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Holt RR, Barile D, Wang SC, Munafo JP, Arvik T, Li X, Lee F, Keen CL, Tagkopoulos I, Schmitz HH. Chardonnay Marc as a New Model for Upcycled Co-products in the Food Industry: Concentration of Diverse Natural Products Chemistry for Consumer Health and Sensory Benefits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15007-15027. [PMID: 36409321 PMCID: PMC9732887 DOI: 10.1021/acs.jafc.2c04519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Research continues to provide compelling insights into potential health benefits associated with diets rich in plant-based natural products (PBNPs). Coupled with evidence from dietary intervention trials, dietary recommendations increasingly include higher intakes of PBNPs. In addition to health benefits, PBNPs can drive flavor and sensory perceptions in foods and beverages. Chardonnay marc (pomace) is a byproduct of winemaking obtained after fruit pressing that has not undergone fermentation. Recent research has revealed that PBNP diversity within Chardonnay marc has potential relevance to human health and desirable sensory attributes in food and beverage products. This review explores the potential of Chardonnay marc as a valuable new PBNP ingredient in the food system by combining health, sensory, and environmental sustainability benefits that serves as a model for development of future ingredients within a sustainable circular bioeconomy. This includes a discussion on the potential role of computational methods, including artificial intelligence (AI), in accelerating research and development required to discover and commercialize this new source of PBNPs.
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Affiliation(s)
- Roberta R Holt
- Department of Nutrition, University of California, Davis, Davis, California 95616, United States
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, Davis, California 95616, United States
| | - Selina C Wang
- Department of Food Science and Technology, University of California, Davis, Davis, California 95616, United States
| | - John P Munafo
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Torey Arvik
- Sonomaceuticals, LLC, Santa Rosa, California 95403, United States
| | - Xueqi Li
- Department of Food Science and Technology, University of California, Davis, Davis, California 95616, United States
| | - Fanny Lee
- Sonomaceuticals, LLC, Santa Rosa, California 95403, United States
| | - Carl L Keen
- Department of Nutrition, University of California, Davis, Davis, California 95616, United States
| | - Ilias Tagkopoulos
- PIPA, LLC, Davis, California 95616, United States
- Department of Computer Science and Genome Center, USDA/NSF AI Institute for Next Generation Food Systems (AIFS), University of California, Davis, Davis, California 95616 United States
| | - Harold H Schmitz
- March Capital US, LLC, Davis, California 95616, United States
- T.O.P., LLC, Davis, California 95616, United States
- Graduate School of Management, University of California, Davis, Davis, California 95616, United States
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Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm. Genes (Basel) 2020; 11:genes11070737. [PMID: 32630730 PMCID: PMC7397172 DOI: 10.3390/genes11070737] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022] Open
Abstract
Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.
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Roach MJ, Johnson DL, Bohlmann J, van Vuuren HJJ, Jones SJM, Pretorius IS, Schmidt SA, Borneman AR. Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS Genet 2018; 14:e1007807. [PMID: 30458008 PMCID: PMC6279053 DOI: 10.1371/journal.pgen.1007807] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/04/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023] Open
Abstract
Chardonnay is the basis of some of the world's most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different Chardonnay clones. There were 1620 markers identified that distinguish the 15 clones. These markers were reliably used for clonal identification of independently sourced genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.
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Affiliation(s)
- Michael J. Roach
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Daniel L. Johnson
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Joerg Bohlmann
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hennie J. J. van Vuuren
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J. M. Jones
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Isak S. Pretorius
- Chancellery, Macquarie University, Sydney, New South Wales, Australia
| | - Simon A. Schmidt
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Anthony R. Borneman
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
- Department of Genetics and Evolution, University of Adelaide, South Australia, Australia
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Quantitative trait loci affecting pathogen resistance and ripening of grapevines. Mol Genet Genomics 2016; 291:1573-94. [PMID: 27038830 DOI: 10.1007/s00438-016-1200-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/12/2016] [Indexed: 10/22/2022]
Abstract
Grapevines (Vitis vinifera L.) form the basis of viticulture, and are susceptible to diseases such as downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator). Therefore, successful viticulture programs require the use of pesticides. Breeding for resistance is the only eco-friendly solution. Marker-assisted selection is currently widely used for grapevine breeding. Consequently, traits of interest must be tagged with molecular markers linked to quantitative trait loci (QTL). We herein present our findings regarding genetic mapping and QTL analysis of resistance to downy and powdery mildew diseases in the progenies of the GF.GA-47-42 ('Bacchus' × 'Seyval') × 'Villard blanc' cross. Simple sequence repeats and single nucleotide polymorphisms of 151 individuals were analyzed. A map consisting of 543 loci was screened for QTL analyses based on phenotypic variations observed in plants grown in the field or under controlled conditions. A major QTL for downy mildew resistance was detected on chromosome 18. For powdery mildew resistance, a QTL was identified on chromosome 15. This QTL was replaced by a novel QTL on chromosome 18 in 2003 (abnormally high temperatures) and 2004. Subsequently, both QTLs functioned together. Additionally, variations in the timing of the onset of veraison, which is a crucial step during grape ripening, were studied to identify genomic regions affecting this trait. A major QTL was detected on linkage group 16, which was supplemented by a minor QTL on linkage group 18. This study provides useful information regarding novel QTL-linked markers relevant for the breeding of disease-resistant grapevines adapted to current climatic conditions.
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Santos S, Oliveira M, Amorim A, van Asch B. A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers. Electrophoresis 2014; 35:3201-7. [PMID: 25146979 DOI: 10.1002/elps.201400107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 11/07/2022]
Abstract
The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.
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Affiliation(s)
- Sara Santos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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A Strategy to Investigate the Intravarietal Genetic Variability in Vitis vinifera L. for Clones and Biotypes Identification and to Correlate Molecular Profiles with Morphological Traits or Geographic Origins. Mol Biotechnol 2011; 52:68-81. [DOI: 10.1007/s12033-011-9475-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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