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Scariolo F, Gabelli G, Magon G, Palumbo F, Pirrello C, Farinati S, Curioni A, Devillars A, Lucchin M, Barcaccia G, Vannozzi A. The Transcriptional Landscape of Berry Skin in Red and White PIWI ("Pilzwiderstandsfähig") Grapevines Possessing QTLs for Partial Resistance to Downy and Powdery Mildews. PLANTS (BASEL, SWITZERLAND) 2024; 13:2574. [PMID: 39339549 PMCID: PMC11434962 DOI: 10.3390/plants13182574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 09/06/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024]
Abstract
PIWI, from the German word Pilzwiderstandsfähig, meaning "fungus-resistant", refers to grapevine cultivars bred for resistance to fungal pathogens such as Erysiphe necator (the causal agent of powdery mildew) and Plasmopara viticola (the causal agent of downy mildew), two major diseases in viticulture. These varieties are typically developed through traditional breeding, often crossbreeding European Vitis vinifera with American or Asian species that carry natural disease resistance. This study investigates the transcriptional profiles of exocarp tissues in mature berries from four PIWI grapevine varieties compared to their elite parental counterparts using RNA-seq analysis. We performed RNA-seq on four PIWI varieties (two red and two white) and their noble parents to identify differential gene expression patterns. Comprehensive analyses, including Differential Gene Expression (DEGs), Gene Set Enrichment Analysis (GSEA), Weighted Gene Co-expression Network Analysis (WGCNA), and tau analysis, revealed distinct gene clusters and individual genes characterizing the transcriptional landscape of PIWI varieties. Differentially expressed genes indicated significant changes in pathways related to organic acid metabolism and membrane transport, potentially contributing to enhanced resilience. WGCNA and k-means clustering highlighted co-expression modules linked to PIWI genotypes and their unique tolerance profiles. Tau analysis identified genes uniquely expressed in specific genotypes, with several already known for their defense roles. These findings offer insights into the molecular mechanisms underlying grapevine resistance and suggest promising avenues for breeding strategies to enhance disease resistance and overall grape quality in viticulture.
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Affiliation(s)
- Francesco Scariolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
| | - Giovanni Gabelli
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
| | - Carlotta Pirrello
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy;
| | - Silvia Farinati
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
| | - Andrea Curioni
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
| | - Aurélien Devillars
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, 35020 Legnaro, Italy; (F.S.); (G.G.); (G.M.); (F.P.); (S.F.); (A.C.); (A.D.); (M.L.); (G.B.)
- Interdepartmental Centre for Research in Viticulture and Enology, University of Padua, Via XXVIII Aprile, 31015 Conegliano, Italy
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Zhang Z, Zhang H, Liu J, Chen K, Wang Y, Zhang G, Li L, Yue H, Weng Y, Li Y, Chen P. The mutation of CsSUN, an IQD family protein, is responsible for the short and fat fruit (sff) in cucumber (Cucumis sativus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112177. [PMID: 38964612 DOI: 10.1016/j.plantsci.2024.112177] [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: 05/11/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The fruit shape of cucumber is an important agronomic trait, and mining regulatory genes, especially dominant ones, is vital for cucumber breeding. In this study, we identified a short and fat fruit mutant, named sff, from an EMS mutagenized population. Compared to the CCMC (WT), sff (MT) exhibited reduced fruit length and increased dimeter. Segregation analysis revealed that the sff phenotype is controlled by a semi-dominant single gene with dosage effects. Through map-based cloning, the SFF locus was narrowed down to a 52.6 kb interval with two SNPs (G651A and C1072T) in the second and third exons of CsaV3_1G039870, which encodes an IQD family protein, CsSUN. The G651A within the IQ domain of CsSUN was identified as the unique SNP among 114 cucumber accessions, and it was the primary cause of the functional alteration in CsSUN. By generating CsSUN knockout lines in cucumber, we confirmed that CsSUN was responsible for sff mutant phenotype. The CsSUN is localized to the plasma membrane. CsSUN exhibited the highest expression in the fruit with lower expression in sff compared to WT. Histological observations suggest that the sff mutant phenotype is due to increased transverse cell division and inhibited longitudinal cell division. Transcriptome analysis revealed that CsSUN significantly affected the expression of genes related to cell division, expansion, and auxin signal transduction. This study unveils CsSUN's crucial role in shaping cucumber fruit and offers novel insights for cucumber breeding.
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Affiliation(s)
- Zhengao Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haiqiang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyan Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kang Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yixin Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lixia Li
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Hongzhong Yue
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Li H, Yang Y, Zhang W, Zheng H, Xu X, Li H, Sun C, Hu H, Zhao W, Ma R, Tao J. Promoter replication of grape MYB transcription factor is associated with a new red flesh phenotype. PLANT CELL REPORTS 2024; 43:136. [PMID: 38709311 DOI: 10.1007/s00299-024-03225-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/30/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE In our study, we discovered a fragment duplication autoregulation mechanism in 'ZS-HY', which may be the reason for the phenotype of red foliage and red flesh in grapes. In grapes, MYBA1 and MYBA2 are the main genetic factors responsible for skin coloration which are located at the color loci on chromosome 2, but the exact genes responsible for color have not been identified in the flesh. We used a new teinturier grape germplasm 'ZhongShan-HongYu' (ZS-HY) which accumulate anthocyanin both in skin and flesh as experimental materials. All tissues of 'ZS-HY' contained cyanidin 3-O-(6″-p-coumaroyl glucoside), and pelargonidins were detected in skin, flesh, and tendril. Through gene expression analysis at different stage of flesh, significant differences in the expression levels of VvMYBA1 were found. Gene amplification analysis showed that the VvMYBA1 promoter is composed of two alleles, VvMYBA1a and 'VvMYBA1c-like'. An insertion of a 408 bp repetitive fragment was detected in the allele 'VvMYBA1c-like'. In this process, we found the 408 bp repetitive fragment was co-segregated with red flesh and foliage phenotype. Our results revealed that the 408 bp fragment replication insertion in promoter of 'VvMYBA1c-like' was the target of its protein, and the number of repeat fragments was related to the increase of trans-activation of VvMYBA1 protein. The activation of promoter by VvMYBA1 was enhanced by the addition of VvMYC1. In addition, VvMYBA1 interacted with VvMYC1 to promote the expression of VvGT1 and VvGST4 genes in 'ZS-HY'. The discovery of this mutation event provides new insights into the regulation of VvMYBA1 on anthocyanin accumulation in red-fleshed grape, which is of great significance for molecular breeding of red-fleshed table grapes.
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Affiliation(s)
- Hui Li
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, 261061, China
| | - Yaxin Yang
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen Zhang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830001, Xinjiang, China
| | - Huan Zheng
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianbin Xu
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haoran Li
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenxu Sun
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haipeng Hu
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanli Zhao
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruiyang Ma
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianmin Tao
- College of Horticulture, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China.
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830001, Xinjiang, China.
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Baranov D, Dolgov S, Timerbaev V. New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches. PLANTS (BASEL, SWITZERLAND) 2024; 13:359. [PMID: 38337892 PMCID: PMC10856997 DOI: 10.3390/plants13030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Sergey Dolgov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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Zheng H, Liang Y, Hong B, Xu Y, Ren M, Wang Y, Huang L, Yang L, Tao J. Genome-Scale Analysis of the Grapevine KCS Genes Reveals Its Potential Role in Male Sterility. Int J Mol Sci 2023; 24:ijms24076510. [PMID: 37047480 PMCID: PMC10095565 DOI: 10.3390/ijms24076510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Very long-chain fatty acid (VLCFA) synthesis in plants, is primarily rate-limited by the enzyme 3-ketoacyl CoA synthase (KCS), which also controls the rate and carbon chain length of VLCFA synthesis. Disruption of VLCFA during pollen development, may affect the pollen wall formation and ultimately lead to male sterility. Our study identified 24 grapevine KCS (VvKCS) genes and provided new names based on their relative chromosome distribution. Based on sequence alignment and phylogenetic investigation, these genes were grouped into seven subgroups, members of the same subgroup having similar motif structures. Synteny analysis of VvKCS genes, showed that the segmental duplication events played an important role in expanding this gene family. Expression profiles obtained from the transcriptome data showed different expression patterns of VvKCS genes in different tissues. Comparison of transcriptome and RT-qPCR data of the male sterile grape ‘Y−14’ and its fertile parent ‘Shine Muscat’, revealed that 10 VvKCS genes were significantly differentially expressed at the meiosis stage, which is a critical period of pollen wall formation. Further, joint analysis by weighted gene co-expression network analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed that five of these VvKCS (VvKCS6/15/19/20/24) genes were involved in the fatty acid elongation pathway, which may ultimately affect the structural integrity of the pollen wall in ‘Y−14’. This systematic analysis provided a foundation for further functional characterization of VvKCS genes, with the aim of grapevine precision breeding improvement.
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