maizegbd.

org
Lisa Harper, curator
USDA ARS PGEC, Albany and University of California, Berkeley, CA

Carolyn Lawrence, PI
Darwin Campbell, database administrator
Taner Sen, computational biologist
Carson Andorf, computer scientist
USDA ARS and Iowa State University, Ames, Iowa

Mary (Polacco) Schaeffer, curator

USDA ARS and University of Missouri, Columbia, MO
 Outline of Talk
1. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position
 Our Mission
•Integrate new maize genetic and genomic data into the
database.
-Expand mutant and phenotype data and tools.
-Expand structural and genetic maps.
-Soon!! Provide a Genome Browser and access to gene models.
-Compile and make accessible at MaizeGDB the annual Maize
Newsletter.

•Provide community support services (e.g., coordinating

Maize Meeting, MGEC Elections, Polls, etc.).
 Coming Soon
•POPCORN:
•A Portal through which you can blast all sources of Maize
sequences at once.
•A Mechanism for Data from ANY project to migrate to
MaizeGDB.
•Community Gene Annotation (complete with “motivation”).
•Beefed up Phenotype Tools, Plant Ontology and PO
annotation.
•Some automated literature mining.
 Coming Soon: MaizeGDB
Genome Browser

*BAC info with links to appropriate MaizeGDB pages

*FPC contigs clearly showing gaps
*Marker data with links to MaizeGD
*Sequence track that shows bases
*Various Gene models will be available as separate tracks
 Outline of Talk
1. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position
Remember to SCROLL DOWN
Remember to SCROLL DOWN
Keep scrolling….
Scroll Down
For more
Goodies!!
 Outline of Talk
1. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position
Remember to
SCROLL DOWN
“Advanced” Searches
Where is lg1 on the genetic map?
x lg1
x lg1
Here is a list of all the genetic maps that contain lg1
Why the Huge difference??
Making the Intermated B73 X MO17 mapping population
B73 Mo17

Single F1
plant was
selfed
 X
Grow up 200 plants,
random mating

Genotype of 5 of those 200 plants

Intermate these F2s, and you “accumulate recombinations”
 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)

x x x x x x
x x x x x x
x x x x x x
x x x x x x
x x x x x x
These plants where used for the
“Intermated B73 Mo17 genetic map
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

EcoR1
PCR + EcoR1

Line10
Mo17
Line1
Line2
Line3
Line4
Line5
Line6
Line7
Line8
Line9
B73

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 Line 4 Line 5 Line 6

MMMMMB Nope!

MBMBMM Nope!

MMBBMM YEAH!
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
Any Questions about Searching for Data
In MaizeGDB?
 Outline of Talk
1. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position
 Outline of Talk
1. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position
 Walking to a Gene for non-geneticists

What is it? A way to identify the sequence of a gene of interest

using genetic and sequence information

Why would you do it? If you have a cool mutant that you
know is heritable and non-allelic to other (cloned) mutants,
you would want to know the sequence of the gene in order to
understand more about the normal function of the gene.

How do you walk? Genetically map your mutation, and

Progressively narrow the region in which the gene is located,
until you are down to sequence.
 Walking to gene is just high resolution
genetic mapping
Left

Genetic map
mutant
 Walking to gene is just high resolution
genetic mapping Right
Left

Genetic map
mutant
 Walking to gene is just high resolution
genetic mapping Right
Left

Genetic map
mutant
 Walking to gene is just high resolution
genetic mappingRight
Left

Genetic map
mutant
 Walking to gene is just high resolution
genetic mappingRight
Left

Genetic map
mutant
 Walking to gene is just high resolution
genetic mapping
Left Right

Genetic map
mutant
 Walking to gene is just high resolution
genetic mapping
Left Right

Genetic map
mutant
 Walking to gene is just high resolution
genetic mapping
Left Right

Genetic map
PCO068796
umc1504 mutant

Sequence umc1504
PCO068796
 An Overview of How To Walk to a Gene
1. Make a Mapping Population (500-1000 progeny).
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) 1:1

xyz(W23) xyz(W23)
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. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position
 Outline of Talk
1. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position
Genetic vs Cytolgical MAPs
 Outline of Talk
1. Brief Introduction- What’s available?
2. General Features from the MaizeGDB homepage
3. Searching the Database
4. Community Curation
5. Usage Example: Walking to genes
6. Case Study: Find SSRs close to mac1
7. Finding QTLs
8. Finding cytological position from genetic position

Open Discussion
THANK YOU!!