Overview

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Genetic and Genomic Resources in Maize Georgia
Davis Asst. Professor Div. Plant
Sciences davisge_at_missouri.edu
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Overview
Genetic map
Anchoring via Molecular Markers
Physical map
INFORMATICS
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What is Genomics? Genomics science that combines
genetics, high through-put robotics and
bioinformatics to derive large amounts of high
quality biological information that will allow a
greater understanding of the organism being
studied.
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Structural Genomics

• Science related to discovery of gene order and
  organization on a chromosome.
• Genetic mapping
• Physical mapping
• In situ hybridization

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Functional Genomics

• Science related to the discovery and definition
  of the function of genes

C16
C18
C20
C22
C24
C26
Aldehydes
Alcohols
Wax Esters
RNA
Whole plant
Cellular
Biochemical
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The Maize Genome in Perspective

• Maize 2500 MB
• Human 2500 MB
• Soybean 1500 MB
• Sorghum 900 MB
• Tomato 950 MB
• Rice 450 MB
• Bacteria 5 MB

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How maize compares to other species in size

• Human equal
• Soybean 1.7X
• Sorghum 2.7X
• Tomato 2.6X
• Rice 5.5X
• Bacteria 500X

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Maize Genetic Resources
al1
d10
gl2
zb7
kn1
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Maize Genetic Resources
mn1
vp1
b1 pl1
te1
tu1
a1 su1 y1 pr1 sh1 wx1
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Maize Genetic Resources

• 1685 mutants with images in MDB
• gt5000 mutants available
• gt10,000 alleles in MDB

www.maizegdb.org
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Maize Genetic Resources

• 49 QTL experiments in MDB
• 59 genetic maps in MDB
• 7850 mapped loci in MDB

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Mapping Maize at UMC

• Genetic mapping is based on DNA fingerprint data
  of offspring from two parents which differ in
  their appearance.
• Similar fingerprint data for two gene indicates
  they are physically close together on a
  chromosome.
• Physical mapping is a laboratory based approach
  and involves identifying small overlapping DNA
  fragment to reconstruct whole maize chromosomes.

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Molecular mapping
Digest DNA
Electrophorese
Hybridize with probe
-
Southern
blot

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Scoring data
A B H H A B A H
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Recombination and Mapping

• Assume that the frequency of crossing-over is
  equal along the chromosome.
• Two genes that are very close to one another
  will have a lower likelihood of having a
  cross-over between them than two genes that are
  very far apart.

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Recombination and Mapping

• So, we can determine the relative distance
  between genes by counting the number of
  recombinant genotypes for each pair of genes.
• Lots of recombinants far apart
• Few recombinants close together

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How Maximum Likelihood Works

• BHBBAHBHHBHHBHB umc157
• HHBBABBHHBBBBAB umc76
• BHBBABHAHHBHBAB asg45
• BHBBABBAHHBHBAB zb4
• BHBBHBHAHHBHBAB csu3

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• BHBBAHBHHBHHBHB umc157
• BHBBABHAHHBHBAB asg45
• HHBBABBHHBBBBAB umc76
• BHBBABBAHHBHBAB zb4
• BHBBHBHAHHBHBAB csu3

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ESTs Defined

• EST is an acronym for Expressed Sequenced Tags.
• cDNAs with map locations.
• ESTs represent the genes active in a particular
  tissue at specific stage of development.
• The cellular function of an EST can often be
  derived by comparison to sequence databases.

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EST Mapping Utility

• ESTs are important markers for physical mapping.
• EST mapping, coupled with trait mapping, will
  help link genes to phenotypes.
• ESTs are the basic building blocks for high
  density gene chips

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Efficient Markers for MaizeSimple Sequence
Repeats(SSRs)

• Develop SSR markers
• Map SSRs genetically
• Use SSRs to anchor physical map to genetic map
• Use SSRs to map QTLs more efficiently

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SSRs What and how?

• Dinucleotide and trinucleotide repeats. ex.
  CACACACACA
• Different corn lines have different numbers of
  repeats. (CA)10, (CA)14
• These differences can be seen on a high
  resolution agarose gel.
• Can be used for mapping.

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SSR Mapping
C A T G
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Trait Mapping

• Links phenotypes to genetic locations
• Precursor to linking phenotypes to genes
• Provides tools for functional analysis of gene
  expression

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Aspergillus flavus
Infection via silk channel wounds in
kernels cracks in kernels
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Aflatoxin
Aflatoxin B1

• Potent carcinogen.
• Associated with liver cancer
• in humans.

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Molecular mapping

• Compare the DNA fingerprint with grain toxin
  levels
• Look for bands on fingerprint associated with
  high toxin and those associated with low toxin

DNA fingerprint
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Mapping Maize at UMC

• Genetic mapping is based on DNA fingerprint data
  of offspring from two parents which differ in
  their appearance.
• Similar fingerprint data for two gene indicates
  they are physically close together on a
  chromosome.
• Physical mapping is a laboratory based approach
  and involves identifying small overlapping DNA
  fragment to reconstruct whole maize chromosomes.

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Mapping Maize at UMCPhysical Mapping

• Large fragments are cloned into Bacterial
  Artificial Chromosomes (BACs).
• DNA fragments can easily be retrieved for gene
  hunting experiments.
• A complete physical map is needed before DNA
  sequencing of the chromosomes can begin.

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Maize HindIII BAC library

• Made at CUGI
• Average insert size is 135 kb.
• Total coverage is 14X.
• Fingerprinting and anchoring of 5X underway.

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Physical Map
Constructed in the laboratory by assembling
overlapping DNA fragments. Each fragment can be
easily retrieved for experiments which can
localize genes of interest.
DNA fragments cloned into Bacterial Artificial
Chromosomes (BACs)
Chromosome 1
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Integrating the Genetic and Physical Maps to Form
a Single Map

• Molecular markers serve as anchor points for the
  two maps since they can be mapped both
  genetically and physically
• Types of Molecular Markers
• RFLPs
• Simple Sequence Repeats (SSRs)
• Expressed Sequence Tags (ESTs)
• Markers from other species

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Maize Physical Mapping

• Whole-genome characterization of HindIII in
  progress.
• Anchor with AFLPs and low copy RFLPs
• Considerations
• Repetitive elements
• Syntenic duplicated regions

B73 Maize BAC library probed by asg20 single copy
clone
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Maize Physical Mapping
CentA-LTR sequence
bnl6.16 - Single copy RFLP
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Integrated Genetic and Physical Map
Genetic
Physical
Plant Height
Disease Resistance
Kernel Color
Tassel Branching
Drought Resistance
Unknown Function (EST)
Chromosome 1
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Synteny in Crop Plants

• The order of genes along chromosomes is conserved
  in many crop plants.
• Maize-Sorghum-Rice
• Tomato-Pepper-Potato
• This is known as synteny and occurs in animals as
  well.
• Mouse-Rat-Humans
• The Missouri Maize Project is working to
  characterize maize-sorghum synteny.

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Maize Synteny With Close Relatives
The Missouri Maize Project is working to
characterize maize-sorghum-rice synteny. This
will allow desirable plant traits to be
transferred across species.
Sorghum
Maize
Rice
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Informatics Tasks What good is the data if you
cant access it?

• Project data curation
• Community curation via MaizeDB
• Dissemination from MaizeDB

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Project Data Curation
Excel Spreadsheets


Scripts
LabDB
Scripts
MaizeDB
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What do we use the tools for?

• Identifying genes for important agronomic traits.
• Insect resistance
• Disease resistance
• Drought tolerance
• Cold/heat tolerance
• Grain quality