Lisa Harper, curator

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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
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Outline of Talk

• 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

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Outline of Talk

• 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

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Objectives for the next 5 years

• Objective 1 Integrate new maize genetic and
  genomic data into the database.
• a. Expand mutant and phenotype data and tools.
• b. Expand structural and genetic map sets.
• c. Provide access to gene models calculated by
• leading gene structure prediction groups
  through
• the MaizeGDB interface.
• d. 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.).

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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

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Outline of Talk

• 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

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Remember to SCROLL DOWN
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Keep scrolling.
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Where is lg1 on the genetic map?
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x
lg1
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x
lg1
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Here is a list of all the genetic maps that
contain lg1
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Making the Intermated B73 X MO17 mapping
population
Mo17
B73
X
Single F1 plant was selfed
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Grow up 200 plants, random mating
Genotype of 5 of those 200 plants
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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.
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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
B73 Mo17 Line1 Line2 Line3 Line4 Line5 Line6 Line7
Line8 Line9 Line10
EcoR1
PCR EcoR1
So, you genes code is MMBBMMBBMB
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Then, the MMPers figure out, with their
computers, where that matches in the genome.
So, you genes code is MMBBMM
Nope!
MMMMMB
Nope!
MBMBMM
MMBBMM
YEAH!
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IBM2 vs IBM2 neighbor map markers added
computationally
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Scroll Down For more Goodies!!
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Outline of Talk

• 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

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• You have found a new liguleless mutant. How do
  you find more mutants like yours?
• Look for liguleless phenotype (variation)
• Look for stocks

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Search Phenotypes
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Sometimes it goes wrong
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Try spelling out the name, or try a different
search criteria, Or go to the complete search page
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Outline of Talk

• 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

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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.
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List of experiments that evaluated the plant
height trait
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List of genetic maps that map ANY QTL
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Outline of Talk

• 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

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An Overview of How To Walk to a Gene

• Make a Mapping Population.
• 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.

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An Overview of How To Walk to a Gene

• Make a Mapping Population.

xyz(B73) xyz(B73)
(Mo17) (Mo17)
x
(Introgressed into B73)
Mapping population B73 alleles with the xyz gene
Aim to get 500-1000 progeny in you mapping
population
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An Overview of How To Walk to a Gene

• Make a Mapping Population.

(Mo17) xyz(W23)
xyz(B73) xyz(W23)
and
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Aim to get 500-1000 progeny in you mapping
population
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An Overview of How To Walk to a Gene

• Make a Mapping Population.
• Map your mutant to a bin.
• -Bulk segregant analysis or standard mapping

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SSR simple sequence repeat (length polymorphism)
PCR Primer
(CA)
(CA)
n
m
variation between strains in number of repeats
at a given locus
PCR yields products of different size

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An Overview of How To Walk to a Gene

• Make a Mapping Population.
• Map your mutant to a bin.
• -Bulk segregant analysis or standard mapping

Lets say your mutant mapped to bin 3.04
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An Overview of How To Walk to a Gene

• Make a Mapping Population.
• 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.

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An Overview of How To Walk to a Gene

• Make a Mapping Population.
• 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
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An Overview of How To Walk to a Gene

• Make a Mapping Population.
• 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
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An Overview of How To Walk to a Gene

• Make a Mapping Population.
• 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.

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Outline of Talk

• 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

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Genetic vs Cytolgical MAPs
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Outline of Talk

• 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!!