q-type C2H2 zinc finger proteins play an important role in plant tolerance to abiotic stresses. Although the Q-type C2H2 gene family has been identified in many plants, little is known about it in potato (Solanum tuberosum). In the present study, a total of 79 Q-type C2H2 proteins in potato (StZFPs) were identified and their distribution on chromosomes, gene structure, and conserved motifs was assessed. According to their protein structural and phylogenetic features, these 79 StZFPs were classified into 12 distinct subclasses. Collinearity analysis showed that tandem and segmental duplication events played a crucial role in expansion of the StZFP gene family. Synteny analysis indicated that 11 and 21 StZFP genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively. RNA-seq data were used to analyze the tissue-specific expression and abiotic stress responses of the StZFP genes. Furthermore, we analyzed the expression of StZFP genes in drought-sensitive and drought-tolerant potato cultivars under drought stress. Subsequently, we used qPCR (Quantitative real-time-PCR) to calculate the relative expression of candidate genes in potato plantlets treated with NaCl (100 mM) and PEG 6000 (10% w/v) for 24 h. Such candidate genes could provide valuable information for abiotic stress resistance research in potato.

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Genome-wide identification and analysis of the Q-type C2H2 gene family in potato (Solanum tuberosum L.)

Abstract

Bibliographical note

Keywords

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