Catalogue of gene symbols for wheat - Plant Ontology Wiki
Catalogue of gene symbols for wheat - Plant Ontology Wiki
Catalogue of gene symbols for wheat - Plant Ontology Wiki
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Investigating trait ontologies to facilitate integrating phenotype and<br />
genome sequence level in<strong>for</strong>mation in <strong>wheat</strong><br />
Rudi Appels, Centre <strong>for</strong> Comparative Genomics, Murdoch University<br />
Outline <strong>of</strong> presentation:<br />
• <strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong> (Y Yamazaki, RA McIntosh)<br />
• CMap <strong>for</strong> projecting trait in<strong>for</strong>mation onto <strong>gene</strong>tic maps and hence<br />
genome sequence (GMOD, D Schibeci, DM Appels,)<br />
• <strong>Plant</strong> <strong>Ontology</strong> definition <strong>of</strong> traits that are projected onto molecular<br />
<strong>gene</strong>tic maps (P Jaiswal, DM Appels)
Outline <strong>of</strong> presentation<br />
• <strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
• CMap <strong>for</strong> projecting trait in<strong>for</strong>mation onto <strong>gene</strong>tic<br />
maps and hence genome sequence<br />
• <strong>Plant</strong> <strong>Ontology</strong> based definition <strong>of</strong> traits that are<br />
projected onto molecular <strong>gene</strong>tic maps
Trait ontologies <strong>for</strong> integrating phenotype and<br />
genome sequence<br />
<strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
RA McIntosh, Y Yamazaki, KM Devos, J Dubcovsky, WJ Rogers, R Appels<br />
The catalogue is a very long standing project led by Bob McIntosh (U <strong>of</strong> Sydney)<br />
• <strong>for</strong> many decades Bob Mcintosh has provided the authority <strong>for</strong> assigning<br />
names to new alleles <strong>for</strong> phenotypes that could be defined as being under<br />
<strong>gene</strong>tic control.<br />
• The Wheat Genetics Symposium held each 4-5 years provides input from the<br />
<strong>wheat</strong> community into the <strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong>.<br />
Basic approach is to characterize traits by their <strong>gene</strong>tic characteristics<br />
(alleles and linked molecular markers, QTL)
<strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
Yukiko Yamazaki
<strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
GeneClass<br />
• Morphological and Physiological Traits<br />
1. Gross Morphology: Spike characteristics<br />
1.1. Squarehead/spelt<br />
1.2. Club/Compact spike<br />
1.3. Sphaerococcum<br />
1.4. Branched spike<br />
1.5. Elongated glume<br />
1.6. Ear length<br />
................<br />
• Proteins<br />
• Pathogenic Disease/Pest Reaction<br />
Gene Nomenclature
<strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
• Gene Nomenclature<br />
• Recommended Rules <strong>for</strong> Gene Symbolization in Wheat<br />
• Guidelines <strong>for</strong> Nomenclature <strong>of</strong> Biochemical, Molecular Loci<br />
• Symbols <strong>for</strong> Loci and Alleles Controlling Quantitative Characters<br />
- Genes identified by segregational analysis:<br />
- Quantitative trait loci (QTLs):<br />
Basic approach is to characterize traits by their <strong>gene</strong>tic characteristics<br />
(alleles and linked molecular markers, QTL)
Outline <strong>of</strong> presentation<br />
• <strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
• CMap <strong>for</strong> projecting trait in<strong>for</strong>mation onto <strong>gene</strong>tic<br />
maps and hence genome sequence<br />
• <strong>Plant</strong> <strong>Ontology</strong> based definition <strong>of</strong> traits that are<br />
projected onto molecular <strong>gene</strong>tic maps
CMap <strong>for</strong> integrating traits and molecular <strong>gene</strong>tic maps<br />
The Cmap project was started (and is maintained) by the GMOD<br />
group in 2001.<br />
For <strong>wheat</strong> and barley CMap provides a basis <strong>for</strong> a more detailed<br />
description <strong>of</strong> traits (as QTL) linked to a large number <strong>of</strong><br />
molecular markers in <strong>gene</strong>tic maps.<br />
A composite molecular <strong>gene</strong>tic map provides a basis <strong>for</strong><br />
compiling published QTL describing plant phenotype and grain<br />
quality traits
CMap <strong>for</strong> integrating traits and molecular <strong>gene</strong>tic maps<br />
CMap Statistics June 2011<br />
Total # Wheat Maps 326<br />
Chromosome # Length cM # markers # Traits<br />
1A Consensus June 2011 131.4 289 40<br />
1B Consensus July 2010 173 372 33<br />
1D Consensus June 2010 153.56 170 14<br />
2A Consensus July 2010 213.5 213 19<br />
2B Consensus July 2010 172.2 360 40<br />
2D Consensus July 2010 94.97 137 21<br />
3A Consensus June 2011 170.1 286 36<br />
3B Consensus April 2011 306.4 527 54<br />
3D Consensus June 2011 226.6 145 20<br />
4A Consensus August 2010 103.18 258 41<br />
4B Consensus August 2010 70.7 98 9<br />
4D Consensus August 2010 84.11 39 3<br />
5A Consensus July 2010 133.5 229 41<br />
5B Consnesus August 2010 158.5 321 36<br />
5D Consensus August 2010 268 143 4<br />
6A Consensus September 2010 112 187 10<br />
6B Consensus July 2010 104.5 152 17<br />
6D Consensus September 2010 149.49 67 10<br />
7A Consensus June 2011 207 300 28<br />
7B ConsensusSeptember 2010 190.65 297 18<br />
7D ConsensusOctober 2010 227 158 24
CMap <strong>for</strong> integrating traits and molecular <strong>gene</strong>tic maps<br />
Relating a<br />
consensus map to<br />
a component map<br />
which was the<br />
source <strong>of</strong> the trait<br />
in<strong>for</strong>mation
CMap <strong>for</strong> integrating traits and molecular <strong>gene</strong>tic maps<br />
International Wheat<br />
Genome Sequencing<br />
Consortium<br />
• BAC end sequencing<br />
• Pooled BAC<br />
sequencing<br />
• Integrate survey<br />
sequencing<br />
•Targeted BAC<br />
sequencing<br />
• Generate markers <strong>for</strong><br />
breeding<br />
7A genome<br />
sequence<br />
7A<br />
Reference<br />
Wheat<br />
7A consensus April 2011<br />
Physical Map Molecular <strong>gene</strong>tic maps<br />
Traits
CMap <strong>for</strong> integrating traits and molecular <strong>gene</strong>tic maps<br />
Map Set: RL4452*AC Domain SO 05/08 (RL4*AC Dom) [ View More Info ]<br />
Species: Wheat (Triticum aestivum) [ View More Info ]<br />
Map Type: Genetic (cM) [ View More Info ]<br />
Reference: McCartney et al (2005); F<strong>of</strong>ana et al (2008) Mapping quantitative trait loci<br />
controlling common bunt resistance in a doubled haploid population derived<br />
from the spring <strong>wheat</strong> cross RL4452 x AC Domain. Mol Breeding 21:317-325<br />
QTL:<br />
<strong>Plant</strong> height: QHt.crc-2D (BE497718-260), QHt.crc-4B (gwm513), QHt.crc-4D<br />
(wmc617-wmc48), QHt.crc-5B (wmc640), QHt.crc-7A (wmc139), QHt.crc-7B<br />
(gwm333) Time to maturity: QMat.crc-3B (wmc231), QMat.crc-4A (Wx-B1),<br />
QMat.crc-4D-4D (wmc617-wmc48), QMat.crc-7D (gwm130) Lodging: QLd.crc-3D<br />
(gwm191), QLd.crc-4B (wmc826-wmc238), QLd.crc-4D (wmc617-wmc48) Grain<br />
yield: QYld.crc-2A (gwm339), QYld.crc-2B (gwm257), QYld.crc-3D (barc71),<br />
QYld.crc-4A (gwm397-wmc650), QYld.crc-4D (wmc617-wmc48) Test weight:<br />
QTwt.crc-1B (gwm374.1), QTwt.crc-1D (gdm126), QTwt.crc-2B (barc183),<br />
QTwt.crc-2D (gwm349-barc59),<br />
Notes: QHt.crc-4B linked to Rht-B1
CMap <strong>for</strong> integrating traits and molecular <strong>gene</strong>tic maps<br />
Map Set: RL4452*AC Domain SO 05/08 (RL4*AC Dom) [ View More Info ]<br />
Species: Wheat (Triticum aestivum) [ View More Info ]<br />
Map Type: Genetic (cM) [ View More Info ]<br />
Reference: McCartney et al (2005); F<strong>of</strong>ana et al (2008) Mapping quantitative trait loci<br />
controlling common bunt resistance in a doubled haploid population derived<br />
from the spring <strong>wheat</strong> cross RL4452 x AC Domain. Mol Breeding 21:317-325<br />
QTL:<br />
<strong>Plant</strong> height: QHt.crc-2D (BE497718-260), QHt.crc-4B (gwm513), QHt.crc-4D<br />
(wmc617-wmc48), QHt.crc-5B (wmc640), QHt.crc-7A (wmc139), QHt.crc-7B<br />
QYld.crc-2B (gwm257)<br />
(gwm333) Time to maturity: QMat.crc-3B (wmc231), QMat.crc-4A (Wx-B1),<br />
QMat.crc-4D-4D (wmc617-wmc48), QMat.crc-7D (gwm130) Lodging: QLd.crc-3D<br />
(gwm191), QLd.crc-4B (wmc826-wmc238), QLd.crc-4D (wmc617-wmc48) Grain<br />
yield: QYld.crc-2A (gwm339), QYld.crc-2B (gwm257), QYld.crc-3D (barc71),<br />
QYld.crc-4A (gwm397-wmc650), QYld.crc-4D (wmc617-wmc48) Test weight:<br />
QTwt.crc-1B (gwm374.1), QTwt.crc-1D (gdm126), QTwt.crc-2B (barc183),<br />
QTwt.crc-2D (gwm349-barc59),<br />
Trait designation lab designation chromosomes linked marker<br />
Notes: QHt.crc-4B linked to Rht-B1
CMap <strong>for</strong> integrating traits and molecular <strong>gene</strong>tic maps<br />
For <strong>wheat</strong> and barley CMap provides a basis <strong>for</strong> a more detailed<br />
description <strong>of</strong> traits (as QTL) linked to a large number <strong>of</strong><br />
molecular markers in <strong>gene</strong>tic maps.
Outline <strong>of</strong> presentation<br />
• <strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
• CMap <strong>for</strong> projecting trait in<strong>for</strong>mation onto <strong>gene</strong>tic<br />
maps and hence genome sequence<br />
• <strong>Plant</strong> <strong>Ontology</strong> based definition <strong>of</strong> traits that are<br />
projected onto molecular <strong>gene</strong>tic maps
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong> Consortium<br />
The value <strong>of</strong> trait descriptions in the <strong>Plant</strong> Onotology Consortium project<br />
is that they have a broad biological basis so that equivalent traits are<br />
identified across a wide range <strong>of</strong> species.<br />
Linked closely with GRAMENE<br />
For example the Zadok scale is widely used to describe stages in plant<br />
development and it has been incorporated into the BBCH scale.<br />
For example the BBCH scale provides the basis <strong>for</strong> describing equivalent<br />
stages in a range <strong>of</strong> other cereals
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong> Consortium<br />
BBCH scale illustration
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong><br />
Consortium<br />
Growth stages <strong>of</strong> mono-and dicotyledonous<br />
plants<br />
BBCH Monograph<br />
Second edition, 2001<br />
Edited by Uwe Meier<br />
Federal Biological Research Centre <strong>for</strong><br />
Agriculture and Forestry
47<br />
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong><br />
Consortium<br />
Growth stages <strong>of</strong> mono-and dicotyledonous<br />
plants<br />
BBCH Monograph<br />
Second edition, 2001<br />
Edited by Uwe Meier<br />
Federal Biological Research Centre <strong>for</strong><br />
Agriculture and Forestry
A stage <strong>of</strong> <strong>wheat</strong> that is <strong>of</strong> particular<br />
interest is early head development:<br />
Z39 = flag-leaf<br />
just visible<br />
Z43 = boot just<br />
visibly swollen<br />
• water deficit<br />
• frost tolerance<br />
(Ji et al 2010),
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong> Consortium
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong> Consortium
Defining the traits – booting stage <strong>of</strong> head development
Defining the traits – booting stage <strong>of</strong> head development
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong> Consortium
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong> Consortium
Defining the traits – <strong>Plant</strong> <strong>Ontology</strong> Consortium
Investigating trait ontologies to facilitate integrating phenotype and<br />
genome sequence level in<strong>for</strong>mation in <strong>wheat</strong><br />
• <strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong> <strong>symbols</strong> <strong>for</strong> <strong>wheat</strong><br />
• CMap <strong>for</strong> projecting trait in<strong>for</strong>mation onto <strong>gene</strong>tic maps<br />
and hence genome sequence<br />
• Defining the traits that are projected onto molecular<br />
<strong>gene</strong>tic maps<br />
PO numbers ( eg PO:0007018) <strong>for</strong> traits in the <strong>Catalogue</strong> <strong>of</strong> <strong>gene</strong><br />
<strong>symbols</strong> and CMap would facilitate the integration <strong>of</strong> biological<br />
in<strong>for</strong>mation <strong>for</strong> molecular analyses
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