How to describe a grapevine experiment
The international metadata standard for Plant Phenotyping experiments is MIAPPE (www.miappe.org, Papoutsoglou et al, 2020). The MIAPPE checklist is a pdf file that lists all the items recommended to describe an experiment, from general characteristics of an investigation/study to biological samples.
A general template (MIAPPEv1.1_training_spreadsheet.xlsx) is available to guide the collection of metadata and proposes descriptors for experimental factors and environmental variables. This template can be used both for greenhouse and vineyard experiments. Experiments based on vineyards in different locations are considered at the “investigation level”, with each vineyard being a “study”.
Some items specific to grapevine cultivation are not yet included in the MIAPPE format but should be provided to fully describe a grapevine experiment. Below are some suggested items.
Technical description of the experiment
- Row and plant spacing
- Planting date
- Training system
- Soil management techniques
Experimental factors specific to grapevine experiments
- Leaf removal
- Training systems
Cultural operations (facultative)
Cultural operations such as pruning, hedging, fertilizing, pesticide spraying, … but also applications of experimental factors, can be stored in the “event” sheet.
Standardizing the variety name
The most commonly used denomination for grapevine material is the variety name. Unfortunately, it has a lot of synonyms and can encompass different genetic material due to homonymy or clonal variation. To at least solve the problem of homonymy and synonymy, we recommend using a standard name, such as the “prime name” extracted from the VIVC database (http://www.vivc.de).
Precise identification of the plant material used in an experiment
The FAO and Biodiversity have developed a standard set of information (metadata) to identify and describe an accession in a genebank collection: the “Multi Crop Passport Descriptors” (MCPD). This standard is also integrated by OIV.
The important fields for identifying an accession are :
- Holding Institute: the name of the institute that maintains the plant material used in the experiment (a genbank or laboratory)
- Accession code: unique ID given by the holding institute to the accession used in the experiment
- Species authority
- The use of DOIs associated with accessions is now highly recommended in order to keep a link with updated information on the accession and has been added in the last MCPD version. This service is provided by EURISCO for European genebanks, the GLIS (Eurisco contributes to the GLIS global list of accessions with DOIs) for international genebanks and sometimes by your Institution.
The recommendations of the plant material used in the MIAPPE standard are also aligned on the MCPD and now recommended by the ELIXIR Plant community for any experiment. Below is an extract with some items requested by MIAPPE v1.1:
Below is an extract with some items requested by MIAPPE v1.1:
|Biological material ID||Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc… This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.||INRA:W95115_inra_2001; INRA:inra_kernel_2351; Rothamsted:rres_GK090847||Unique identifier|
An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.
|Genus||Genus name for the organism under study, according to standard scientific nomenclature.||Zea|
|Species||Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.||mays|
|Infraspecific name|| |
Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: ‘subsp.’ (subspecies); ‘convar.’ (convariety); ‘var.’ (variety); ‘f.’ (form); ‘Group’ (cultivar group).
|vinifera Pinot noirB73|
subspecies:vinifera ; cultivar:Pinot noir
subsp. vinifera var. Pinot Noir
|Free text, or key-value pair list, or MCPD-compliant format|
|Material source ID (Holding institute/stock centre, accession)||An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: “mother_accession X father_accession”, or, if father is unknown, as “mother_accession X UNKNOWN”. For in situ material, the region of provenance may be used when an accession is not available.||INRA:W95115_inra|
|Material source DOI||Digital Object Identifier (DOI) of the material source||doi:10.15454/1.4658436467893904E12||DOI|
MIAPPE differentiates between:
- the “Material source ID” (e.g. cuttings provided by a genebank used in the experiment) allows to trace the original genebank accession with a code composed of the holding institute name and the accession code
- the “Biological material ID” is the material that was actually experimented with a unique code. If built manually (not using a PUID such as a DOI), we recommend to build it with three fields separated by an underscore “_”: Institution_Type of plant material_Local code
Field 2: Type of plant material
- the VIVC code with five digits: VIVCxxxxx (http://www.vivc.de) for identified varieties
- “PRO” for genotypes from bi-parental crosses
- “TL” for transgenic lines
- “ESL” for lines regenerated from anthers or somatic tissues
- Nothing when the type of plant material is not characterized
Field 3: code used to identify the accession in your institute
- FRA038_VIVC10077_274Col49 for the clone number 49 of Riesling available at INRAE Colmar.
- FRA038_PRO_41207Col0011E for a genotype in the progeny from a cross between Riesling and Gewurztraminer.
- DEU098_VIVC22828_DEU098-2010-083 and Infraspecific name: Calardis blanc
MIAPPE recommends providing a unique ID to the taxon. Please refer to:
- NCBI taxonomy https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
Example : NCBI:txid694578 for Vitis coignetiae.
- or the GRIN database https://npgsweb.ars-grin.gov/gringlobal/taxonomybrowse.aspx
Example : GRIN:41864 for Vitis coignetiae
If necessary, a list of species and corresponding abbreviations (originally designed for genes) is available at: http://www.vivc.de/docs/dataonbreeding/AbbrevVitaceae%208Dez10.pdf
If the accession/genotype is the product of an interspecific crossing, we can distinguish two cases. If a taxon already exists in NCBI taxonomy database (NCBI:txid2018007 for V. riparia x V. cinerea for example), it should be used in priority. For simple crossings, we propose to use a clear descriptor such as “Vitis riparia x Vitis rupestris”. For complex crossings, we propose to use the term “xVitis”.
A reliable description of biological samples requires a shared vocabulary for the organ collected (see also the MIAPPE format).
We propose to refer to:
- the grapevine ontology anatomy, with a working document available at https://docs.google.com/spreadsheets/d/1uK77WFwUZCoGP0zrGVZ9RgTZvJQ2motGrbI6E6cxXts/edit?usp=sharing and https://doi.org/10.15454/SBXYSV
- or to the Plant Ontology: https://www.ebi.ac.uk/ols/ontologies/po and Agroportal:
Several scales to describe developmental stages are available (Baggiolini 1952; Coombe 1995, Lorenz et al. 1995) and can be used. We propose here to add some accuracy to the descriptions of these stages.
Dates for the main development stages
A working group in France proposes recommendations for the determination of budbreak, flowering and véraison dates (https://doi.org/10.15454/1.5514275483910464e12, in French, https://doi.org/10.20870/IVES-TR.2019.2586, in English). A proceedings paper with the detailed recommendations for budbreak and flowering dates, is also available in English.
To summarize these recommendations :
- A bud is counted as “broken” if a green (or red) tip is visible (BBCH 07, Baggiolini C). The budbreak date is determined by interpolation between several successive records, as the day when 50% of the buds left after pruning had reached this stage.
- For flowering (BBCH 65, Baggiolini I), the flowering date is determined as the day when 50% of the flower caps were detached or fallen.
- For véraison (BBCH 85, Baggiolini M), the most relevant definition is “softening” and not “color change” in order to record values that can be compared between white and colored genotypes. The date of véraison is determined as the day when 50% of the berries are soft. A reliable estimation of the percentage of soft berries should rely on touching at least 100 berries (20 on 5 plants for example).
Phenological descriptors for the berries
Four types of berry samples can be distinguished:
- Green berries
- Ripening berries
- Mix of green and ripening berries
- Harvested berries
In order to allow comparisons between experiments, we propose to provide the following data to best characterize a sample, by priority.
For green berries :
- Number of days after flowering or before véraison (as defined above)
- Heat sums calculated with degree days (usually above 10°C, otherwise to be specified), starting at flowering
- Single berry weight
- Single berry volume
For ripening berries :
- Number of days after véraison (as defined above)
- Heat sums (usually base 10°C, otherwise to be specified) after véraison
- Single berry weight
- Single berry volume
- Sugar concentration
- Acidity parameters (pH, titratable acidity, malic acid concentration, tartaric acid concentration, potassium concentration)
For harvested berries (Post ripening berries, BBCH 99) Number of days after harvest
Phenological descriptors for the leaves
- Age (number of leaves above, when the apex is active)
- Position (from the base of the shoot)
Baggiolini M (1952) Les stades repères dans le développement annuel de la vigne et leur utilisation pratique. Revue Romande d’Agriculture et de Viticulture 8:4-6.
Coombe BG. 1995. Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1(2): 104-110.
Lorenz DH, Eichhorn KW, Bleiholder H, Klose R, Meier U, Weber E (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale. Aust J Grape Wine Res 1:100-103.
Papoutsoglou, E.A., Faria, D., Arend, D., Arnaud, E., Athanasiadis, I.N., Chaves, I., Coppens, F., Cornut, G., Costa, B.V., Cwiek-Kupczynska, H., Droesbeke, B., Finkers, R., Gruden, K., Junker, A., King, G.J., Krajewski, P., Lange, M., Laporte, M.A., Michotey, C., Oppermann, M., Ostler, R., Poorter, H., Ramirez-Gonzalez, R., Ramsak, Z., Reif, J.C., Rocca-Serra, P., Sansone, S.A., Scholz, U., Tardieu, F., Uauy, C., Usadel, B., Visser, R.G.F., Weise, S., Kersey, P.J., Miguel, C.M., Adam-Blondon, A.F., and Pommier, C. (2020) Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytologist 227, 260-273.