Transcript Lisa Harper, curator Carolyn Lawrence, PI Trent Seigfried, bioinformatics engineer

maizegbd.org
Lisa Harper, curator
USDA ARS PGEC, Albany and University of California, Berkeley, CA
Carolyn Lawrence, PI
Trent Seigfried, bioinformatics engineer
Darwin Campbell, database administrator
Taner Sen, computational biologist
USDA ARS and Iowa State University, Ames, Iowa
Mary (Polacco) Schaeffer, curator
USDA ARS and University of Missouri, Columbia, MO
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
Objectives for the next 5 years
•Objective 1: Integrate new maize genetic and genomic data into
the database.
a.
b.
c.
d.
Expand mutant and phenotype data and tools.
Expand structural and genetic map sets.
Provide access to gene models calculated by
leading gene structure prediction groups through
the MaizeGDB interface.
Compile and make accessible at MaizeGDB the
annual Maize Newsletter.
•Objective 2: Provide community support services (e.g.,
coordinating Maize Meeting, MGEC Elections, Polls, etc.).
Outside our Scope
•Project data from “stand alone” studies are not well integrated
•Literature is not systematically curated
•Experimental data on development and on plant structure and growth are not
current
•Community curation is uneven and requires professional closure of gaps
•Plant Ontology or PO annotation is limited to genes in MaizeGDB that have
mutant phenotypes
•Metabolic pathway curation and representation are poor and/or altogether
absent
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
Remember to SCROLL DOWN
Remember to SCROLL DOWN
Keep scrolling….
Remember to
SCROLL DOWN
Where is lg1 on the genetic map?
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lg1
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lg1
Here is a list of all the genetic maps that contain lg1
Why the Huge difference??
Why the Huge difference??
Making the Intermated B73 X MO17 mapping population
Mo17
B73
X
Single F1
plant was
selfed
X
Grow up 200 plants,
random mating
Genotype of 5 of those 200 plants
Select 100 ears, pick 5 kernals from each ear. Put in a
bag, shake, plant, more random matings (2nd generation).
Repeat, repeat. Intermating was done 4 times.
From these lines, generate Recombinant Inbred lines by repeated selfing (5x or more)
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There are 288 lines in the IBM population. To make the map, MMP project
researchers mapped thousands of markers. They use primers that amplify a
different length fragment in Mo17 vs B73.
B73
Mo17
PCR + EcoR1
B73
Mo17
Line1
Line2
Line3
Line4
Line5
Line6
Line7
Line8
Line9
Line10
EcoR1
So, you gene’s ‘code’ is: MMBBMMBBMB…
Then, the MMPers figure out, with their computers, where
that matches in the genome.
So, you gene’s ‘code’ is: MMBBMM …
Line 1
Line 2
Line 3
MMMMMB
Nope!
MBMBMM
Nope!
MMBBMM
YEAH!
Line 4
Line 5
Line 6
IBM2 vs IBM2 neighbor map: markers added computationally
Scroll Down
For more
Goodies!!
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
You have found a new liguleless mutant. How
do you find more mutants like yours?
1. Look for “liguleless” phenotype (variation)
2. Look for stocks
Search Phenotypes
Genes which when mutated have
liguleless phentoype
Liguleless alleles
Stocks
Sometimes it goes wrong…
Try spelling out the name, or try a different search criteria,
Or go to the complete search page
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
QTLs, or Quantitative Trait Loci, are loci that contribute a
measurable phenotypic effect to a particular trait.
Plant height is a trait, and there are many QTLs that
contribute to this trait.
QTLs can be genetically mapped to a region. In MaizeGDB
they are all on the “bins map”. Some are on other maps.
They are not on the IBM or other high resolution map.
Scroll Down
Scroll Down
QTL loci start with a q (usually)
Scroll Down…
List of experiments that evaluated the
plant height trait
List of genetic maps that map ANY QTL
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
2. Map your mutant to a bin.
-Bulk segregant analysis or standard mapping
3. Use MaizeGDB to find markers in that bin that are likely to
work with the inbreds in your mapping population.
4. Use the markers to do fine structure mapping (using the
same mapping populations) then relate your genetic
position to the BAC map (currently requires other
databases).
5. Once you are down to a reasonable number of genes on
one-three BACs, use RT-PCR or sequence to find
differences in wt vs. mutant.
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
xyz(B73) x + (Mo17)
xyz(B73)
+ (Mo17)
(Introgressed into B73)
+ (Mo17) x xyz(W23)
xyz(B73)
xyz(W23)
Mapping population: B73 alleles with the xyz gene
Aim to get 500-1000 progeny in you mapping population
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
+ (Mo17) x xyz(W23)
xyz(B73)
xyz(W23)
+ (Mo17) and xyz(B73)
xyz(W23)
xyz(W23)
1:1
Aim to get 500-1000 progeny in you mapping population
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
2. Map your mutant to a bin.
-Bulk segregant analysis or standard mapping
SSR: simple sequence repeat
(length polymorphism)
PCR Primer
(CA)n
(CA)m
variation between strains in number of repeats
at a given locus
PCR yields products of different size:
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
2. Map your mutant to a bin.
-Bulk segregant analysis or standard mapping
Lets say your mutant mapped to bin 3.04
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
2. Map your mutant to a bin.
-Bulk segregant analysis or standard mapping
3. Use MaizeGDB to find markers in that bin that are likely to
work with the inbreds in your mapping population.
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
2. Map your mutant to a bin.
-Bulk segregant analysis or standard mapping
3. Use MaizeGDB to find markers in that bin that are likely to
work with the inbreds in your mapping population.
Heres another way to get to close SSRs
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
2. Map your mutant to a bin.
-Bulk segregant analysis or standard mapping
3. Use MaizeGDB to find markers in that bin that are likely to
work with the inbreds in your mapping population.
4. Use the markers to do fine structure mapping (using the
same mapping populations) then relate your genetic
position to the BAC map (currently requires other
databases).
Lets say that your mutant is between two markers:
umc1504 and PCO068796
(genetically right next too each other).
Go to MaizeSequence.org to find the BAC sequences
An Overview of How To Walk to a Gene
1. Make a Mapping Population.
2. Map your mutant to a bin.
-Bulk segregant analysis or standard mapping
3. Use MaizeGDB to find markers in that bin that are likely to
work with the inbreds in your mapping population.
4. Use the markers to do fine structure mapping (using the
same mapping populations) then relate your genetic
position to the BAC map (currently requires other
databases).
5. Once you are down to a reasonable number of genes on
one-three BACs, use RT-PCR or sequence to find
differences in wt vs. mutant.
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
Genetic vs Cytolgical MAPs
Outline of Talk
1.
2.
3.
4.
5.
6.
7.
Brief Introduction
General Features from the MaizeGDB homepage
Usage example: Finding more mutants like yours
Usage example: Finding QTLs
Usage example: Walking to genes
Usage example: Cytological to Genetic Distance
Open Discussion
Thank You!!