Chicken QTL Phenotype Ontology

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Chicken QTL Phenotype Ontology
Wilfrid Carré, Jan Aerts, Dave Burt, Andy
Law Roslin Institute, Genetics and Genomics
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ENSEMBL Project

• What are we trying to achieve
• Add function over the genome sequence.
• Integrate the QTL data to the Chicken Genome.

• How are we going to that?
• Get and organise all the QTL data.
• Make it easily available (via cMap, ArkDB,
  ENSEMBL, UCSC).
• Work out where it maps on the genome.
• Allow cross species comparison with synteny
  comparison.

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Mapping QTL data
Use Cases

• Map the QTL on Consensus linkage Map, Genome
  assembly, RH Map, Cytogentic Map.
• ?based on position on common flanking markers.

? Browse by chromosome numbers or animal trait
ontology tree
? Retrieve all available information for each QTL.
? Search by chromosomes, trait names and/or
key-words in the publication.
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Mapping QTL data
Chicken QTL data in ArkDB http//www.thearkdb.or
g/
QTL study
QTL
Linkage Map
QTL map
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Chicken QTL data
QTL data collected for Chicken - 111
Publications - 227 different traits -
1508 chicken QTL/Associations found
Different kind of data - Association study (439
Associations, 40 studies) - QTL analysis (1058
QTLs, 60 studies) - Causative genes (11 genes,
11 studies)
Data - QTL description (Trait, Age, Chromosome,
Position, Flanking markers, Significance, Genome
/ Chromosome wise, QTL effect on the trait, ) -
Parameters of the study (Type of Cross, Number of
animals in the study, Breed, Description,
Statistic / Software used .) - References
(Title of the publication, Authors, Journal,
PubMed ID, Laboratory, Contact e-mail)
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Classification of Traits
Trait Ontology
- Mammalian Phenotype Ontology (MGI website) not
suitable for production traits.
- Define a 3 level Ontology based on the
different publications ? Body traits ?
Behavior ? Immune response ? Reproduction
- Define a 3 level Ontology based on the
different publications ? Body traits
? Carcass traits ? Fat ?
Growth traits ? Meat quality
? Metabolic traits ? Muscular
system ? Nervous system ?
Organs ? Plumage ?
Skeletal system
- Define a 3 level Ontology based on the
different publications ? Body traits
? Fat ? Abdominal fat
weight ? Abdominal fat weight ?
Abdominal fat weight / BW ? Abdominal
fat width ? Fat distribution ?
Skin fat weight ? Skin fatness
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Classification of Traits
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Issues with Traits

• Interactions between traits / Traits belonging
  to different group
• ? Thigh meat / bone ratio.
• ? Meat colour adjusted for body weight.
• ? Weights of heart, liver and gizzard (g).

• Trait given at a specific age or stage
• Body weight at 5 weeks of age under Ascites
  Condition (g).
• Feed intake in a fixed weight interval.

• Environmental conditions
• Same trait in different environmental condition
  not necessary the same meaning.
• Body weight at 5 weeks of age (g)
• Body weight at 5 weeks of age under Ascites
  Condition (g)
• Body weight post transport to the processing
  factory

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Issues with Traits

• Different way to look at and to classify traits

ROSLIN Body traits Skeletal system Body traits
Skeletal system Body traits Skeletal
system Body traits Carcass traits Body traits
Muscular system
ATO Egg Quality Production traits Egg
Quality Production traits Growth Production
traits Growth Production traits
Tibia width Tibia length Thigh bone Thigh
weight Thigh muscle
ROSLIN Reproduction fem Egg prod Reproduction
fem Egg prod Reproduction fem Egg
shell Reproduction fem Egg comp Body traits
Growth
Egg weight Total Egg Number Shell weight Albumen
weight Test end Body weight
ATO Egg production Production traits Egg
Quality Production traits Egg Quality Production
traits Egg production Production traits Egg
production Production traits
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Other phenotype databases

• Several other databases oriented on trait
  OMIM, for human, or MGI for mouse.

• Online Mendelian Inheritance in Animals (OMIA)
  is a database of genes, inherited disorders and
  traits in more than 135 animal species (other
  than human and mouse, which have their own
  resources).

• The database of Genotype and Phenotype (dbGaP)
  was developed to archive and distribute the
  results of studies that have investigated the
  interaction of genotype and phenotype.

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Conclusion

• QTL identified in Human, Mouse and Rat are
  disease or physiology oriented. Same trait
  defined differently in farm animals.
• How to make the connection between different
  traits?

• How to integrate OMIA and OMIM data to the trait
  ontology?

? In order to do some comparative mapping
necessity to have a similar ontology from one
species to an other one. Common trait should be
in the same super classe and have almost the same
subcategories even if they reflect different
production in different species.
? Necessity to standardize abbreviations of
traits.
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Example of Comparative Mapping