Molecular Plant Breeding 2024, Vol.15 http://genbreedpublisher.com/index.php/mpb © 2024 GenBreed Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher
Molecular Plant Breeding 2024, Vol.15 http://genbreedpublisher.com/index.php/mpb © 2024 GenBreed Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. GenBreed Publisher is an international Open Access publisher specializing in molecular genetics, plant genes or traits, and plant breeding registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher GenBreed Publisher Editedby Editorial Team of Molecular Plant Breeding Email: edit@mpb.genbreedpublisher.com Website: http://genbreedpublisher.com/index.php/mpb Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Molecular Plant Breeding (ISSN 1923-8266) is an international, open access, peer reviewed journal published online by BioPublisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all areas of transgene, molecular genetics, crop QTL analysis, germplasm genetic diversity, and advanced breeding technologies. Molecular Plant Breeding is archived in LAC (Library and Archives Canada) and deposited in CrossRef. The Journal has been indexed by ProQuest as well. The Journal is expected to be indexed by PubMed and other databases in near future. All the articles published in Molecular Plant Breeding are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. GenBreed Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Molecular Plant Breeding (online), 2024, Vol. 15 ISSN 1923-8266 http://genbreedpublisher.com/index.php/mpb © 2024 GenBreed Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher Latest Content Research Progress of WRKY Transcription Factor Family in Plant Stress Resistance Qingqing Ji, Xia An, Guanghui Du, Xiahong Luo, Changli Chen, Tingting Liu, Lina Zou, Guanlin Zhu Molecular Plant Breeding, 2024, Vol. 15, No. 2, pp.42-51 The Current Situation and Future of Using GWAS Strategies to Accelerate the Improvement of Crop Stress Resistance Traits Wenzhong Huang Molecular Plant Breeding, 2024, Vol. 15, No. 2, pp.52-62 Starch Biosynthesis and Engineering Starch Yield and Properties in Cassava Youzhi Li Molecular Plant Breeding, 2024, Vol. 15, No. 2, pp.63-69 Precision Editing: Revolutionary Applications of Genome Editing Technology in Tree Breeding Xiuying Zhao Molecular Plant Breeding, 2024, Vol. 15, No. 2, pp.70-80 Application of CRISPR/Cas9 Technology in Editing Poplar Drought Resistance Genes YepingHan Molecular Plant Breeding, 2024, Vol. 15, No. 2, pp.81-89
Molecular Plant Breeding 2024, Vol.15, No.2, 42-51 http://genbreedpublisher.com/index.php/mpb 42 Review and Progress Open Access Research Progress of WRKY Transcription Factor Family in Plant Stress Resistance Qingqing Ji 1,2, XiaAn1 , Guanghui Du2, Xiahong Luo1, Changli Chen1, Tingting Liu1, LinaZou1, Guanlin Zhu1 1 Zhejiang Xiaoshan Institute of Cotton & Bast Fiber Crops, Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311251, Zhejiang, China 2 College of Agriculture, Yunnan University, Kunming, 650091, Yunnan, China Corresponding author: anxia@zaas.ac.cn Molecular Plant Breeding, 2024, Vol.15, No.2 doi: 10.5376/mpb.2024.15.0006 Received: 08 Jan., 2024 Accepted: 26 Feb., 2024 Published: 09 Mar., 2024 Copyright © 2024 Ji et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Ji Q.Q., An X., Du G.H., Luo X.H., Chen C.L., Liu T.T., Zou L.N., and Zhu G.L., 2024, Research progress of WRKY transcription factor family in plant stress resistance, Molecular Plant Breeding, 15(2): 42-51 (doi: 10.5376/mpb.2024.15.0006) Abstract Transcription factors are a group of regulatory proteins that play significant roles in biological processes. They are the seventh largest family of transcription factors in higher plants, and are essential in plant growth, development, and response to biotic and abiotic stresses. This study provides a brief overview of the evolution of WRKY transcription factors in response to various abiotic stresses such as drought, high salt, temperature, inorganic elements, and oxidation, as well as biotic stresses such as infection by pathogenic bacteria and feeding by phytophagous insects. Furthermore, the research prospects and directions of WRKY transcription factors are envisioned. Keywords WRKY; Transcription factor; Biotic stress; Abiotic stress 1 Introduction Throughout their growth and development, plants are vulnerable to various stresses such as drought, flooding, high and low temperatures, salinity, oxidation, inorganic elements, as well as infestation by pathogenic bacteria and phytophagous insects. To maintain their normal life processes and adapt to the ever-changing external environment, plants have evolved a range of complex and effective defense mechanisms. One of the primary ways that plants deal with stress is through the transcription of specific genes, whereby transcription factors play a crucial role in regulating various developmental and physiological processes in plants by directly or indirectly binding to the cis-acting elements in genes that are involved in the stress signal transduction pathways. WRKY is a unique and novel transcription factor specific to plants. Its members play a crucial role in enhancing plant stress tolerance. The WRKY protein comprises a 60-amino-acid conserved region known as the WRKY conserved region. The N-terminal of this region contains a core sequence of WRKYGQK, which is responsible for DNA binding and forms a positively charged concave surface. On the other hand, the C-terminal of the WRKY protein is a zinc-finger structure that can be linked to the W-box (C/TTGACT/C). This structure is responsible for DNA binding. The N-terminal region is positively charged and mainly responsible for DNA binding, while the C-terminal region is responsible for specific binding to DNA. WRKY is induced by pathogens, mechanical damage, and the signaling molecule salicylic acid. Initially, the WRKY family was classified into three subfamilies based on the number of WRKY regions and zinc-finger structures, which are known as subfamily I, II, and III. Subfamily I contains two WRKY structural domains, family II contains one WRKY structural domain and one C2H2-type zinc-finger structure, and family III contains one WRKY structural domain and one C2HC-type zinc-finger structure. Later, Zhang and Wang (2005) reclassified the family into five families based on the differences in the conserved structures and the positions of their introns. These are Ⅰ, Ⅱa+Ⅱb, Ⅱc, Ⅱd+Ⅱe, and Ⅲ, which are distinguished by the differences in the conserved structures and the positions of their introns.
Molecular Plant Breeding 2024, Vol.15, No.2, 42-51 http://genbreedpublisher.com/index.php/mpb 43 In 1994, the first member of the WRKY transcription factors was discovered in sweet potato (Ipomoea batatas). Since then, researchers have identified numerous WRKY transcription factor members in many plants. Arabidopsis has over 100 WRKY members, each with one or two WRKY structural domains. Rice has 102 WRKY members, soybean has 197, cotton has 116, oilseed rape has 46, tomato has 81, poplar has 104, and rubber tree has 81 members. The WRKY structural domain is a sequence of 60 amino acids that includes a highly conserved amino acid sequence, WRKYGQK, at the N-terminus and a zinc finger domain. Most WRKY proteins bind to the W-box [TGAC(C/T)], which is present in the promoters of various genes related to plant defense responses. This binding helps in mediating transcriptional responses induced by pathogens. When the plant is infected with viruses, bacteria, or fungi, or treated with signaling agents like salicylic acid, mRNA and protein synthesis of WRKY transcription factors increases and enhances their DNA-binding activity (Dong et al., 2003). The W-box and WRKY transcription factors work together to regulate the expression of downstream gene products that provide protection and defense against pathogens. 2 Role of WRKY Transcription Factors in Abiotic Stresses Abiotic stresses can affect normal physiological and biochemical processes in plants. Research has shown that WRKY transcription factors play a significant role in regulating plant responses to abiotic stresses. WRKY proteins are one of the largest families of transcription factors in higher plants, and they participate in complex signaling pathways and response mechanisms. Moreover, individual WRKY proteins can regulate multiple stress responses, and they may even play a role in both biotic and abiotic stresses. WRKY transcription factors are involved in the response to abiotic stresses such as drought, high salt and temperature (Figure 1) (Wu et al., 2020). For example, transcriptome analysis showed that 41 OsWRKY genes in rice, 20 AtWRKY genes in Arabidopsis, and 74 BnWRKY genes in oilseed rape were involved in the response to abiotic stress (Ramamoorthy et al., 2008; Chen et al., 2012). Figure 1 The function of WRKY in plant abiotic stress signaling network (Adopted from Wu et al., 2020) 2.1 Drought stress Drought stress has been found to be the most detrimental abiotic stress on plant growth and development, according to studies. Drought causes stomatal closure and lowers plant water content, reducing transpiration and affecting photosynthesis and solute accumulation. The WRKY family of transcription factors is essential for plant drought tolerance.
Molecular Plant Breeding 2024, Vol.15, No.2, 42-51 http://genbreedpublisher.com/index.php/mpb 44 The expression of some WRKY family transcription factors in the tomato genome can be induced by drought stress, including SlWRKY1, SlWRKY25, SlWRKY31, SlWRKY32, and SlWRKY74.SlWRKY81 reduced proline synthesis and lowered drought tolerance in tomatoes, and the expression of SlWRKY81 was up-regulated under drought conditions. The silencing of SlWRKY81 accelerated the closure of tomato stomata under drought stress and significantly reduced drought-induced damage (Dong et al., 2023). It has been observed in a study that the overexpression of CmWRKY10 in chrysanthemum leads to a significant increase in the expression of drought-related genes (Jaffar et al., 2016). Additionally, CmWRKY1 has been reported to play a role in drought tolerance in chrysanthemums by down-regulating PP2C, ABI1, and ABI2, and up-regulating genes in the ABA signaling pathway such as PYL2, SnRK2.2, ABF4, MYB2, RAB18, andDREB1A(Fan et al., 2016). Plants can regulate the expression of drought-related genes by controlling the accumulation of ROS (reactive oxygen species). In cotton, the GhWRKY25 gene reduces drought tolerance by increasing MDA and ROS levels while decreasing the activities of SOD, POD, and CAT enzymes (Liu et al., 2016). On the other hand, overexpression of the MbWRKY5 gene from Zingiber officinale in tobacco plants increases their chlorophyll, proline, glutathione, and ascorbic acid contents, as well as the activities of POD, SOD, and CAT enzymes, resulting in improved drought tolerance (Han et al., 2019). After being subjected to drought stress, WRKY-like transcription factors may have a negative impact on the expression of related genes. Some transgenic plants exhibited less resistance to drought stress, with lower leaf water content and higher levels of transpiration water loss, resulting in lower survival rates than wild-type plants. For instance, transgenic plants that had overexpressed GhWRKY25 showed a decreased resistance to grey mould (Liu, 2015). In addition, a single WRKY transcription factor can correspond to multiple physiological processes. For instance, in land cotton, the expression of the WRKY4 gene is induced under both salt and drought stress, while WRKY5 is induced only under drought stress. 2.2 High salt stress In our country, plants not only suffer from drought stress, but also from high salt stress. This salt stress negatively affects the nutritional and reproductive growth of plants, causing primary and secondary salt damage. It destroys their normal morphological structure, and can even result in serious consequences such as plant death. Salt stress has become a major obstacle to the construction of a healthy ecological environment, as well as the sustainable development of agriculture in China, alongside drought stress. First, WRKY transcription factors may be directly involved in regulating salt stress response to alleviate damage caused by high salt. For example, overexpression of the SmWRKY28 gene in Arabidopsis thaliana enhances resistance to saline salts such as NaCl and NaHCO3 and reduces oxidative toxicity (Wang, 2016); overexpression of GsWRKY15 gene can significantly enhance alfalfa alkali tolerance (Zhu et al., 2017); Overexpression of GmWRKY34 in Arabidopsis thaliana (Zhou et al., 2015), as well as overexpression of GhWRKY41 (Chu et al., 2016) and GhWRKY25(Liu et al., 2016) in tobacco, can improve salt tolerance. Plants have the ability to respond to salt stress by producing signaling molecules like ABA and H2O2. For instance, when ZmWRKY17 is overexpressed, it can reduce the sensitivity of transgenic plants to ABA while increasing their sensitivity to salt stress. Additionally, with the addition of an ABA synthesis inhibitor, the seeds of transgenic lines can recover the phenotype of strongly inhibited germination under high salt stress (Cai, 2016). OsWRKY50 in rice contains a WRKY structural domain and acts as a transcriptional repressor in the nucleus. OsWRKY50 participates in the salt stress response of rice by regulating stress-responsive genes and decreasing the ABA sensitivity of the plant, and it plays a positive role in the regulation of salt stress in rice (Fan et al., 2023). WRKY transcription factors are known to play a role in various abiotic stress responses. For instance, TaWRKY44 expression in tobacco has been shown to enhance resistance to drought, salt stress, and osmotic stress (Han et al., 2015). In the case of ginseng, PgWRKYs transcript levels respond significantly to salt stress treatment (Xiu et al., 2016). Furthermore, the promoter sequence of GhWRKY25 contains cis-acting elements that are associated with low temperature, drought, endosperm, and gibberellin elements, and are induced by high salinity and low
Molecular Plant Breeding 2024, Vol.15, No.2, 42-51 http://genbreedpublisher.com/index.php/mpb 45 temperature (4 °C), while being inhibited by polyethylene glycol (PEG) and mechanical damage. It is worth noting that the hormonal signaling molecules GA3, 6-BA, ABA and SA strongly induce gene expression in GhWRKY25 (Liu, 2015). The interaction of WRKY transcription factors with other proteins is very important in regulating salt tolerance responses in plants. For instance, in Arabidopsis, the transcription factor WRKY8 interacts with VQ9, a member of the VQ protein family, to regulate salt tolerance responses in plants (Han et al., 2015). WRKY transcription factors can be induced by multiple stressors, including salt stress. For example, the overexpression of cotton GHWRKY39-1 in tobacco increased the tolerance of the transgenic plants to salt stress (Shi et al., 2014). The overexpression of the tomato SlWRKY39 gene in tomato plants also increased their proline content significantly, thereby improving their resistance to salt damage and drought caused by multiple stress factors such as PstDC3000, salt damage, and drought (Sun et al., 2015). WRKY transcription factors are also negatively regulated by salt stress. For example, overexpression of OsWRKY45-1 reduced rice tolerance to high salt (Tao et al., 2011); in transgenic Arabidopsis thaliana and chrysanthemum, chrysanthemumGmWRKY17 negatively regulated its salt tolerance (Li et al., 2015). 2.3 Temperature stress Temperature is a crucial factor that affects plant growth and development. High and low temperatures can cause stress on plants, which is referred to as abiotic stress. When plants are subjected to high or low temperatures, specific transcription factors known as WRKY transcription factors regulate the expression of related genes to reduce the damage caused by the temperature. For instance, the expression of transcription factors WRKY5 and WRKY24 in the highly cold-tolerant variety 'Dongnong Winter Wheat 1', varied significantly between different low-temperature treatments, indicating that this transcription factor plays a vital role in regulating the cold tolerance of plants. Furthermore, the chili CaWRKY13 gene plays a crucial role in coping with abiotic stresses, including low and high temperatures (Wei et al., 2017). The WRKY family of genes plays a crucial role in the response of plants to temperature-related stress by regulating the ABA signaling pathway. For instance, in the tea tree, 50 genes belonging to the WRKY family are identified, most of which are induced by cold stress. Among these genes, CsWRKY2 is responsible for enhancing plant cold resistance by regulating the ABA signaling pathway (Wu et al., 2016). Overexpression of VpWRKY1 and VpWRKY2 in Arabidopsis thaliana has been found to increase the plant's response to cold stress, salt stress, and frost, thus aiding in better cold resistance in transgenic plants. In addition to this, VpWRKY2 also enhances plant resistance to downy mildew (Li et al., 2010a). Similarly, in oilseed rape, the BcWRKY46 gene responds to strong induction of NaCl and drought and enhances cold resistance by regulating the ABA signaling pathway (Wang et al., 2012). The phytohormone JA, which is involved in the plant's response to various stressors, also reduces the damage caused by low temperatures in fruit. The MaWRKY26 gene found in bananas is activated by low-temperature stress and MeJA. This activation helps to improve the cold resistance of banana fruits. Additionally, when combined with its promoter, MaWRKY26 can also be reverse-activated to promote the synthesis of JA. This can reduce the damage caused by low temperatures on banana fruits. The transcription factors of the WRKY family, HbWRKY2, HbWRKY3, HbWRKY4, and HbWRKY9, respond to abiotic stresses such as PEG, high salinity, and low temperature. This response helps in improving the plant's resistance to these conditions (Xie, 2013; Zhao et al., 2015). Moreover, chili CaWRKY40 is involved in plant response to high-temperature stress (Dang et al., 2013). In Arabidopsis, high temperature inhibited the expression of the AtWRKY33 gene with a repressive effect, but induced the expression of the AtWRKY25 and AtWRKY26 genes. Among them, constitutive expression of AtWRKY25 andAtWRKY26 enhanced plant expression by activating Hsfs (Heat shock factors), Hsps (Heat shock proteins), Zat10 (Transcription factor), and MBF1c (Multiprotein bridging factor 1) enhance plant resistance to heat stress (Ohama et al., 2017); heat treatment induces the expression of AtWRKY39, which positively regulates the signalling pathways involved in SA (salicylic acid) and JA (jasmonic acid) through the activation of MBF1c, thereby increasing plant heat tolerance (Li et al., 2010b; Ohama et al., 2017).
Molecular Plant Breeding 2024, Vol.15, No.2, 42-51 http://genbreedpublisher.com/index.php/mpb 46 2.4 Inorganic element stress During low phosphorus stress, WRKY28 directly regulates phosphorus uptake and translocation from roots to crowns (Zhang, 2015). Similarly, WRKY42 regulates the expression of PHO1 and PHT1;1, which are involved in the plant's response to low phosphorus stress (Su et al., 2015). Additionally, AtWRKY6 (Xu et al., 2012) and AtWRKY33 (Ding et al., 2013) are associated with low boron stress and aluminum ion stress in Arabidopsis, respectively. It has been found that WRKY transcription factors play a negative role in regulating the expression of transcription factors related to elemental stress. This means that when plants are exposed to cadmium toxicity, their respiratory system is adversely affected. AtWRKY18, AtWRKY40, and AtWRKY60 are known to negatively regulate the plant response to cadmium toxicity (Liu, 2015). Similarly, WRKY6 and WRKY42 genes are capable of directly binding to and negatively regulating the expression of the PH01 promoter, which makes the plant more sensitive to low phosphorus levels (Zhang, 2015). 2.5 Oxidative stress Plants are exposed to various environmental stressors that cause the production and accumulation of reactive oxygen species (ROS) in their mitochondria. ROS is a highly oxidative molecule that can function as a signaling molecule and either positively or negatively regulate the plant's response to oxidative stress. In a study conducted on transgenic tobacco, it was found that the overexpression of FcWRKY40 increased the plant's resistance to oxidative stress. 2.6 Other abiotic stresses Apart from the five abiotic stresses mentioned earlier, there are several other abiotic stresses that plants have to endure such as light exposure, UV-B radiation, and sugar deprivation. For instance, WRKY proteins are responsible for regulating the reaction of most bamboo species to intense light (Zhao et al., 2016). Moreover, GmWRKY30 can respond to various inducers in Gentiana macrophylla, including arachidonic acid, salicylic acid, and silver ions, in order to cope with abiotic stress (He et al., 2018). 3 WRKY Transcription Factors and Biotic Stresses Plants face two main biological stresses - pathogenic bacteria infestation and feeding by phytophagous pests. When plants are exposed to these stresses, their metabolism and signal transduction processes change. Various signaling molecules, such as SA, JA, ET (ethylene), ABA, etc., get altered. This also affects the transcription levels of a large number of genes and proteins in the plant. All these lead to the plant's defense response to biotic stress. 3.1 WRKY transcription factors and pathogenic bacteria Several studies conducted on Arabidopsis and other crops have identified multiple WRKY genes that play a vital role in regulating plant resistance to pathogenic bacteria. These genes include WRKY3, WRKY33, WRKY40, WRKY46, WRKY18, WRKY53, WRKY70, and WRKY75. Therefore, these genes can be seen as a valuable source for genetically enhancing crop resistance against bacterial infections. Several studies have shown that overexpression of certain genes in Arabidopsis can enhance its resistance to various pathogens. For instance, Arabidopsis lines overexpressing AtWRKY28 and AtWRKY75 have been found to show enhanced resistance to Dictyostelium nucleatum (Chen et al., 2013). Similarly, overexpression of AtWRKY33 in Arabidopsis thaliana has been found to confer resistance against the necrotrophic fungus Staphylococcus griseus (Sham et al., 2017). Late blight is caused by Phytophthora infestans, and transcription factors such as StWRKY5 and StWRKY59 have important regulatory roles in potato resistance to late blight. StWRKY1 may mediate defense against infection of potato by Botrytis cinerea (Tian et al., 2023). The PsnWRKY70 gene in poplar may interact with specific members of the MAPK cascade to enhance resistance to leaf blight in poplar (Populussimonii × Populusnigra) (Zhao et al., 2017). It was shown that VlWRKY3 could enhance resistance to leaf blight pathogen live nutrients by increasing the expression of PR1 and NPR1 genes
Molecular Plant Breeding 2024, Vol.15, No.2, 42-51 http://genbreedpublisher.com/index.php/mpb 47 associated with disease resistance while down-regulating the expression of PDF1.2 and LOX3 (Guo et al., 2018). Sequential expression of CaWRKY40 in chickpea increased plant resistance to Fusarium oxysporumf. sp. ciceri Race1 (Foc1) (Chakraborty et al., 2019). Upon being infected with pathogenic bacteria, plants and organisms respond by using signaling molecules such as SA, JA, ET, and ABA as well as modifying the signal transduction process. TaWRKY70 may play a role in the resistance of high-temperature wheat nursery plants (HTSP) to striped stalk rust (Puccinia striiformis f. sp. tritici, Pst) infestation-induced stripe rust (Wang et al., 2017a). TaWRKY70 showed a significant increase during the initial symptomatic stage of Pst infection and was induced by high temperature, ET, SA, and low-temperature stress (4 °C) treatments. However, its expression was down-regulated in plants treated with methyl jasmonate (MeJA) and heat stress (40 °C) (Wang et al., 2017a). OsWRKY13 is involved in resistance to infection by rice blast fungus (Magnaporthe grisea) by activating the SA signaling pathway and repressing the JA signaling pathway, directly or indirectly regulating the expression of genes upstream and downstream of SA and JA (Schluttenhofer and Yuan, 2014). All these WRKY genes are involved in controlling the control of defense responses in plants through JA or SA-mediated signaling pathways. 3.2 WRKY transcription factors and phytophagous insects There are few reports available on the association of WRKY transcription factors with phytophagous insects in plants. Certain WRKY transcription factors have been shown to influence the feeding behavior of phytophagous insects (Ganbaatar et al., 2016). For instance, when H2O2 and ET levels were increased in OsWRKY45 antisense repressor lines, the feeding and egg-laying preferences of Nilaparvata lugens (Stal) were diminished, leading to an anthelmintic effect. This indicates that WRKY transcription factors play a role in the plant's defense response to feeding by phytophagous insects (Huangfu, 2015). Additionally, GhWRKY18 and GhWRKY70 not only reduce cotton resistance to phytophagous insects, but also affect the fundamental growth and development of cotton (Chang, 2018). Finally, some of the WRKY transcription factors related to phytophagous insects were summarized in this study (Table 1) (Wu et al., 2020). Table 1WRKYs involved in herbivoreinduced defense responses (Adopted from Wu et al., 2020) Gene Species Research methods Stress type AtWRKY8 Arabidopsis Mutation Improve resistance to aphids AtWRKY40 Arabidopsis Expression analysis Improve resistance toBrevicoryne brassicae OsWRKY45 Rice Expression analysis Improve resistance toNilaparvata lugens OsWRKY53, OsWRKY70 Rice Expression analysis Induced by SSB larva 4 Conclusions WRKY is a class of plant-specific transcription factors that play a crucial role in the life activities of plants. With the advancements in genomics, bioinformatics, and genetic engineering, research on WRKY has become increasingly extensive and thorough. It's now known that WRKY transcription factors not only impact plant growth and development but also have a sophisticated and effective regulatory mechanism for external stresses. The WRKY gene can regulate a variety of stresses through synergistic or antagonistic mechanisms. Moreover, the co-expression of WRKY produces a complex regulatory network to counteract stress via multiple expressions. The use of WRKY transcription factors to screen stress-resistant plant varieties and enhance plant stress tolerance holds enormous potential in terms of economic and scientific value.
Molecular Plant Breeding 2024, Vol.15, No.2, 42-51 http://genbreedpublisher.com/index.php/mpb 48 Authors’ Contributions QJ, GD, XA, LZ, and CC conceived the idea; XA organized the data; QJ and GD conducted the formal analyses; XA obtained the funding. QJ, GD, and TL conducted the research; QJ, GD, and XL provided the methodology; XA and QJ, GD obtained the resources; XA and QJ and GD wrote the original manuscript, and XA wrote, reviewed, and edited the manuscript. All authors read and approved the final manuscript. Acknowledgments This research was funded by Zhejiang Province "San Nong Jiu Fang" Science and Technology Cooperation Plan Project (2024SNJF005), China Agriculture Research System of MOF and MARA, China Agriculture Research System for Bast and Leaf Fiber Crops (CARS-16-S05), and National Natural Science Foundation of China (32202506). Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Cai R.H., 2016, Identification of stress-resistance related genes of group Ⅱd WRKY transcription factor family in maize and function analysis of ZmWRKY17, Dissertation for Ph.D., Anhui Agricultural University, Supervisor: Xiang Y., pp.77. Chakraborty J., Ghosh P., Sen S., Nandi A.K., and Das S., 2019, CAMPK9 increases the stability of CaWRKY40 transcription factor which triggers defense response in chickpea upon Fusarium oxysporumf. sp. ciceri Race1 infection, Plant Mol. Biol., 100(3): 411-431. https://doi.org/10.1007/s11103-019-00868-0 PMid:30953279 Chang Y.Q., 2018, Cloning and functional verification of genes related to cotton and Bemisia tabaci, Thesis for M.S., Huazhong Agricultural University, Supervisor: Jin S.X., pp.23-45. Chen L.G., Song Y., Li S.J., Zhang L.P., Zou C.S., and Yu D.Q., 2012, The role of WRKY transcription factors in plant abiotic stresses, Biochim Biophys Acta, 1819(2): 120-128. https://doi.org/10.1016/j.bbagrm.2011.09.002 PMid:21964328 Chen X.T., Liu J., Lin G.F., Wang A.R., Wang Z.H., and Lu G.D., 2013, Overexpression of AtWRKY28 and AtWRKY75 in Arabidopsis enhances resistance to oxalic acid and Sclerotinia sclerotiorum, Plant Cell Rep., 32(10): 1589-1599. https://doi.org/10.1007/s00299-013-1469-3 PMid:23749099 Chu X., Wang C., Chen X., Lu W., Li H., Wang X., Hao L., and Guo X., 2016, Correction: the cotton WRKY gene GhhWRKY41 positively regulates salt and drought stress tolerance in transgenic Nicotiana benthamiana, PLoS One, 11(6): e0157026. https://doi.org/10.1371/journal.pone.0157026 PMid:27253990 PMCid:PMC4890847 Dang F.F., Wang Y.N., Yu L., Eulgem T., Lai Y., Liu Z.Q., WangX., Qiu A.L., Zhang T.X., Lin J., Chen Y.S., Guan D.Y, Cai H.Y., Mou S.L., and He S.L., 2013, CaWRKY40, a WRKY protein of pepper, plays an important role in the regulation of tolerance to heat stress and resistance to Ralstonia solanacerum infection, Plant Cell Environ., 36(4): 757-774. https://doi.org/10.1111/pce.12011 PMid:22994555 Ding Z.J., Yan J.Y., Xu X.Y., Li G.X., and Zheng S.J., 2013, WRKY46 functions as a transcriptional repressor of ALMT1, regulating aluminum-induced malate secretion in Arabidopsis, Plant J., 76(5): 825-835. https://doi.org/10.1111/tpj.12337 PMid:24118304 Dong J., Chen C., and Chen Z., 2003, Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response, Plant Mol. Boil., 51(2): 21-37. https://doi.org/10.1023/A:1020780022549 PMid:12602888 Dong S.C, Ling J.Y., Zhao L.P., Song L.X., Wang Y.L., and Zhao T.M., 2023, Progress of transcription factors regulating drought resistance in tomato, Jiangsu Agricultural Science, (9): 9-16. Fan Q.Q., Song A.P., Jiang J.F., Zhang T., Sun H.N., Wang Y.J., Chen S.M., and Chen F.D., 2016, CmWRKY1 enhances the dehydration tolerance of chrysanthemum through the regulation of ABA-associated genes, PLoS One, 11(3): e150572. https://doi.org/10.1371/journal.pone.0150572 PMid:26938878 PMCid:PMC4777562
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Molecular Plant Breeding 2024, Vol.15, No.2, 52-62 http://genbreedpublisher.com/index.php/mpb 52 Review and Progress Open Access The Current Situation and Future of Using GWAS Strategies to Accelerate the Improvement of Crop Stress Resistance Traits Wenzhong Huang Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding email: Wenzhonghuang@126.com Molecular Plant Breeding, 2024, Vol.15, No.2 doi: 10.5376/mpb.2024.15.0007 Received: 26 Jan., 2024 Accepted: 01 Mar., 2024 Published: 15 Mar., 2024 Copyright © 2024 Huang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Huang W.Z., 2024, The current situation and future of using GWAS strategies to accelerate the improvement of crop stress resistance traits, Molecular Plant Breeding, 15(2): 52-62 (doi: 10.5376/mpb.2024.15.0007) Abstract This study explores the current state and future prospects of accelerating crop resistance trait improvement through Genome-Wide Association Studies (GWAS) strategies. With the rapid development of high-throughput sequencing technology and bioinformatics, GWAS has emerged as a powerful tool for linking DNA variations to important crop traits. This research particularly emphasizes the strategies for integrating multi-omics data, as well as the application of precision breeding and gene editing technologies based on GWAS findings, offering new directions and strategies for the improvement of crop resistance traits. Additionally, the emergence of methods such as Transcriptome-Wide Association Studies (TWAS) provides robust tools for identifying genes associated with complex traits, suggesting a more comprehensive understanding of genomic regulation and genetically regulated genes in the future. These advancements not only propel the scientific research of crop genetic improvement but also provide a solid scientific foundation for the sustainable development of crop production and food safety. Keywords Genome-wide association studies (GWAS); High-throughput sequencing technology; Bioinformatics; Crop resistance traits; Transcriptome-wide association studies (TWAS) 1 Introduction The genetic diversity of crops is the basis of breeding efforts, and by identifying beneficial alleles and useful variations in target traits, new varieties can be developed that can meet global agricultural challenges (Alison et al., 2022). In this context, technologies such as whole-genome resequencing, genome excerpts, partial-genome sequencing strategies, and high-density genotyping arrays have enabled large-scale assessment of the genetic diversity of a wide range of species, including major and “orphan” crops (Alison et al., 2022). However, unless these technologies are combined with adaptive and functional improvements in crops, their value will be limited. With the advancement of high-throughput phenotyping technology, the “phenotypic bottleneck” has been overcome, making powerful phenotypic data points that accurately characterize crop agronomic and physiological attributes available (Alison et al., 2022). A growing number of studies are leveraging these scientific advances and data science techniques to reveal the relationship between the genome and phenotype, unlocking the breeding potential of plant genetic resources. Genome -wide association studies (GWAS) and genomic selection (GS) are methods to explore marker - trait associations, The powerful data science method of MTAs can accelerate the rate of genetic gain of crops and shorten the breeding cycle in a cost-effective manner (Xu et al., 2021). For example, a GWAS analysis of 217 upland cotton varieties revealed genetic variation and candidate genes for traits related to salt tolerance (Rafael et al., 2021). These findings provide breeders with a rich toolbox for developing new varieties. In addition, new methods using new library preparation technologies and single-molecule long-read sequencing technologies (such as PacBio and Oxford Nanopore Technologies) have rapidly developed, making it possible to align sequences from multiple individuals, and due to the read length and be able to characterize missing sequences in the reference genome (Rafael et al., 2021). Furthermore, the creation of pan-genome references enables the characterization of structural variation in a non-reference-biased manner. Access to multiple reference-quality genome assemblies provides the opportunity for analysis of SVs (structural variation) in crop species, although doing so is problematic in some crop species. Its large and complex genome is costly.
Molecular Plant Breeding 2024, Vol.15, No.2, 52-62 http://genbreedpublisher.com/index.php/mpb 53 By exploring the application of GWAS in improving crop stress resistance traits, we can clearly see the potential of this strategy in understanding crop genetic diversity, accelerating crop breeding cycles, and developing new varieties that can adapt to changing environments. Future research needs to further explore and optimize GWAS methods to overcome challenges such as large data volumes and high computational costs, while improving the accuracy and applicability of GWAS results. This will help improve crop productivity and sustainability globally, especially in the face of climate change and increased food demand. 2 Basic Concepts of Crop Stress Resistance Traits 2.1 Define stress resistance traits of crops In contemporary agriculture, the study of crop stress resistance traits is particularly important. These traits enable crops to maintain growth and yield in the face of various biotic and abiotic stresses. With the intensification of global climate change and environmental pressure, it has become particularly urgent to study and improve crop stress resistance traits. The stress resistance traits of crops can be mainly divided into two categories: biotic stress resistance and abiotic stress resistance. Biological stress resistance includes the resistance to biological pressures such as pathogens and insect pests, while abiotic stress resistance covers the tolerance to environmental stresses such as drought, salinity, cold, and heat stress (Brandes et al., 2020). The basis of these traits is the complex physiological and molecular mechanisms formed by plants in order to adapt to changing environments during the long evolutionary process. In response to these stresses, crops exhibit stress resistance mechanisms that include, but are not limited to, regulating growth patterns, stimulating immune responses, enhancing antioxidant systems, adjusting osmotic pressure balance, and initiating processes to repair damaged tissues. In addition, the interaction between plants and their microbial symbionts also plays an important role in improving stress resistance. For example, certain plant bacteria can help crop growth under salt stress conditions. Systematically improving stress-resistant traits in crops requires not only understanding the fundamentals of these complex mechanisms, but also transferring knowledge gained from model plants to crops and applying this knowledge through modern plant breeding techniques. This requires closer collaboration between researchers, breeders and policymakers to achieve effective translation and application of knowledge. Regarding future research directions, considering the changing climate and environmental pressure, it is necessary to continue to explore the deep-seated mechanisms of crop stress resistance traits, and at the same time, we must also focus on interdisciplinary and multi-angle research methods to comprehensively improve the stress resistance of crops, ensuring the sustainable development of agricultural production (Thomas and Hückelhoven, 2018). 2.2 Classification of stress resistance traits As global climate changes and population grows, developing crop varieties with strong stress-resistant traits becomes increasingly important. Through the comprehensive application of traditional breeding technology and modern biotechnology, such as gene editing and transgenic technology, we are expected to improve the stress resistance traits of crops to ensure food security and sustainable agricultural development. However, this process requires interdisciplinary collaboration, including the combined efforts of genetics, biotechnology, ecology and agricultural sciences. Drought resistance refers to the ability of a crop to maintain growth, development and yield under drought conditions. Improving drought-resistant traits often involves enhancing a plant's water use efficiency, root depth, and leaf transpiration efficiency. For example, through gene editing technology, scientists have successfully improved the root growth of certain crop varieties so that they can more effectively absorb water from deep soil, thus increasing their drought resistance. Salt tolerance refers to the ability of plants to maintain their growth and development under salt stress conditions. Crops' tolerance to salt can be improved by adjusting salt absorption by roots, increasing salt distribution in the body, and enhancing the balance of salt inside and outside cells. Examples include genetically modified tomatoes
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