A Transcriptomic Comparison of Late- Ripening Cabernet Sauvignon - - PowerPoint PPT Presentation

▶

Jun 22, 2023 216 likes •325 views

A Transcriptomic Comparison of Late- Ripening Cabernet Sauvignon Berry Skins from Bordeaux and Reno Grant R. Cramer Department of Biochemistry and Molecular Biology University of Nevada, Reno Talk Outline Experimental conditions

SLIDE 1

Grant R. Cramer Department of Biochemistry and Molecular Biology University of Nevada, Reno

A Transcriptomic Comparison of Late- Ripening Cabernet Sauvignon Berry Skins from Bordeaux and Reno

SLIDE 2

Talk Outline

Experimental conditions
Transcriptomic analysis and results
Conclusions

SLIDE 3

Reno and Bordeaux Experimental Conditions

Environmental Variable BOD (2013) RNO (2012) Elevation (m) 25 1,373 Average Daily Solar Radiation (kW-hr m-2) 1.17 5.86 Day length Starting Harvest Date 12:25:36 12:38:34 Day length Ending Harvest Date 11:20:57 11:57:37 Maximum Temperature Starting Harvest Date 19 30.5 Minimum Temperature Starting Harvest Date 13 13.9 Maximum Temperature Ending Harvest Date 18 27.8 Minimum Temperature Ending Harvest Date (°C) 11 6.7 Ave September Maximum Temperature (°C) 23.9 30.2 Ave September Minimum Temperature (°C) 13.9 10.2 Latitude 44°47’23.83’’ N 39°52’96’’ N Longitude 0°34’39.3’’ W 119°81’38’’ W September Precipitation (mm) 65.5 2.03 Average Monthly Relative Humidity (%) 74 34 Soil Type Gravelly soil Sandy Loam Soil pH 6.2 6.7 Root stock SO4 Own-rooted

Grapes harvested at 4 different °Brix levels at physiological maturity RNA-seq analysis of berry skins using Illumina technology

SLIDE 4

Experimental Design

Three experimental replicates collected for

berry skins at 4° Brix levels at or near physiological maturity for grapes of the respective location

BOD = 19.5, 20.5, 21.5, and 22.5 °Brix
RNO = 20, 22, 24 and 26 °Brix

SLIDE 5

Transcriptomic Method

50 bp Illumina reads
Read alignment using the V2 assembly of the

PN40024 Vitis vinifera reference genome

Transcripts per million (TPM) calculated using

Salmon

Differentially expressed genes (DEGs)

determined using DESeq2

Gene Set Enrichment Analysis (GSEA)

performed with BinGO

SLIDE 6 response to UV-B response to UV response to blue light shade avoidance response to light stimulus response to red or far red light response to red light response to sucrose stimulus response to disaccharide stimulus response to carbohydrate stimulus response to monosaccharide stimulus response to chitin response to hexose stimulus response to fructose stimulus response to salicylic acid stimulus response to organic substance cellular response to salicylic acid stimulus response to jasmonic acid stimulus response to hormone stimulus response to ethylene stimulus response to auxin stimulus cellular response to hormone stimulus response to cadmium ion cellular response to abscisic acid stimulus cellular response to auxin stimulus abscisic acid mediated signaling pathway response to metal ion response to abscisic acid stimulus cellular response to ethylene stimulus response to chemical stimulus response to water response to endogenous stimulus cellular response to jasmonic acid stimulus cellular response to organic substance cellular response to endogenous stimulus response to ozone response to inorganic substance transmembrane receptor protein serine/threonine kinase signaling pathway enzyme linked receptor protein signaling pathway auxin mediated signaling pathway cell surface receptor linked signaling pathway salicylic acid mediated signaling pathway hormone-mediated signaling pathway response to oxidative stress water transport nucleobase transport anion transport neutral amino acid transport proline transport

rganic anion transport

ion transport purine nucleoside transport transition metal ion transport iron ion transport di-, tri-valent inorganic cation transport monovalent inorganic cation transport cation transport terpenoid transport lead ion transport metal ion transport response to bacterium response to fungus response to external stimulus defense response to bacterium signal transmission systemic acquired resistance response to other organism defense response to oomycetes signal transduction cellular response to stimulus cellular response to biotic stimulus cellular response to stress defense response response to stimulus response to endoplasmic reticulum stress regulation of catalytic activity two-component signal transduction system (phosphorelay) intracellular signaling pathway regulation of hydrolase activity negative regulation of hydrolase activity regulation of peptidase activity auxin transport auxin efflux isoprenoid transport negative regulation of catalytic activity negative regulation of peptidase activity auxin polar transport cellular response to chemical stimulus signaling pathway ethylene mediated signaling pathway jasmonic acid mediated signaling pathway flavone biosynthetic process flavonoid metabolic process cinnamic acid biosynthetic process chlorophyll biosynthetic process flavonoid biosynthetic process chlorophyll metabolic process fat-soluble vitamin metabolic process fat-soluble vitamin biosynthetic process plastid localization regulation of hormone levels respiratory burst hormone metabolic process chloroplast relocation chloroplast organization Golgi organization purine transport fluid transport amino acid transport carboxylic acid transport

rganic acid transport

nucleobase, nucleoside, nucleotide and nucleic acid transport lipid transport nucleoside transport amine transport chemical homeostasis protein complex assembly macromolecular complex assembly protein complex biogenesis cellular macromolecular complex assembly homeostatic process plastid organization cell wall biogenesis cellular cell wall organization or biogenesis protein targeting cellular macromolecule localization transmembrane transport intracellular transport reproductive structure development protein targeting to membrane

ligosaccharide biosynthetic process

hormone biosynthetic process cellular hormone metabolic process cinnamic acid metabolic process

rganelle localization

immune system process regulation of anatomical structure size cell wall organization or biogenesis innate immune response stomatal movement multi-organism process signaling process lipid localization protein transport cellular protein localization hormone transport ion transmembrane transport transport cytokinin transport intracellular protein transport protein localization trichoblast maturation trichoblast differentiation root hair cell differentiation gene silencing by miRNA ion homeostasis cell development cell maturation cellular developmental process indole and derivative metabolic process phenylpropanoid metabolic process porphyrin biosynthetic process phenylpropanoid biosynthetic process L-phenylalanine catabolic process L-phenylalanine metabolic process tryptophan metabolic process chorismate metabolic process tryptophan catabolic process indole derivative catabolic process amine catabolic process cellular biogenic amine catabolic process cellular amino acid catabolic process purine ribonucleoside metabolic process indolalkylamine catabolic process thiamin metabolic process aromatic amino acid family catabolic process indolalkylamine metabolic process aromatic compound biosynthetic process vitamin biosynthetic process cellular aromatic compound metabolic process vitamin metabolic process porphyrin metabolic process tetrapyrrole metabolic process water-soluble vitamin biosynthetic process indole derivative metabolic process cellular amino acid biosynthetic process carboxylic acid catabolic process amine biosynthetic process cellular amino acid metabolic process amine metabolic process sulfur amino acid metabolic process S-adenosylmethionine metabolic process heterocycle catabolic process serine family amino acid metabolic process nucleoside metabolic process purine nucleotide metabolic process purine nucleoside metabolic process ribonucleoside metabolic process purine nucleotide catabolic process purine nucleoside triphosphate metabolic process purine ribonucleotide metabolic process thiamin and derivative metabolic process heterocycle metabolic process cellular amine metabolic process carboxylic acid metabolic process cellular amino acid derivative metabolic process thiamin and derivative biosynthetic process sulfur metabolic process cellular amino acid derivative catabolic process carboxylic acid biosynthetic process sulfur compound biosynthetic process cellular nitrogen compound biosynthetic process aromatic amino acid family metabolic process cellular biogenic amine metabolic process aromatic compound catabolic process aromatic amino acid family biosynthetic process vitamin E biosynthetic process dicarboxylic acid metabolic process water-soluble vitamin metabolic process vitamin E metabolic process monosaccharide metabolic process generation of precursor metabolites and energy RNA biosynthetic process cellular macromolecule biosynthetic process protein metabolic process nucleic acid metabolic process cellular carbohydrate catabolic process pyridine nucleotide metabolic process cysteine biosynthetic process

xidoreduction coenzyme metabolic

process nucleotide metabolic process cysteine metabolic process serine family amino acid biosynthetic process sulfur amino acid biosynthetic process nucleoside phosphate metabolic process nucleotide catabolic process nucleoside triphosphate catabolic process ribonucleotide catabolic process nucleoside triphosphate metabolic process ribonucleotide metabolic process purine nucleoside triphosphate catabolic process ribonucleoside triphosphate catabolic process ribonucleoside triphosphate metabolic process purine ribonucleotide catabolic process alcohol biosynthetic process cellular lipid metabolic process cellular metabolic compound salvage lipid biosynthetic process glyceraldehyde-3-phosphate metabolic process pyruvate metabolic process lipid metabolic process alcohol metabolic process starch metabolic process mRNA cleavage starch catabolic process glucan biosynthetic process glucan catabolic process RNA processing mRNA metabolic process cellular glucan metabolic process mRNA processing small molecule catabolic process nucleotide-sugar biosynthetic process isoprenoid biosynthetic process fatty acid biosynthetic process nucleotide-sugar metabolic process nucleobase, nucleoside, nucleotide and nucleic acid catabolic process nucleobase, nucleoside and nucleotide metabolic process coenzyme metabolic process nucleobase, nucleoside and nucleotide catabolic process cellular nitrogen compound catabolic process hexose biosynthetic process monosaccharide biosynthetic process isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway cellular aldehyde metabolic process photorespiration gluconeogenesis alcohol catabolic process glycolysis phosphorus metabolic process steroid biosynthetic process macromolecule modification cellular protein metabolic process lipoprotein metabolic process photosynthetic electron transport chain lipoprotein biosynthetic process ATP metabolic process ATP catabolic process purine ribonucleoside triphosphate catabolic process purine ribonucleoside triphosphate metabolic process cellular polysaccharide catabolic process gene expression photosynthesis, light reaction RNA metabolic process transcription nucleic acid phosphodiester bond hydrolysis isoprenoid metabolic process phospholipid biosynthetic process phospholipid metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process electron transport chain macromolecule metabolic process carbohydrate metabolic process cellular carbohydrate metabolic process cellular polysaccharide biosynthetic process transcription, DNA-dependent photosynthesis cellular macromolecule metabolic process polysaccharide biosynthetic process cellular protein complex assembly

xidation reduction

indoleacetic acid biosynthetic process

ligosaccharide metabolic process

photosynthesis, dark reaction cell wall polysaccharide metabolic process cellular cell wall macromolecule metabolic process transcription from plastid promoter reductive pentose-phosphate cycle disaccharide metabolic process hemicellulose metabolic process

rganophosphate metabolic process

catabolic process cellular carbohydrate biosynthetic process auxin biosynthetic process glycoside metabolic process glycoside biosynthetic process carbohydrate biosynthetic process macromolecule catabolic process cell wall macromolecule catabolic process macromolecule biosynthetic process primary metabolic process cellular metabolic process cellular biosynthetic process cellular ketone metabolic process

rganic acid metabolic process

small molecule metabolic process monocarboxylic acid metabolic process cellular amino acid and derivative metabolic process small molecule biosynthetic process carbohydrate catabolic process biosynthetic process

rganic substance metabolic process

metabolic process auxin metabolic process secondary metabolic process maltose metabolic process carbon fixation epidermis development cell wall macromolecule metabolic process pigment biosynthetic process pigment metabolic process indole derivative biosynthetic process cofactor biosynthetic process cellular amino acid derivative biosynthetic process cofactor metabolic process nitrogen compound metabolic process flavone metabolic process heterocycle biosynthetic process tetrapyrrole biosynthetic process indoleacetic acid metabolic process photosystem II assembly polysaccharide metabolic process polysaccharide catabolic process cellular polysaccharide metabolic process glucan metabolic process

rganic acid catabolic process

cellular catabolic process fatty acid metabolic process

rganic acid biosynthetic process

cellular nitrogen compound metabolic process

xoacid metabolic process

iron ion homeostasis mRNA cleavage involved in gene silencing by miRNA di-, tri-valent inorganic cation homeostasis cation homeostasis xyloglucan metabolic process protein modification process NADP metabolic process nicotinamide nucleotide metabolic process pentose-phosphate shunt glucose catabolic process hexose catabolic process NADPH regeneration protein amino acid autophosphorylation protein ubiquitination protein amino acid phosphorylation protein modification by small protein conjugation post-translational protein modification phosphorylation protein modification by small protein conjugation or removal protein amino acid acylation peptidyl-amino acid modification N-terminal protein amino acid modification protein amino acid myristoylation N-terminal protein myristoylation starch biosynthetic process protein amino acid lipidation N-terminal protein lipidation peptide or protein amino-terminal blocking protein myristoylation isopentenyl diphosphate biosynthetic process isopentenyl diphosphate metabolic process sterol metabolic process steroid metabolic process monosaccharide catabolic process phosphate metabolic process glucose metabolic process photosynthetic electron transport in photosystem I sterol biosynthetic process hexose metabolic process regulation of dephosphorylation regulation of secondary metabolic process positive regulation of flavonoid biosynthetic process regulation of cellular protein metabolic process regulation of phosphate metabolic process regulation of flavonoid biosynthetic process regulation of protein amino acid dephosphorylation regulation of protein modification process regulation of programmed cell death regulation of plant-type hypersensitive response regulation of cellular response to stress positive regulation of cellular process regulation of protein metabolic process positive regulation of response to stimulus positive regulation of biological process regulation of metabolic process regulation of cellular process negative regulation of metabolic process negative regulation of biological process regulation of biological process negative regulation of cellular process regulation of macromolecule metabolic process regulation of cell differentiation response to radiation hyperosmotic response response to temperature stimulus response to water deprivation response to cold response to salt stress regulation of defense response regulation of response to stress regulation of immune system process regulation of response to stimulus negative regulation of defense response regulation of cell death regulation of innate immune response regulation of immune response negative regulation of response to stimulus regulation of primary metabolic process regulation of biosynthetic process regulation of cellular metabolic process positive regulation of biosynthetic process regulation of cellular biosynthetic process regulation of hormone metabolic process positive regulation of cellular biosynthetic process positive regulation of metabolic process positive regulation of hormone metabolic process regulation of phosphorus metabolic process positive regulation of cellular metabolic process defense response, incompatible interaction response to nematode negative regulation of macromolecule metabolic process regulation of developmental process defense response to fungus response to biotic stimulus intracellular signal transduction response to stress response to wounding response to mechanical stimulus response to osmotic stress response to abiotic stimulus positive regulation of auxin biosynthetic process regulation of auxin biosynthetic process positive regulation of auxin metabolic process positive regulation of hormone biosynthetic process regulation of auxin metabolic process regulation of hormone biosynthetic process immune response regulation of molecular function signaling negative regulation of molecular function establishment of protein localization macromolecule localization establishment of localization establishment of localization in cell establishment of organelle localization localization cellular localization establishment of plastid localization cell wall organization

rganelle organization

cellular component organization cellular component biogenesis cellular component assembly cellular macromolecular complex subunit organization macromolecular complex subunit

rganization

cellular process biological_process cellular homeostasis regulation of gene expression reproductive process in a multicellular organism posttranscriptional regulation of gene expression regulation of gene expression, epigenetic multicellular organism reproduction biological regulation dehiscence negative regulation of gene expression tropism response to oomycetes multicellular organismal process reproduction regulation of cellular component size gene silencing growth regulation of cell size reproductive process posttranscriptional gene silencing cell growth developmental growth developmental cell growth posttranscriptional gene silencing by RNA multidimensional cell growth gene silencing by RNA negative regulation of developmental process anther dehiscence flower morphogenesis floral whorl development negative regulation of cell differentiation developmental process reproductive developmental process developmental maturation stem cell development meristem maintenance root hair elongation cell differentiation stem cell differentiation multicellular organismal development regulation of biological quality mitochondrion localization immune effector process respiratory burst involved in defense response root morphogenesis tissue development ectoderm development root development maintenance of root meristem identity

rgan development

vasculature development post-embryonic root development root system development root epidermal cell differentiation epidermal cell differentiation meristem development post-embryonic morphogenesis lateral root development post-embryonic organ development stamen development androecium development anatomical structure development anatomical structure morphogenesis post-embryonic development system development flower development stem cell maintenance floral organ development anther development maintenance of meristem identity

Response to Stimulus Biosynthesis Process Response to Stress

Temperature Light Water Fungus

Gene Ontology Enrichment

4455 DEGs

100s of GO categories

SLIDE 7

Autophagy genes indicate BOD grapes ripen at lower sugar levels than RNO grapes

ATG18g (Vitvi07g00210)

20 22 24 26 4.0 4.5 5.0 5.5 6.0

Average log2 TPM Reno Bordeaux

ATG11 (Vitvi11g00777)

20 22 24 26 3.5 4.0 4.5 5.0 5.5

°Brix Average log2 TPM

APG9 (Vitvi07g00580)

20 22 24 26 3.0 3.5 4.0 4.5 5.0

Average log2 TPM

ATG2 (Vitvi03g00492)

20 22 24 26 3.0 3.5 4.0 4.5 5.0

°Brix Average log2 TPM

SLIDE 8

TPS35 (Vitvi12g00574)

20 22 24 26 1 2 3 4 5 Average log2 TPM Bordeaux Reno

TPS28 (Vitvi19g00391)

20 22 24 26 1 2 3 4 Average log2 TPM

TPS10 (Vitvi18g02449)

20 22 24 26 0.0 0.2 0.4 0.6 0.8 Average log2 TPM

TPS07 (Vitvi18g02446)

20 22 24 26 0.0 0.5 1.0 1.5 2.0 2.5 Average log2 TPM

TPS04 (Vitvi18g02298)

20 22 24 26 0.0 0.5 1.0 1.5 2.0 2.5 °Brix Average log2 TPM

TPS14 (Vitvi18g02452)

20 22 24 26 0.0 0.5 1.0 1.5 2.0 Average log2 TPM

TPS26 (Vitvi19g01791)

20 22 24 26 1.0 1.5 2.0 2.5

Average log2 TPM

TPS55 (Vitvi10g02174)

20 22 24 26 1 2 3 4 5 Average log2 TPM

TPS68 (Vitvi07g00130)

20 22 24 26 1 2 3 4 5

Average log2 TPM

TPS69 (Vitvi19g01734)

20 22 24 26 3.0 3.2 3.4 3.6 3.8 4.0

°Brix Average log2 TPM

PR10 (Vitvi05g01760)

20 22 24 26 2 4 6 8 10

Average log2 TPM Bordeaux Reno

PR3 (Vitvi05g01575)

20 22 24 26 1 2 3 4 5

°Brix Average log2 TPM

MLA10 (Vitvi12g01802)

20 22 24 26 1.0 1.5 2.0 2.5 3.0

Average log2 TPM

PR5 (Vitvi02g01405)

20 22 24 26 7 8 9 10

°Brix Average log2 TPM

PAL4 (Vitvi16g00054)

20 22 24 26 2 4 6 8

Average log2 TPM Reno Bordeaux

BCAT3 (Vitvi00g00789)

20 22 24 26 3.5 4.0 4.5 5.0 5.5 6.0

°Brix Average log2 TPM

DHS1 (Vitvi07g03049)

20 22 24 26 4 5 6 7 8

Average log2 TPM

TAT7 (Vitvi19g00186)

20 22 24 26 2 3 4 5 6 7

°Brix Average log2 TPM

Terpene Synthases Phenylpropanoid Metabolism Powdery Mildew Responsive

SLIDE 9

1) BOD berries reached maturity at lower sugar levels than RNO berries 2) Transcriptomic responses were dynamic and very sensitive to the environment 3) Temperature, light, water status and fungal infection were identified as some of the most influential factors affecting DEGs 4) Many flavor- and aroma-associated pathways were differentially affected

Conclusions

SLIDE 10

Acknowledgements

Aude Habran Serge Delrot University of Bordeaux Agnès Destrac-Irvine University of Nevada, Reno Noé Cochetel Ryan Ghan