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Vodiasova E, Sinchenko A, Khvatkov P, Dolgov S. Genome-Wide Identification, Characterisation, and Evolution of the Transcription Factor WRKY in Grapevine ( Vitis vinifera): New View and Update. Int J Mol Sci 2024; 25:6241. [PMID: 38892428 PMCID: PMC11172563 DOI: 10.3390/ijms25116241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
WRKYs are a multigenic family of transcription factors that are plant-specific and involved in the regulation of plant development and various stress response processes. However, the evolution of WRKY genes is not fully understood. This family has also been incompletely studied in grapevine, and WRKY genes have been named with different numbers in different studies, leading to great confusion. In this work, 62 Vitis vinifera WRKY genes were identified based on six genomes of different cultivars. All WRKY genes were numbered according to their chromosomal location, and a complete revision of the numbering was performed. Amino acid variability between different cultivars was assessed for the first time and was greater than 5% for some WRKYs. According to the gene structure, all WRKYs could be divided into two groups: more exons/long length and fewer exons/short length. For the first time, some chimeric WRKY genes were found in grapevine, which may play a specific role in the regulation of different processes: VvWRKY17 (an N-terminal signal peptide region followed by a non-cytoplasmic domain) and VvWRKY61 (Frigida-like domain). Five phylogenetic clades A-E were revealed and correlated with the WRKY groups (I, II, III). The evolution of WRKY was studied, and we proposed a WRKY evolution model where there were two dynamic phases of complexity and simplification in the evolution of WRKY.
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Affiliation(s)
- Ekaterina Vodiasova
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia
| | - Anastasiya Sinchenko
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Pavel Khvatkov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Sergey Dolgov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 142290 Puschino, Russia
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Gao Z, Sun B, Fan Z, Su Y, Zheng C, Chen W, Yao Y, Ma C, Du Y. Vv-circSIZ1 mediated by pre-mRNA processing machinery contributes to salt tolerance. THE NEW PHYTOLOGIST 2023; 240:644-662. [PMID: 37530126 DOI: 10.1111/nph.19181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023]
Abstract
CircRNAs exist widely in plants, but the regulatory mechanisms for the biogenesis and function of plant circRNAs remain largely unknown. Using extensive mutagenesis of expression plasmids and genetic transformation methods, we analyzed the biogenesis and anti-salt functions of a new grape circRNA Vv-circSIZ1. We identified Vv-circSIZ1 that is mainly expressed in the cytoplasm of xylem. CircSIZ1 is species-specific, and genomic circSIZ1-forming region of seven tested species could be backspliced in Nicotiana benthamiana, but not in Arabidopsis. The retention length of Vv-circSIZ1 flanking introns was significantly positively correlated with its generation efficiency. The precise splicing of Vv-circSIZ1 does not depend on its mature exon sequence or internal intron sequences, but on the AG/GT splicing signal sites and branch site of the flanking introns. The spliceosome activity was inversely proportional to the expression level of Vv-circSIZ1. Furthermore, RNA-binding proteins can regulate the expression of Vv-circSIZ1. The overexpression of Vv-circSIZ1 improved salt tolerance of grape and N. benthamiana. Additionally, Vv-circSIZ1 could relieve the repressive effect of VvmiR3631 on its target VvVHAc1. Vv-circSIZ1 also promoted transcription of its parental gene. Overall, these results broaden our understanding of circRNAs in plants.
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Affiliation(s)
- Zhen Gao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Baozhen Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zongbao Fan
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Yifan Su
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Weiping Chen
- Institute of Horticulture, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 750002, China
| | - Yuxin Yao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuanpeng Du
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
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Wang P, Zhao F, Zheng T, Liu Z, Ji X, Zhang Z, Pervaiz T, Shangguan L, Fang J. Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1102695. [PMID: 36844076 PMCID: PMC9947647 DOI: 10.3389/fpls.2023.1102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Grape rootstocks play critical role in the development of the grape industry over the globe for their higher adaptability to various environments, and the evaluation of their genetic diversity among grape genotypes is necessary to the conservation and utility of genotypes. METHODS To analyze the genetic diversity of grape rootstocks for a better understanding multiple resistance traits, whole-genome re-sequencing of 77 common grape rootstock germplasms was conducted in the present study. RESULTS About 645 billion genome sequencing data were generated from the 77 grape rootstocks at an average depth of ~15.5×, based on which the phylogenic clusters were generated and the domestication of grapevine rootstocks was explored. The results indicated that the 77 rootstocks originated from five ancestral components. Through phylogenetic, principal components, and identity-by-descent (IBD) analyses, these 77 grape rootstocks were assembled into ten groups. It is noticed that the wild resources of V. amurensis and V. davidii, originating from China and being generally considered to have stronger resistance against biotic and abiotic stresses, were sub-divided from the other populations. Further analysis indicated that a high level of linkage disequilibrium was found among the 77 rootstock genotypes, and a total of 2,805,889 single nucleotide polymorphisms (SNPs) were excavated, GWAS analysis among the grape rootstocks located 631, 13, 9, 2, 810, and 44 SNP loci that were responsible to resistances to phylloxera, root-knot nematodes, salt, drought, cold and waterlogging traits. DISCUSSION This study generated a significant amount of genomic data from grape rootstocks, thus providing a theoretical basis for further research on the resistance mechanism of grape rootstocks and the breeding of resistant varieties. These findings also reveal that China originated V. amurensis and V. davidii could broaden the genetic background of grapevine rootstocks and be important germplasm used in breeding high stress-resistant grapevine rootstocks.
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Affiliation(s)
- Peipei Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Fanggui Zhao
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ting Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhongjie Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinglong Ji
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Zhichang Zhang
- Shandong Zhichang Agricultural Science and Technology Development Co. LTD, Rizhao, China
| | - Tariq Pervaiz
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States
| | - Lingfei Shangguan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jinggui Fang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Wang FP, Zhao PP, Zhang L, Zhai H, Abid M, Du YP. The VvWRKY37 Regulates Bud Break in Grape Vine Through ABA-Mediated Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:929892. [PMID: 35783936 PMCID: PMC9245421 DOI: 10.3389/fpls.2022.929892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/24/2022] [Indexed: 06/12/2023]
Abstract
Dormancy is a common survival strategy in plants to temporarily suspend visible growth under unsuitable conditions. The elaborate mechanism underlying bud break in perennial woody plants is gradually illustrated. Here, we identified a grape vine WRKY transcription factor, VvWRKY37, which was highly expressed in dormant buds. It was particularly induced by the application of exogenous abscisic acid, and depressed on exposure to gibberellin and low temperature (4°C) stress at the transcript level. The yeast one-hybrid assay confirmed that VvWRKY37 had a transcriptional activity. Ectopic over-expression of VvWRKY37 significantly delayed bud break of transgenic poplar plants. As an ABA-inducible gene, VvWRKY37 also depressed the expression of ABA catabolic gene CYP707As and enhanced the accumulation of endogenous ABA in transgenic poplar plants. The molecular pieces of evidence showed that VvWRKY37 preferentially recognized and bound W-box 5'-G/CATTGACT/C/G-3' cis-element in vitro. Additionally, VvABI5 and VvABF2 acted as the upstream transcriptional activators of VvWRKY37 via protein-DNA interactions. Taken together, our findings provided valuable insights into a new regulatory mechanism of WRKY TF by which it modulates bud break through ABA-mediated signaling pathways.
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Affiliation(s)
- Feng-Pan Wang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Pan-Pan Zhao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Lei Zhang
- College of Biological and Enology Engineering, Taishan University, Tai’an, China
| | - Heng Zhai
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Muhammad Abid
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Yuan-Peng Du
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
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Wang WN, Min Z, Wu JR, Liu BC, Xu XL, Fang YL, Ju YL. Physiological and transcriptomic analysis of Cabernet Sauvginon (Vitis vinifera L.) reveals the alleviating effect of exogenous strigolactones on the response of grapevine to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:400-409. [PMID: 34411779 DOI: 10.1016/j.plaphy.2021.08.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Drought stress can significantly affect the growth and yield of grapevine. The application of exogenous strigolactone can relieve the drought symptoms of grapevine; however, little is known about the transcription levels in grapevine under drought stress following exogenous strigolactone application. The mitigative effect of exogenous strigolactone on grapevine leaves under drought stress was studied by transcriptome analysis based on RNA sequencing. On the 10th day of drought stress, the strigolactone treatment group had a higher relative water content and lower electrical conductivity, which significantly alleviated the drought damage. Compared to the drought (D) group, a total of 5955 differentially expressed genes (DEGs) (2966 up-regulated genes and 2989 down-regulated genes) were detected in the exogenous strigolactone (DG) groups. Based on Gene Ontology analysis, the DEGs in the D and DG treatments were enriched in the processes of photosynthesis and organic acid catabolism. Pathway analysis showed that the DEGs in the D and DG treatments were enriched in carbon metabolism, ribosome, starch and sucrose metabolism, flavonoid biosynthesis, and circadian rhythm. Additionally, in the DG group, the antioxidant enzyme genes of CAT1, GSHPX1, GSHPX2, POD42, APX6, and SODCP were up-regulated, two NAC, three WRKY, and four MYB transcription factor genes were down-regulated, and the key gene of strigolactone synthesis D14 was up-regulated, compared with that in the D group. The results provide a new perspective for studying the adaptation of plants to drought stress.
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Affiliation(s)
- Wan-Ni Wang
- College of Enology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Zhuo Min
- Department of Brewing Engineering, Moutai University, Renhuai, Guizhou, 564507, China
| | - Jin-Ren Wu
- College of Enology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Bo-Chen Liu
- College of Enology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Xue-Lei Xu
- College of Enology, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yu-Lin Fang
- College of Enology, Northwest A & F University, Yangling, 712100, Shaanxi, China; Heyang Viti-viniculture Station, Northwest A & F University, Yangling, 712100, Shaanxi, China.
| | - Yan-Lun Ju
- College of Enology, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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Comparative Transcriptome Analysis of Two Root-Feeding Grape Phylloxera ( D. vitifoliae) Lineages Feeding on a Rootstock and V. vinifera. INSECTS 2020; 11:insects11100691. [PMID: 33053741 PMCID: PMC7601026 DOI: 10.3390/insects11100691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
Simple Summary Grape phylloxera is an American native insect pest that caused heavy damages to the vineyards worldwide since its spreading to wine regions since the 1850s. This insect, able to feed on leaves and roots, induces plant galls and manipulates the grapevine physiology leading to plant damage and may cause plant death. The most successful treatment was the use of mostly partially resistant rootstocks. The degree of resistance is affected by environment, grapevine management and the insect biotype. In this study, we analyse the interaction of insect biotypes feeding on particular host plants. Therefore we evaluated the gene expression of Phylloxera feeding on a susceptible host versus feeding on a rootstock in two different developmental stages. We discovered (mainly in advanced insect developmental stages) genes expressed in higher proportion in one insect compared to the other. These genes related to chemosensory; in plant physiology manipulation and root deformation and insect digestive traits may play a role in the plant-insect interaction determining plant resistance in response to the pest attack. Abstract Grape phylloxera is one of the most dangerous insect pests for worldwide viticulture. The leaf- and root-galling phylloxerid has been managed by grafting European grapevines onto American rootstock hybrids. Recent reports pinpoint the appearance of host-adapted biotypes, but information about the biomolecular characteristics underlying grape phylloxera biotypisation and its role in host performance is scarce. Using RNA-sequencing, we sequenced the transcriptome of two larval stages: L1 (probing) and L2-3 (feeding) larvae of two root-feeding grape phylloxera lineages feeding on the rootstock Teleki 5C (biotype C) and V. vinifera Riesling (biotype A). In total, 7501 differentially expressed genes (DEGs) were commonly modulated by the two biotypes. For the probing larvae, we found an increased number of DEGs functionally associated with insect chemoreception traits, such as odorant-binding proteins, chemosensory proteins, ionotropic, odorant, and gustatory receptors. The transcriptomic profile of feeding larvae was enriched with DEGs associated with the primary metabolism. Larvae feeding on the tolerant rootstock Teleki 5C exhibited higher numbers of plant defense suppression-associated DEGs than larvae feeding on the susceptible host. Based on the identified DEGs, we discuss their potential role for the compatible grape phylloxera–Vitis interaction belowground. This study was the first to compare the transcriptomes of two grape phylloxera lineages feeding on a tolerant and susceptible host, respectively, and to identify DEGs involved in the molecular interaction with these hosts. Our data provide a source for future studies on host adaptation mechanisms of grape phylloxera and help to elucidate grape phylloxera resistance further.
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Deng B, Wang W, Ruan C, Deng L, Yao S, Zeng K. Involvement of CsWRKY70 in salicylic acid-induced citrus fruit resistance against Penicillium digitatum. HORTICULTURE RESEARCH 2020; 7:157. [PMID: 33082964 PMCID: PMC7527965 DOI: 10.1038/s41438-020-00377-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 06/23/2020] [Accepted: 07/07/2020] [Indexed: 05/11/2023]
Abstract
Penicillium digitatum causes serious losses in postharvest citrus fruit. Exogenous salicylic acid (SA) can induce fruit resistance against various pathogens, but the mechanism remains unclear. Herein, a transcriptome-based approach was used to investigate the underlying mechanism of SA-induced citrus fruit resistance against P. digitatum. We found that CsWRKY70 and genes related to methyl salicylate (MeSA) biosynthesis (salicylate carboxymethyltransferase, SAMT) were induced by exogenous SA. Moreover, significant MeSA accumulation was detected in the SA-treated citrus fruit. The potential involvement of CsWRKY70 in regulating CsSAMT expression in citrus fruit was studied. Subcellular localization, dual luciferase, and electrophoretic mobility shift assays and an analysis of transient expression in fruit peel revealed that the nucleus-localized transcriptional activator CsWRKY70 can activate the CsSAMT promoter by recognizing the W-box element. Taken together, the findings from this study offer new insights into the transcriptional regulatory mechanism of exogenous SA-induced disease resistance in Citrus sinensis fruit.
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Affiliation(s)
- Bing Deng
- College of Food Science, Southwest University, 400715 Chongqing, China
| | - Wenjun Wang
- College of Food Science, Southwest University, 400715 Chongqing, China
| | - Changqing Ruan
- College of Food Science, Southwest University, 400715 Chongqing, China
- Research Center of Food Storage & Logistics, Southwest University, 400715 Chongqing, China
| | - Lili Deng
- College of Food Science, Southwest University, 400715 Chongqing, China
- Research Center of Food Storage & Logistics, Southwest University, 400715 Chongqing, China
| | - Shixiang Yao
- College of Food Science, Southwest University, 400715 Chongqing, China
- Research Center of Food Storage & Logistics, Southwest University, 400715 Chongqing, China
| | - Kaifang Zeng
- College of Food Science, Southwest University, 400715 Chongqing, China
- Research Center of Food Storage & Logistics, Southwest University, 400715 Chongqing, China
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