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Cantu D, Massonnet M, Cochetel N. The wild side of grape genomics. Trends Genet 2024; 40:601-612. [PMID: 38777691 DOI: 10.1016/j.tig.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.
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Affiliation(s)
- Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
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2
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Wang Y, Ding K, Li H, Kuang Y, Liang Z. Biography of Vitis genomics: recent advances and prospective. HORTICULTURE RESEARCH 2024; 11:uhae128. [PMID: 38966864 PMCID: PMC11220177 DOI: 10.1093/hr/uhae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/25/2024] [Indexed: 07/06/2024]
Abstract
The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers have explored the domestication and origins of the grape and clarified the gene flow that occurred during its dispersed history. Moreover, genome-wide association studies and other methods have been used to identify more than 900 genes related to resistance, quality, and developmental phases of grape. These findings have benefited grape studies and provide some basis for smart genomic selection breeding. Moreover, the grape genome has played a great role in grape studies and the grape industry, and the importance of genomics will increase sharply in the future.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Kangyi Ding
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayang Li
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangfu Kuang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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3
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Wang X, Tu M, Wang Y, Zhang Y, Yin W, Fang J, Gao M, Li Z, Zhan W, Fang Y, Song J, Xi Z, Wang X. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. HORTICULTURE RESEARCH 2024; 11:uhad260. [PMID: 38288254 PMCID: PMC10822838 DOI: 10.1093/hr/uhad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/26/2023] [Indexed: 01/31/2024]
Abstract
Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.
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Affiliation(s)
- Xianhang Wang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxing Tu
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yali Zhang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghao Fang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Zhan
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an 710116, China
| | - Yulin Fang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyang Song
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhumei Xi
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Zou C, Sapkota S, Figueroa-Balderas R, Glaubitz J, Cantu D, Kingham BF, Sun Q, Cadle-Davidson L. A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus. PLANT PHYSIOLOGY 2023; 193:2321-2336. [PMID: 37706526 DOI: 10.1093/plphys/kiad494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/10/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023]
Abstract
Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here, we employed a multitiered haplotypic marker system to increase fine mapping accuracy by constructing a chromosome-level, haplotype-resolved parental genome, accurate detection of recombination sites, and allele-specific characterization of the transcriptome. In the first tier of this system, we applied the preexisting panel of 2,000 rhAmpSeq core genome markers that is transferable across the entire Vitis genus and provides a genomic resolution of 200 kb to 1 Mb. The second tier consisted of high-density haplotypic markers generated from Illumina skim sequencing data for samples enriched for relevant recombinations, increasing the potential resolution to hundreds of base pairs. We used this approach to dissect a novel Resistance to Plasmopara viticola-33 (RPV33) locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.46 Mb. In the third tier, we used allele-specific RNA-seq analysis to identify a cluster of 3 putative disease resistance RPP13-like protein 2 genes located tandemly in a nonsyntenic insertion as candidates for the disease resistance trait. In addition, combining the rhAmpSeq core genome haplotype markers and skim sequencing-derived high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana 'PI 588149' assembly, initially built solely from Pacific Biosciences (PacBio) high-fidelity (HiFi) reads, leading to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs and will likely be widely adopted in highly heterozygous species.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Surya Sapkota
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Jeff Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Brewster F Kingham
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
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Miao BB, Dong W, Gu YX, Han ZF, Luo X, Ke CH, You WW. OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data. HORTICULTURE RESEARCH 2023; 10:uhad195. [PMID: 38023482 PMCID: PMC10673651 DOI: 10.1093/hr/uhad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023]
Abstract
With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, Mutation Annotation Format, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source: https://github.com/OmicsSuite/, Website: https://omicssuite.github.io, v1.3.9).
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Affiliation(s)
- Ben-Ben Miao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wei Dong
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou 510055, Guangdong, China
| | - Yi-Xin Gu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China
| | - Zhao-Fang Han
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Cai-Huan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wei-Wei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
- Fujian Institute for Sustainable Oceans, Xiamen University, Xiamen 361102, Fujian, China
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Huff M, Hulse-Kemp AM, Scheffler BE, Youngblood RC, Simpson SA, Babiker E, Staton M. Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. BMC Genomics 2023; 24:409. [PMID: 37474911 PMCID: PMC10357881 DOI: 10.1186/s12864-023-09514-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Muscadine grape (Vitis rotundifolia) is resistant to many of the pathogens that negatively impact the production of common grape (V. vinifera), including the bacterial pathogen Xylella fastidiosa subsp. fastidiosa (Xfsf), which causes Pierce's Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf, but the mechanism is unknown. RESULTS We assembled and annotated a new, long-read genome assembly for 'Carlos', a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the 'Carlos' and common grape genomes indicates an expansion of resistance (R) genes in 'Carlos.' We further identified genes involved in Xfsf response by transcriptome sequencing 'Carlos' plants inoculated with Xfsf. We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf, we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome. CONCLUSIONS Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf, within and between muscadine and common grape.
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Affiliation(s)
- Matthew Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, 27606, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27606, USA
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Ebrahiem Babiker
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, 39470, USA.
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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Seedlessness Trait and Genome Editing—A Review. Int J Mol Sci 2023; 24:ijms24065660. [PMID: 36982733 PMCID: PMC10057249 DOI: 10.3390/ijms24065660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Parthenocarpy and stenospermocarpy are the two mechanisms underlying the seedless fruit set program. Seedless fruit occurs naturally and can be produced using hormone application, crossbreeding, or ploidy breeding. However, the two types of breeding are time-consuming and sometimes ineffective due to interspecies hybridization barriers or the absence of appropriate parental genotypes to use in the breeding process. The genetic engineering approach provides a better prospect, which can be explored based on an understanding of the genetic causes underlying the seedlessness trait. For instance, CRISPR/Cas is a comprehensive and precise technology. The prerequisite for using the strategy to induce seedlessness is identifying the crucial master gene or transcription factor liable for seed formation/development. In this review, we primarily explored the seedlessness mechanisms and identified the potential candidate genes underlying seed development. We also discussed the CRISPR/Cas-mediated genome editing approaches and their improvements.
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Cheng G, Wu D, Guo R, Li H, Wei R, Zhang J, Wei Z, Meng X, Yu H, Xie L, Lin L, Yao N, Zhou S. Chromosome-scale genomics, metabolomics, and transcriptomics provide insight into the synthesis and regulation of phenols in Vitis adenoclada grapes. FRONTIERS IN PLANT SCIENCE 2023; 14:1124046. [PMID: 36760645 PMCID: PMC9907855 DOI: 10.3389/fpls.2023.1124046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Vitis adenoclada is a wild grape unique to China. It exhibits well resistance to heat, humidity, fungal disease, drought, and soil infertility. Here, we report the high-quality, chromosome-level genome assembly of GH6 (V. adenoclada). The 498.27 Mb genome contained 221.78 Mb of transposable elements, 28,660 protein-coding genes, and 481.44 Mb of sequences associated with 19 chromosomes. GH6 shares a common ancestor with PN40024 (Vitis vinifera) from approximately 4.26-9.01 million years ago, whose divergence occurred later than Vitis rotundifolia and Vitis riparia. Widely-targeted metabolome and transcriptome analysis revealed that the profiles and metabolism of phenolic compounds in V. adenoclada varieties significantly were differed from other grape varieties. Specifically, V. adenoclada varieties were rich in phenolic acids and flavonols, whereas the flavan-3-ol and anthocyanin content was lower compared with other varieties that have V. vinifera consanguinity in this study. In addition, ferulic acid and stilbenes content were associated with higher expressions of COMT and STSs in V. adenoclada varieties. Furthermore, MYB2, MYB73-1, and MYB73-2 were presumably responsible for the high expression level of COMT in V. adenoclada berries. MYB12 (MYBF1) was positively correlated with PAL, CHS, FLS and UFGT.Meanwhile, MYB4 and MYBC2-L1 may inhibit the synthesis of flavan-3-ols and anthocyanins in two V. adenoclada varieties (YN2 and GH6). The publication of the V. adenoclada grape genome provides a molecular foundation for further revealing its flavor and quality characteristics, is also important for identifying favorable genes of the East Asian species for future breeding.
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Affiliation(s)
- Guo Cheng
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Daidong Wu
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongrong Guo
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hongyan Li
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongfu Wei
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jin Zhang
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zhiyong Wei
- Bureau of Agriculture and Rural Affairs of Luocheng Mulao Autonomous County, Hechi, China
| | - Xian Meng
- Bureau of Agriculture and Rural Affairs of Luocheng Mulao Autonomous County, Hechi, China
| | - Huan Yu
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Linjun Xie
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ling Lin
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ning Yao
- Guangxi Luocheng Maoputao Experimental Station, Hechi, China
| | - Sihong Zhou
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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9
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Lytkin K, Nosulchak V, Agakhanov M, Matveikina E, Lushchay E, Karzhaev D, Raines E, Vasylyk I, Rybachenko N, Grigoreva E, Volkov V, Volynkin V, Gentzbittel L, Potokina E. Development of a High-Density Genetic Map for Muscadine Grape Using a Mapping Population from Selfing of the Perfect-Flowered Vine 'Dixie'. PLANTS (BASEL, SWITZERLAND) 2022; 11:3231. [PMID: 36501271 PMCID: PMC9738875 DOI: 10.3390/plants11233231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Intraspecific diversity of the immune grape Muscadinia rotundifolia Michaux. can serve as a rich source of valuable resistance loci to the most widespread pathogens and pests of grapevine. While only one Run1/Rpg1 resistance locus has been introgressed from M. rotundifolia to the Vitis vinifera gene pool, a number of other genes conferring resistance to powdery mildew and downy mildew have been identified in various Muscadinia cultivars. A larger introduction of Muscadinia varieties to the European continent would greatly facilitate experiments of interspecific crosses as well as stimulate biotechnological efforts to overcome the main barrier to F1 fertility caused by the differences in chromosome number. For the successful introduction of Muscadinia into the new European environment, it is necessary to overcome the difficulties associated with the physiological characteristics of the species, such as insufficient cold tolerance and very late fruit ripening. To facilitate the further discovery of valuable loci in Muscadinia and their transfer to grapevine breeding programs, we constructed a high-density linkage map using an S1 mapping population obtained from the self-pollination of M. rotundifolia cv. Dixie maintained on the southern coast of Crimea. Using ddRADseq, 3730 SNPs were ordered across 20 linkage groups spanning 2753.6 cM of the total map length. No segregation in resistance to diseases and pests was observed among the 'Dixie' S1 population, suggesting the presence of homozygous non-segregating resistant loci in the genetic background of 'Dixie'. Markers with high segregation distortion showed a bias towards chromosomal intervals on linkage groups 10 and 20, where loci affecting the survival of 'Dixie' S1 progeny may be localized. QTLs with significant additive and dominance effects were discovered on LG14 and LG18, affecting the morphological traits associated with the vigor of growth and adaptability of young Muscadinia vines in the conditions of Crimea.
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Affiliation(s)
- Kirill Lytkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vasily Nosulchak
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Magamedgusein Agakhanov
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Elena Matveikina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Ekaterina Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Dmitry Karzhaev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Evgenii Raines
- Information Technologies and Programming Faculty, ITMO University, St. Petersburg 197101, Russia
| | - Irina Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Nataliya Rybachenko
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Elizaveta Grigoreva
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Vladimir Volkov
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vladimir Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | | | - Elena Potokina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
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10
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Ismail A, Gajjar P, Park M, Mahboob A, Tsolova V, Subramanian J, Darwish AG, El-Sharkawy I. A recessive mutation in muscadine grapes causes berry color-loss without influencing anthocyanin pathway. Commun Biol 2022; 5:1012. [PMID: 36153380 PMCID: PMC9509324 DOI: 10.1038/s42003-022-04001-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Anthocyanins, a major class of flavonoids, are important pigments of grape berries. Despite the recent discovery of the genetic cause underlying the loss of color, the metabolomic and molecular responses are unknown. Anthocyanin quantification among diverse berry color muscadines suggests that all genotypes could produce adequate anthocyanin quantities, irrespective of berry color. Transcriptome profiling of contrasting color muscadine genotypes proposes a potential deficiency that occurs within the anthocyanin transport and/or degradation mechanisms and might cause unpigmented berries. Genome-wide association studies highlighted a region on chromosome-4, comprising several genes encoding glutathione S-transferases involved in anthocyanin transport. Sequence comparison among genotypes reveals the presence of two GST4b alleles that differ by substituting the conserved amino acid residue Pro171-to-Leu. Molecular dynamics simulations demonstrate that GST4b2–Leu171 encodes an inactive protein due to modifications within the H-binding site. Population genotyping suggests the recessive inheritance of the unpigmented trait with a GST4b2/2 homozygous. A model defining colorless muscadines’ response to the mutation stimulus, avoiding the impact of trapped anthocyanins within the cytoplasm is established. Transcriptome profiling and mutational analysis suggest a potential deficiency in anthocyanin transport by glutathione S-transferases and/or degradation mechanisms that might cause unpigmented berries.
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11
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Park M, Darwish AG, Elhag RI, Tsolova V, Soliman KFA, El-Sharkawy I. A multi-locus genome-wide association study reveals the genetics underlying muscadine antioxidant in berry skin. FRONTIERS IN PLANT SCIENCE 2022; 13:969301. [PMID: 35991419 PMCID: PMC9386419 DOI: 10.3389/fpls.2022.969301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Muscadine berries display enhanced nutraceutical value due to the accumulation of distinctive phytochemical constituents with great potential antioxidant activity. Such nutritional and health merits are not only restricted to muscadine, but muscadine berries accumulate higher amounts of bioactive polyphenolics compared with other grape species. For the genetic study of the antioxidant trait in muscadine, a multi-locus genome-wide association study (GWAS) with 350 muscadine genotypes and 1,283 RNase H2 enzyme-dependent amplicon sequencing (rhAmpSeq) markers was performed. Phenotyping was conducted with several antioxidant-related traits, including total phenolic content (TPC), total flavonoid content (TFC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, and FRAP antioxidant assay in muscadine berry skin. The correlation coefficient analysis revealed that the TPC, and DPPH/FRAP activities were significantly correlated. Through the GWAS analysis, 12 QTNs were identified from the four traits, of which six were pleiotropic QTNs. Two pleiotropic QTNs, chr2_14464718 and chr4_16491374, were commonly identified from the TPC and DPPH/FRAP activities. Co-located genes with the two pleiotropic QTNs were isolated, and two candidate genes were identified with transcriptome analysis. UDP-glycosyltransferase and 4-hydroxy-4-methyl-2-oxoglutarate aldolase were the candidate genes that are positively and negatively correlated to the quantitative property of traits, respectively. These results are the first genetic evidence of the quantitative property of antioxidants in muscadine and provide genetic resources for breeding antioxidant-rich cultivars for both Muscadinia and Euvitis species.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Ahmed G. Darwish
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
- Department of Biochemistry, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Rashid I. Elhag
- College of Science and Technology, Florida A&M University, Tallahassee, FL, United States
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Karam F. A. Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
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12
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Varanasi A, Worthington M, Nelson L, Brown A, Chizk TM, Threlfall R, Howard L, Conner P, Figueroa-Balderas R, Massonnet M, Cantu D, Clark JR. Glutathione S-transferase: a candidate gene for berry color in muscadine grapes (Vitis rotundifolia). G3 (BETHESDA, MD.) 2022; 12:6550507. [PMID: 35302606 PMCID: PMC9073687 DOI: 10.1093/g3journal/jkac060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/09/2022] [Indexed: 01/27/2023]
Abstract
Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n = 40) belong to the Muscadinia subgenus of Vitis, while other cultivated grape species belong to the subgenus Euvitis (2n = 38). The muscadine berry color locus was mapped to a 0.8 Mbp region syntenic with chromosome 4 of Vitis vinifera. In this study, we identified glutathione S-transferase4 as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and Kompetitive allele-specific PCR genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline to leucine mutation within the muscadine glutathione S-transferase4 (VrGST4) that differentiated black (CC and CT) from bronze (TT) muscadines in 126 breeding selections, 76 cultivars, and 359 progeny from 3 mapping populations. Anthocyanin profiling on a subset of the progeny indicated a dominant VrGST4 action. VrGST4 was expressed in skins of both black and bronze muscadines at similar levels. While nonsynonymous polymorphisms between black and bronze muscadines were discovered in VrGSTF12, another Type I GST-coding gene in the muscadine color locus, this gene was ruled out as a possible candidate for berry color because RNA sequencing indicated it is not expressed in berry skins at véraison from black or bronze genotypes. These results suggest that the bronze phenotype in muscadines is regulated by a mechanism distinct from the MybA gene cluster responsible for berry color variation in Vitis vinifera.
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Affiliation(s)
- Aruna Varanasi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Lacy Nelson
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Autumn Brown
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Thomas Mason Chizk
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Renee Threlfall
- Department of Food Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Luke Howard
- Department of Food Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Patrick Conner
- Department of Horticulture, University of Georgia, Tifton, GA 31793, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - Mélanie Massonnet
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture & Enology, University of California, Davis, Davis, CA 95616, USA
| | - John R Clark
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
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13
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Buck K, Worthington M. Genetic Diversity of Wild and Cultivated Muscadine Grapes ( Vitis rotundifolia Michx.). FRONTIERS IN PLANT SCIENCE 2022; 13:852130. [PMID: 35419015 PMCID: PMC8996184 DOI: 10.3389/fpls.2022.852130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The muscadine (Vitis rotundifolia syn. Muscadinia rotundifolia) is an American grape species native to the southeastern United States that has been cultivated for centuries. Muscadines are one of three grape species in subgenus Muscadinia with a chromosome number of 2n = 40 (V. rotundifolia, Vitis munsoniana, and Vitis popenoei), making them genetically distinct from the European wine and table grape (Vitis vinifera) and other species in subgenus Euvitis. Crop improvement efforts have been continuous since the late 19th century, yet the germplasm that served as the foundation for early muscadine breeding efforts was sourced from a relatively small portion of their native range, mostly in the coastal plains of North Carolina. This study used the rhAmpSeq Vitis core panel haplotype markers to genotype 194 Muscadinia accessions from five cultivated populations and 15 wild populations collected across their native range. Wild populations from the western half of the native range were generally less genetically differentiated than hypothesized, but were genetically distinct from the material used in both past and present breeding efforts. One population collected from coastal North Carolina grouped closely with V. munsoniana accessions despite being well outside the reported range for that species. Principal coordinate and structure analyses revealed three main groups within the 194 accessions: one for cultivated material, one for wild V. rotundifolia, and one for V. munsoniana and V. popenoei. At K = 5, structure results showed that more recent muscadine cultivars are further differentiated from wild accessions and varieties. These analyses confirmed our hypothesis that muscadine cultivars are genetically differentiated from their wild counterparts. This study also showed that genetic diversity in V. rotundifolia is not equally distributed across its native range and that the limited number of genotypes used in crop improvement efforts has not fully utilized the genetic diversity within the species.
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14
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Ismail A, Darwish AG, Park M, Gajjar P, Tsolova V, Soliman KFA, El-Sharkawy I. Transcriptome Profiling During Muscadine Berry Development Reveals the Dynamic of Polyphenols Metabolism. FRONTIERS IN PLANT SCIENCE 2021; 12:818071. [PMID: 35185966 PMCID: PMC8849228 DOI: 10.3389/fpls.2021.818071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/31/2021] [Indexed: 05/17/2023]
Abstract
Muscadine grapes accumulate higher amounts of bioactive phenolics compared with other grape species. To identify the molecular events associated with polyphenolic accumulation that influence antioxidant capacity, two contrasting muscadine genotypes (C5 and C6) with varied phenolic/flavonoid content and antioxidant activity were investigated via RNA-sequencing during berry development. The results showed that berry development is concomitant with transcriptome profile changes, which was more pronounced at the véraison (V) stage. Despite that the downregulation pattern of gene expression dominated the upregulation through berry development, the C5 genotype maintained higher expression levels. Comparative transcript profiling allowed the identification of 94 differentially expressed genes with potential relevance in regulating fruit secondary metabolism, including 18 transcription factors and 76 structural genes. The genes underlying the critical enzymes in the modification reactions of polyphenolics biosynthetic pathway, including hydroxylation, methylation, and glycosylation were more pronounced during the immature stages of prevéraison (PrV), V, and postvéraison (PoV) in the C5 genotype, resulting in more accumulation of biologically active phenolic/flavonoid derivatives. The results suggested that muscadine grapes, as in bunch grapes (Vitis sp.); possess a similar mechanism that organizes polyphenolics accumulation; however, the set of total flavonoids (TFs) and structural genes coordinating the pathway varies between the two species.
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Affiliation(s)
- Ahmed Ismail
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
- Department of Horticulture, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Ahmed G. Darwish
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
- Department of Biochemistry, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Pranavkumar Gajjar
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Karam F. A. Soliman
- College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL, United States
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
- *Correspondence: Islam El-Sharkawy,
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