Genetic and Genomic Resources in Genetic and Genomic Resources in MaizeMaize

Georgia DavisGeorgia Davis

Asst. ProfessorAsst. Professor

Div. Plant SciencesDiv. Plant Sciences

davisge@missouri.edudavisge@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