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Genetic and Genomic Resources in Genetic and Genomic Resources in MaizeMaize
Georgia DavisGeorgia Davis
Asst. ProfessorAsst. Professor
Div. Plant SciencesDiv. Plant Sciences
[email protected]@missouri.edu
Overview
Genetic map
Physical map
Anchoring via Molecular Markers
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.
Structural Genomics
Science related to Science related to discovery of gene discovery of gene order and order and organization on a organization on a chromosome.chromosome. Genetic mappingGenetic mapping Physical mappingPhysical mapping In situIn situ hybridization hybridization
Functional Genomics
Science related to the discovery and Science related to the discovery and definition of the function of genesdefinition of the function of genes
Whole plant Cellular Biochemical RNA
C16
C18
C20
C22
C24
C26
Aldehydes Alcohols
Wax Esters
The Maize Genome in Perspective
Maize 2500 MBHuman 2500 MBSoybean 1500 MBSorghum 900 MBTomato 950 MBRice 450 MBBacteria 5 MB
How maize compares to other species in size
Human equalSoybean 1.7XSorghum 2.7XTomato 2.6XRice 5.5XBacteria 500X
Maize Genetic Resources
zb7
d10
gl2
al1
kn1
Maize Genetic Resources
orp1
mn1
tu1
a1 su1 y1 pr1 sh1 wx1
b1 pl1 vp1 te1
Maize Genetic Resources
1685 mutants with images in MDB
>5000 mutants available
>10,000 alleles in MDB
www.maizegdb.orgwww.maizegdb.org
Maize Genetic Resources
49 QTL experiments in MDB
59 genetic maps in MDB
7850 mapped loci in MDB
Mapping Maize at UMC
Genetic mapping Genetic mapping is based on DNA fingerprint is based on DNA fingerprint data of offspring from two parents which differ data of offspring from two parents which differ in their appearance. in their appearance. Similar fingerprint data for two gene indicates they Similar fingerprint data for two gene indicates they
are physically close together on a chromosome. 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.
Molecular mapping
Digest DNA
Electrophorese
-
+
Southern
blot
Hybridizewith probe
Scoring data
A B H H A B A H
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.
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
BHBBAHBHHBHHBHB umc157HHBBABBHHBBBBAB umc76BHBBABHAHHBHBAB asg45BHBBABBAHHBHBAB zb4BHBBHBHAHHBHBAB csu3
How Maximum Likelihood Works
BHBBAHBHHBHHBHB umc157BHBBABHAHHBHBAB asg45HHBBABBHHBBBBAB umc76BHBBABBAHHBHBAB zb4BHBBHBHAHHBHBAB csu3
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.
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”
EST Mapping: Utility
Efficient Markers for Maize
Simple 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
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.
SSR Mapping
C A T G
Trait Mapping
Links phenotypes to genetic locations
Precursor to linking phenotypes to genes
Provides tools for functional analysis of gene expression
Aspergillus flavus
Infection via silk channel wounds in kernels cracks in kernels
Aflatoxin
Aflatoxin B1
Potent carcinogen.Associated with liver cancer
in humans.
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 fingerprintGene 1
Mp3
13E
Va3
5
1 2 3 4 5 6
Lo Hi Int. Lo LoHi Int. Int.
Lo Hi Int. Lo LoHi Int. Int.
Gene 2
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 mappingPhysical mapping is a laboratory based is a laboratory based approach and involves identifying small approach and involves identifying small overlapping DNA fragment to reconstruct overlapping DNA fragment to reconstruct whole maize chromosomes.whole maize chromosomes.
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.
Maize HindIII BAC library
Made at CUGIAverage insert size
is 135 kb.Total coverage is
14X.Fingerprinting and
anchoring of 5X underway.
Physical Map
Constructed in the laboratory by assembling overlapping DNAfragments. Each fragment can be easily retrieved for experiments
which can localize genes of interest.
DNA fragments cloned into Bacterial Artificial
Chromosomes (BACs)
Chromosome 1
Integrating the Genetic and Physical Maps Integrating the Genetic and Physical Maps to Form a Single Mapto 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
Maize Physical Mapping
Whole-genome characterization of HindIII in progress.
Anchor with AFLPs and low copy RFLPs
Considerations: Repetitive elements
Syntenic duplicated regionsB73 Maize BAC library probedB73 Maize BAC library probedby asg20 single copy cloneby asg20 single copy clone
Maize Physical Mapping
CentA-LTR sequenceCentA-LTR sequence bnl6.16 - Single copy RFLPbnl6.16 - Single copy RFLP
Integrated Genetic and Physical Map
Plant Height
Disease Resistance
Kernel Color
Tassel Branching
Drought Resistance
Unknown Function(EST)
Chromosome 1
Genetic Physical
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.
Maize Synteny With Close RelativesThe Missouri Maize Project is working to characterize
maize-sorghum-rice synteny. This will allow desirable planttraits to be transferred across species.
SorghumMaize Rice
Informatics Tasks What good is the data if you
can’t access it?
Project data curation
Community curation via MaizeDB
Dissemination from MaizeDB
Excel SpreadsheetsExcel Spreadsheets
Project Data CurationProject Data Curation
LabDBLabDB
MaizeDBMaizeDB
ScriptsScripts
ScriptsScripts
What do we use the tools for?
Identifying genes for important agronomic traits.
Insect resistance
Disease resistance
Drought tolerance
Cold/heat tolerance
Grain quality