Goal 3. Wood qualities and phenotypes

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Contents

Neighboring ontologies of the PO: Describing Traits and Phenotypes

Unlike goals 1 and 2, this goal goes beyond the current domain of the PO, but as we discussed in the sessions, we are closely linked to the Trait Ontology and utilize the PATO extensively.

Each of these have their own SourceForge trackers and repositories.

Background

  • What is a trait? What is a quality?
  • What is the difference between an entity and a phenotype?
  • How do the TO and PATO differ from the PO? How are they similar? How do they interact?

For more explanations, please see: File:PO Walls wood meeting short.pdf

Domain of Trait Ontology (TO)

The Trait Ontology is hosted by Gramene.

The TO consists of precomposed terms to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature individual. TO is specific to plants (should be called Plant Trait Ontology).

Examples are glutinous endosperm, disease resistance, plant height, photosensitivity, male sterility, etc.

The TO is organized around 9 main parent terms or categories:

File:TO top.png

Domain of Phenotypic Quality Ontology (PATO)

PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation and is applicable to all organisms.

From PATO Wiki:

PATO is an ontology of *phenotypic qualities*, intended for use in a number of applications, primarily phenotype annotation.

The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities.

PATO is designed to be used in conjunction with ontologies of "quality-bearing entities". An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality 'red' (PATO:0000322). This combination is the "red eye" phenotype.

We say that the phenotype term is 'post-coordinated', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. See below for a more formal treatment.

Other ontologies of content bearers include the OBO Cell ontology (CL), the GO biological process or cellular component ontologies, and ontologies of anatomical entities (such as the PO).

Describing wood traits, qualities and phenotypes:

Priorities: User needs and accessing genomic data:

  • How should we prioritize which traits are the most important, which to focus on first?

-ones used in the literature, to describe QTL or transcriptome datasets

  • Wood traits for which genomic data are currently being collected should be a priority:
  • AG will contact some of the other database groups and survey which terms they are using: see below

From AG: "The 'biofuel' biochemical traits and basic measures of wood development and quality are the ones that will have the most genetic and genomic data associated with them. Some of the more derived traits that are in the long list that have to do with wood physical properties are more used by wood physical scientists and engineers, and not so much by geneticists. I can't think of any datasets looking at the genetics of board checking, gluing properties, and those sorts of traits."

  • How will quality/phenotype terms be used and by who? Will we develop annotations to them and where will they be stored?
  • Are we creating a separate "Wood Quality Ontology" versus describing phenotypes on the fly using cross products?

List of terms needed

See link to Google Doc for wood traits

At the Workshop we started compiling a list (in Google doc) of trait and quality terms from various sources and tried to categorize them based the nine main headings of the TO.

Sources:

List from BL: Media:WQ traits (BL 2-6-12) .pdf

List from AW: Media:Andrew_Wood_traits_mapped_to_TO_Sheet1.pdf‎

List from MS:

Database groups:

TRY Database

A global database of plant traits

See link to the Core traits and related data they are interested: link

ORNL Plant Genomics Group

Gerald Tuskan

Bioenergy traits measured on (primarily) Populus: Wet weight core + bark

Wet weight core

Dry weight core

Wet weight bark

Dry weight bark

Diameter with bark

Diameter without bark

Wet thickness

Dry thickness

Water displacement of core

Populus Genome Consortium

Wood Science, University of British Columbia

Shawn Mansfield and Carl Douglas, Wood and Fibre Quality Department

Fibre length

Fibre width

Wood density

Wood microfibril angle

Cell wall crystallinity

Total lignin

Acid soluble lignin

Acid insoluble lignin

Lignin S:G ratio

Arabinose

Rhamnose

Galactose

Glucose

Xylose

Mannose

Alpha Cellulose

Holocellulose

Acetate content

Any any ratio of the above

PopGenie.org

Nathaniel Street, Umea, Sweden

List of traits measured for QTL and association mapping studies at UPSC:

Stem diameter

Stem height

Stem volume

Wood density

Wood stiffness

Xylem vessel width (angiosperms)

Xylem vessel length (angiosperms)

Xylem vessel cell wall thickness (angiosperms)

Xylem fiber width (angiosperms)

Xylem fiber length (angiosperms)

Xylem fiber cell wall thickness (angiosperms)

Tracheid width (gymnosperms)

Tracheid length (gymnosperms)

Tracheid cell wall thickness (gymnosperms)

Radial width of the living xylem

Microfibril angle

Total lignin content

S/G lignin ratio

Total carbohydrate content

Total extractives content

Amount of cellulose

Cellulose crystallinity

Degree of cellulose polymerisation

Amount of xylan

Amount of soluble sugars (glucose, fructose, saccharose)

Amount of uronic acids Sugar release during saccharification

Existing glossaries:

See list of links at Inside Wood site: IAWA glossaries

References from literature:

Sannigrahi, P., Ragauskas, A.J., and Tuskan, G.A. (2010). Poplar as a feedstock for biofuels: A review of compositional characteristics. Biofuels, Bioprod. Bioref. 4, 209–226. link

To do:

  • We will do preliminary edits to the TO for wood traits, depending upon the priorities for the PO and TO
  • Survey other database groups about terms needed in the TO/Plant Ontology- AG: see info above, JW will also follow up with some she works with
  • Prioritize the list of trait and quality terms by user need, access to genomic data, commercial importance: add these to the TO by September 2012 (LC)
  • Work with GO to get terms needed for wood traits, based on priorities above (LC, others?)
  • Work with ChEBI to get terms needed for wood chemical compounds
  • Add measurements to trait ontology (focus on the wood) '???
  • Add biofuel traits from the Sannigrahi et al (2010), Poplar paper
  • Consult with domain experts about how traits are measured eg. specific plant diseases

Notes and questions that came up:

  • fiber in pulp and paper can include any type of cell, e.g. "pulp fiber" not the same as "fiber cell"
  • susceptibility vs resistance are two sides of the same trait or are they?
  • Is the lignin network part of the cell (GO) or is it extracellular (belongs in PO)?? See above
  • What should be done about concerns over TO general structure?


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