A5076325223- Horticultural and Viticultural Research
- Plant Pathogens and Fungal Diseases
- Fermentation and Sensory Analysis
- Plant and Fungal Interactions Research
- Mycorrhizal Fungi and Plant Interactions
- Plant Virus Research Studies
- Plant biochemistry and biosynthesis
- Plant Disease Resistance and Genetics
- Plant-Microbe Interactions and Immunity
- Plant Reproductive Biology
- Wine Industry and Tourism
- Genetic Mapping and Diversity in Plants and Animals
- Plant Gene Expression Analysis
- Powdery Mildew Fungal Diseases
- Yeasts and Rust Fungi Studies
- Plant Pathogenic Bacteria Studies
- Plant Physiology and Cultivation Studies
- Molecular Biology Techniques and Applications
- Cocoa and Sweet Potato Agronomy
- Plant and animal studies
- Photosynthetic Processes and Mechanisms
- Phytoplasmas and Hemiptera pathogens
- Plant tissue culture and regeneration
- Plant Disease Management Techniques
- Fungal Biology and Applications
University of California, Davis
2016-2025
Universidad Nacional Autónoma de México
2006-2007
Pretty or Sweet The grocery-store tomato that looks beautiful but tastes like tart cardboard arises from selection processes favoring phenotypes make commercial production more reliable. Significant in process was a mutation reduced the mottled color variations of unripe green tomatoes, leaving them uniform, pale, green. Powell et al. (p. 1711 ) analyzed molecular biology mutation. uniform ripening turns out to disable transcription factor called Golden 2-like ( GLK2 ). expression increases...
Abstract It remains a major challenge to identify the genes and mutations that lead plant sexual differentiation. Here, we study structure evolution of sex-determining region (SDR) in Vitis species. We report an improved, chromosome-scale Cabernet Sauvignon genome sequence phased assembly nine wild cultivated grape genomes. By resolving twenty SDR haplotypes, compare male, female, hermaphrodite haplotype structures sex-linked regions. Coupled with gene expression data, candidate...
Grapevine red blotch-associated virus (GRBaV) is a major threat to the wine industry in USA. GRBaV infections (aka blotch disease) compromise crop yield and berry chemical composition, affecting flavor aroma properties of must wine. In this study, we combined genome-wide transcriptional profiling with targeted metabolite analyses biochemical assays characterize impact disease on red-skinned ripening metabolism. Using naturally infected berries collected from two vineyards, were able identify...
Lipopolysaccharides (LPS) are among the known pathogen-associated molecular patterns (PAMPs). LPSs potent elicitors of PAMP-triggered immunity (PTI), and bacteria have evolved intricate mechanisms to dampen PTI. Here we demonstrate that Xylella fastidiosa (Xf), a hemibiotrophic plant pathogenic bacterium, possesses long chain O-antigen enables it delay initial recognition, thereby allowing effectively skirt elicitation innate establish itself in host. Lack modifies perception Xf hallmarks...
Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in are performed using the available genome sequence, PN40024, as reference. However, differences gene content among accessions, which contribute phenotypic cultivars, suggest that a single reference does not represent species' entire space. Though whole assembly and annotation can reveal relatively unique or "private" space of any particular cultivar, transcriptome...
Abstract Background Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature mutations throughout genome. Fifteen Zinfandel winegrape genomes were sequenced compared one another using a highly contiguous genome reference produced from clones, 03. Results Though most heterozygous variants shared, accumulated in individual subsets clones. Overall, frequent intergenic space more introns than...
Abstract In this genome report, we describe the sequencing and annotation of wine grape Carménère (clone 02, VCR-702). Long considered extinct, old French variety is now cultivated mostly in Chile where it was imported 1850s just before European phylloxera epidemic. Genomic DNA sequenced using Single Molecule Real Time technology assembled with FALCON-Unzip, a diploid-aware assembly pipeline. To optimize contiguity completeness assembly, tested about thousand combinations parameters,...
Abstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because species are valuable sources agronomic traits that essential to enhance sustainability and adaptability domesticated cultivars. Genetic across a genus can be captured in super-pangenomes, which provide framework interpreting genomic variations. Results Here we report sequencing, assembly, annotation nine North American grape genomes, phased scaffolded at chromosome scale. We generate...
Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections grape (Vitis vinifera cv. 'Béquignol') variegated berries found that accumulation products from branches the phenylpropanoid isoprenoid pathways showed an opposite tendency. Light-responsive flavonol monoterpene levels increased anthocyanin-depleted areas correlation with increasing MYB24 expression. Cistrome analysis suggested binds to promoters 22 terpene synthase...
Abstract Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in southeastern United States. M. rotundifolia is resistant to many of pathogens that detrimentally affect Vitis vinifera, grape species commonly used winemaking. For this reason, a valuable genetic resource breeding. Single-molecule real-time reads were combined with optical maps reconstruct two haplotypes each 20 cv. Trayshed chromosomes. The completeness and accuracy assembly confirmed using...
The ascomycete Neofusicoccum parvum, one of the causal agents Botryosphaeria dieback, is a destructive wood-infecting fungus and serious threat to grape production worldwide. capability colonize woody tissue, combined with secretion phytotoxic compounds, thought underlie its pathogenicity virulence. Here, we describe repertoire virulence factors their transcriptional dynamics as feeds on different substrates colonizes stem. We assembled annotated highly contiguous genome using...
Grapevine trunk diseases cause important economic losses in vineyards worldwide. Neofusicoccum parvum, one of the most aggressive causal agents disease Botryosphaeria dieback, colonizes cells and tissues grapevine wood, leading to formation an internal canker. Symptoms then extend distal shoots, with wilting leaves bud mortality. Our aim was characterize transcriptional dynamics genes woody stem during parvum colonization. Genome-wide profiling at seven distinct time points (0, 3, 24 hours;...
Abstract While genome assembly projects have been successful in a number of haploid or inbred species, one the current main challenges is assembling non-inbred rearranged heterozygous genomes. To address this critical need, we introduce open-source FALCON and FALCON-Unzip algorithms ( https://github.com/PacificBiosciences/FALCON/ ) to assemble Single Molecule Real-Time (SMRT ® Sequencing data into highly accurate, contiguous, correctly phased diploid We demonstrate quality approach by new...
Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified panel of V. accessions from Central Asia with partial resistance to PM possess Ren1-like local haplotype. In this study, we show in addition typical Ren1-associated late post-penetration resistance, these display range different levels development suggesting alternative alleles or additional genes contribute...
With the increasing frequency of wildfires, vineyards are more often exposed to smoke, resulting in a higher risk smoke taint wine. This imparts undesirable "smoky" and "ashy" aromas causes significant economic losses. Smoke-derived volatile phenols (VPs) grape berries, metabolized into stable, non-volatile glycoconjugates via glycosyltransferases (GTs), underlie formation. Here, we present dwarf grapevine cultivar Pixie as model system for research. We generated phased, telomere-to-telomere...
While grapevine is an exceptional perennial model for studying host-microbiome interactions, the host genome's role in microbiome assembly often masked by environmental factors. This research provides a first insight into genetic mechanisms shaping berry-associated microbial communities. Using QTL mapping newly established population of 140 F1-progeny genotypes complete random block design, we were able to control abiotic effects and investigate how genome influences grape bacterial fungal...
The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. isolates has been reported, but underlying genetic basis phenotypic variability remains unknown. goal this study was to characterize intraspecific diversity explore its potential impact on functions associated with secondary metabolism, cellular transport, cell wall decomposition. We generated chromosome-scale genome...
DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous planta-detection of multiple pathogens associated with disease complexes, such as grapevine trunk diseases. Profiling pathogen communities diseases particularly challenging, due to presence within an individual wood lesion co-infecting and other wood-colonizing fungi, which span broad range taxa fungal kingdom. As such, we designed metabarcoding primers, using template...
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and woody tissues. Mature grapevines typically contract more than one disease often multiple grapevine pathogens (GTPs) recovered from infected The co-existence of different GTP species in complex dynamic microbial communities complicates study molecular mechanisms underlying development, especially under vineyard conditions. objective this was to develop optimize a community-level...
Abstract Phytophthora megakarya and P. palmivora are oomycete pathogens that cause black pod rot of cacao (Theobroma cacao), the most economically important disease on globally. While is a cosmopolitan pathogen, megakarya, which more aggressive than palmivora, has been reported only in West Central Africa where it spreading devastating farms since 1950s. In this study, we reconstructed complete diploid genomes multiple isolates both species using single-molecule real-time sequencing....
Abstract Grapevine leafroll‐associated virus (GLRaV) infections are accompanied by symptoms influenced host genotype, rootstock, environment, and which individual or combination of GLRaVs is present. Using a dedicated experimental vineyard, we studied the responses to in ripening berries from Cabernet Franc grapevines grafted different rootstocks with zero, one, pairs leafroll infection(s). RNA sequencing data were mapped high‐quality genome reference assembled carry out this study...