Ontologies for describing Solanaceae phenotypes

Solanaceae phenotypes

Information collection process

Annotation

Using controlled vocabularies

Future at SOL Genomics Network (SGN)

Available resources

Solanaceae gene nomenclature

Solanaceae germplasms

Mutants

Mapping populations

Wild species

Varieties

Solanaceae are linked by a syntenic genome

2n=2x=24 950 Mb

2n=2x=24 950 Mb

2n=2x=24 3000 Mb

2n=4x=24 1800 Mb

2n=2x=24 1300 Mb

2n=2x= 22 ca. 1000 Mb

Solanaceae share phenotypes

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Phenotypic mutant resources

Tomato:

960 monogenic mutants at TGRC http://tgrc.ucdavis.edu/

Chemical and physical mutagenesis: 15,000 M2 lines http://zamir.sgn.cornell.edu/mutants/

3,400 microtom mutants (INRA)

Eggplant, pepper, and potato : chemical mutagenesis: 1,000 M2 lines each.

Potato : 6392 activation tagged line http://www.cpgp.ca/

“Real Time” phenotyping

Information collection

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Accession# : e3406m2

Phenotype: yellow leaf-virescence, light-yellow flowers, orange fruit pericarp	and flesh

Mode of inheritance: recessive

http://zamir.sgn.cornell.edu/mutants/

Annotation – use controlled vocabulary

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Gene : tangerine allele (TGRC gene)

Tomato phenotypic catalog:

leaf color (sub category : yellow leaf)

flower color (sub category : pale yellow flower)

fruit color (sub category : orange fruit)

Annotations: GO

Biological process:

Involved in:

carotenoid biosynthesis	GO:0016117 etioplast organization and biogenesis GO:0009662

Cellular component:

located in: chloroplast	GO:0009507

Molecular function:

has: carotenoid isomerase activity	GO:0046608

tangerine: carotenoid isomerase

Annotations: PO

Whole plant growth: expressed in:

leaf production PO:0007133	flowering PO:0007016	late stage of ripening PO:0007050

Plant structure development: expressed during:

leaf expansion PO:0001052 anthesis	PO: 0007616 fruit maturation	PO: ?

Plant structure: expressed in:

leaf PO:0009025	flower PO:0009046	fruit PO:0009001

Tomato vocabulary is mapped to PO terms:

lycopersicon invertase 5 (lin5)

Fridman et al, Science 2004

LIN5 expression is in the conductive tissue of the flower’s ovary, fruit placenta, and pericarp during the early stage of cell division

Whole plant growth: expressed in:

immature green fruit PO:0007032 (fruit size 10%)	flowering PO:0007016

Plant structure development: expressed during:

anthesis	PO: 0007616 fruit cell division stage PO: ?

Plant structure: expressed in:

ovary vascular system PO: ?	fruit placenta PO: ? fruit mesocarp PO:0009087

Common ontologies for phenotypes

Solanaceae gene nomenclature

~1,200 tomato gene and allele names

Naming conventions required for facilitating functional and	comparative genomics

One unique locus name – many synonyms, alleles, transcripts

Gene name registry at SGN:

Provide consistency

Avoid duplications

Track history

Future at SGN

Framework for searching across Solanaceae phenotypes

Comparative searches using common vocabularies (GO and PO)

Online gene/phenotype submission and annotation

Online gene registry platform

Phenotype

Gene

Expression

Robert Buels

2005-09-20T17:13:01