Mapping - phenotypic
        Relative position of two genes on the chromosome is reflected by the frequency of 
                        recombination between two mutants.
        m1m1 x m2m2 -> in F1  a m1m2 progeny is a recombinant phenotype
                                        a m1wt, and wt m2 is a parental phenotype
                -if markers are unlinked (separate chromosomes)- all progeny are recombinant
                -if markers are on the same chromosome,

                    the closer genes m1 and m2 are, the fewer recombinants since they require

                    crossing over- recombination between chromosomes  

        Phenotypic mapping
                        - the only marker of the gene is the phenotype
                        -the polymorphism that allows distinction between parents at 
                                one locus is the mutant or wt phenotype
example- Arabidopsis classical genetic map (zoom in on an area of a chromosome to see details)

Mapping- molecular markers
        -polymorphism’s based upon DNA sequence rather than phenotype

        RFLP- Restriction length polymorphisms
                -restriction site mapping of a region of DNA provides a marker of that 
                        region
                -the polymorphism that allows distinction of that region being from 
                        one parent or the other is the difference in restriction map
                -a region is defined by the cloned DNA probe, not necessarily a gene
                -provides a DNA handle on the location
                

        PCR-based- allows use of small amounts of DNA
                RAPDS- Random Amplification of Polymorphic DNA
                        -a randomly-chosen primer that amplifies a certain size of DNA 
                                defines one locus
                        -polymorphisms in DNA sequence determine size and presence 
                                of amplified DNA
                        -AFLP a variant- anchored at restriction sites
                CAPS- Cleaved Amplified Polymorphic Sequence
                        -amplify random sequence, then look at restriction digest of that amplified 
                                fragment for polymorphisms
			-examples from Arabidopsis
			-can develop new ones from sequencing data- Single Nucleotide polymorphism
                              such as that for Arabidopsis			

        	SSLP- Small Sequence Length Polymorphisms
                	-uses dinucleotide repeats in genome
                	-polymorphisms are on the variation in small sequence repeats located 
                        around genome
   			example from maize- slow loading




	Combined genetic map- example from Arabidopsis(zoom in on an area of a chromosome to see details)

 Map-based Cloning
        Use molecular markers to connect a phenotype with a physical location on 
                the genome
                1) Find a molecular marker that maps close to your phenotypic marker 
                        (represents the gene you want to clone)- provides link- genetic 
                        and physical marker
                2) Walk along the chromosome towards gene
                3) Find gene when you can transform that DNA into the mutant plant 
                        and produce a wild-type phenotype.

	

Physical Maps
        -YAC or BAC libraries of genomic DNA with overlaps and contigs identifed 
                -ordering of clones- walking by cross hybridization(hard),
			 restriction enzyme fingerprinting (quicker)
              		
                -example- Arabidopsis physical map (zoom in on an area of a chromosome to see details)
  -easy to go from map position to YAC clone to gene	
		See example in class Jirage et al 1999 PNAS 23: 13583

Links:
Exercise in Phenotypic Mapping MIT Hypertext
Mapping and Sequencing the Human Genome
List of Genome Mapping Projects for Arabidopsis
List of Genes found from Sequencing Chromosome V of Arabidopsis
Arabidopsis Resources- maps, genes from a number of databases
Maize genome database
Listing and links of genes cloned in Snapdragon
Mapping and discussion of markers- PLSC431 NDSU
Mapping with molecular markers- PLSC731 NDSU
Analysis of plant genomes with molecular markers- PLSC731 NDSU
Map-based cloning-PLSC731 NDSU
AFLP markers- another molecular marker soewhere inbetween RAPD and RFLP

Last revised: Feb 4, 1999- Straney