Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

1. Introduction

Sweetpotato (Ipomoea batatas (L.) Lam.) is an important food crop with ultra-high yield characteristics, and sweetpotato is rich in protein, dietary fiber, polyphenols, vitamins, mineral elements, and other nutrients needed by the human body. It is one of the globally recognized nutrients (Neela and Fanta, 2019). The sweetpotato planting area can reach 7.4 million hectares, with an annual production of about 88.9 million tonnes of storage roots (SRs). As the main edible tissue of sweetpotato, the production and development of SR are their most important agronomic traits (Du et al., 2023). However, adverse abiotic factors like salt and drought severely restrict the sweetpotato plant’s growth, development, and output (Zhang et al., 2023). Transcription factors play an important regulatory role in the transmission of plant stress signals, regulating the expression of multiple stress related genes and improving plant stress resistance. The regulatory effects of many transcription factors have been reported, for example, the MYB transcription factor (Dubos et al., 2010; Li et al., 2016), the WRKY transcription factor (Chen et al., 2009; Raineri et al., 2015), the NAC transcription factor (Yuan et al., 2019; Diao et al., 2020), the bHLH transcription factor (Guo et al., 2021; Qian et al., 2021), the bZIP transcription factor (Joo et al., 2021; Han et al., 2023), and zinc finger transcription factor (Kiełbowicz-Matuk, 2012; Yin et al., 2017), etc. Zinc finger proteins (ZFPs) the largest transcription factor family in plants, are present in many different species. In controlling plant growth and development and responding to varied environmental challenges, they serve a critical regulatory role (Han et al., 2021).

ZFPs can be categorized into many subfamilies, such as C2H2, C3H, C3HC4, etc., depending on the quantity and arrangement of cysteine and histidine residues in their secondary structure. C2H2 zinc finger proteins (C2H2-ZFPs) are one of them that have undergone more in-depth study (Jiao et al., 2020). The EPF1 gene of Petunia is the earliest zinc finger protein found in plants with a C2H2 zinc finger structure (Takatsuji et al., 1992). Numerous C2H2-ZFPs have so far been found in plants, including Arabidopsis thaliana 176 (Englbrecht et al., 2004), Sorghum bicolor 145 (Cui et al., 2022), Vitis vinifera 98 (Arrey-Salas et al., 2021), and Panax ginseng 115 (Jiang et al., 2022). The length of the long spacer between the two zinc fingers in plant-specific C2H2-ZFP (Q-type C2H2-ZFP) is different from that of other eukaryotes (Ciftci-Yilmaz and Mittler, 2008). A highly conservative QALGGH sequence is typically found in Q-type C2H2-ZFPs, allowing ZFPs to detect target genes and control their expression levels (Wang et al., 2019). There are several distinct classification types and standards used for C2H2-ZFPs. Usually, the number of zinc finger domains, the spacing between them, the series or dispersion of zinc finger domains, and the QALGGH sequence are used to categorize C2H2-ZFPs (Liu et al., 2022b).

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C2H2-ZFP genes can regulate plants to cope with various abiotic stresses such as high salinity, drought, cold, etc. and plays a very important role in plant adaptation to the environment (Han et al., 2020). C2H2-ZFPs can typically interact with plant hormones to affect the phenotype of plants under stress. (Kiełbowicz-Matuk, 2012; Liu et al., 2022b). For example, overexpression of OsZFP179 enhances the salt tolerance of rice, transgenic seedlings show hypersensitivity to exogenous ABA (Sun et al., 2010), OsZFP36 is a key participant in rice abscisic acid induced antioxidant defense and oxidative stress tolerance (Zhang et al., 2014), and PtrZPT2-1 encodes C2H2-ZFP from Poncirus trifoliata, which can enhance the tolerance of plants to various abiotic stresses (Liu et al., 2017).

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In addition, C2H2-ZFP can also participate in the growth and development of many plant organs and structures. For instance, during seed germination and plant development, Arabidopsis thaliana AtZFP3 interferes with the transmission of abscisic acid and light signals (Joseph et al., 2014), Arabidopsis thaliana AtZFP1 acts upstream of the key trichome initiation factors GL3 and TRY, and overexpression of AtZFP1 significantly increases the number of trichomes on the stem, leaf, lateral branch, and main stem (Zhang et al., 2020). AtZFP5 is associated with ethylene signaling and regulates root hair development induced by phosphate and potassium deficiency in Arabidopsis thaliana (Huang et al., 2020).

In this study, we identified 178 C2H2 zinc-finger proteins (IbZFPs) from the genome of sweetpotato and analyzed their phylogenetic relationship, chromosome location, collinearity with other species, gene structure, conservative motif promoter cis-regulatory element, and subcellular location. In addition, we also analyzed the expression profile of IbZFP genes in sweetpotato SR development and salt stress. Some IbZFP genes were detected by real-time quantitative polymerase chain reaction (qRT-PCR). And overexpression of IbZFP105 in Arabidopsis thaliana was revealed to enhance its tolerance to salt and ABA stress. These results should provide a very important theoretical basis for studying the function of IbZFP genes in the future.

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