Mapping and Mapping Populations

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Mapping and Mapping Populations

Transcript Of Mapping and Mapping Populations

Mapping and Mapping Populations

Types of mapping populations
• F2 o Two F1 individuals are intermated
• Backcross o Cross of a recurrent parent to a F1
• Recombinant Inbred Lines (RILs; F2-derived lines) o Developed by single seed descent through multiple generations of selfing

Homozygosity of Recombinant Inbred Lines

RI Population

% within-line homozygosity at

Degree of Inbreeding

each locus













Value of Recombinant Inbred Populations
• Eternal population • Phenotypic data can be collected from replicated trials to ensure
accuracy • Large field trials can be performed for major production traits • Only problem
o Dominance and epistasis cannot be measured because no heterozygotes are available

Segregation Ratios for Mapping Populations

Population F2 Backcross Recombinant inbred

Codominant marker 1:2:1 1:1 1:1

Dominant marker 3:1 1:1* 1:1

* To score a dominant marker in a backcross population, you must cross the recessive parent with the F1 plant. Therefore to score a dominant marker (such as a RAPD), you would need to create two populations, each one developed by backcrossing to one of the two parents. For this reason, backcross populations have not been used for mapping dominant markers.

One of the first molecular mapping papers (Bernatzky and Tanksley. 1986. Genetics 112:887)

One of the first molecular marker maps for plants (tomato). (Bernatzky and Tanksley. 1986. Genetics 112:887)
A first plant molecular marker map • cDNA map of tomato • Notice the limited number of markers • Isozyme markers also included

Arabidopsis RAPD map (Reiter et al. 1992. Proc. Natl. Acad. Sci., USA 89:1477) Segregating population gel
Examples • (A and B) Two dominant loci segregating • (C) One dominant locus segregating

Linkage map
• First “dense” RAPD map o Developed by DuPont Compant  Developers of RAPD concept and the RAPD map

Mapping Efficiencies of Different Mapping Populations

Other Mapping Populations
Association Mapping (AM) Population
Limits of traditional bi-parental populations
• Limited number of recombination events o F2 population  One round of recombination o Recombinant inbred population  Two rounds of recombination
• Allele richness of F2 and RI populations o Poor  Only alleles of parents sampled • Limits discovery of all factors controlling a quantitative trait in a species
• But the advance of F2/RI populations o With limited recombination
 Fewer markers needed to discover relevant genetic

What is an association mapping (AM) population?
• Collection of genotypes from any level of organization from a species o Represent the genetic background for which you want to make inferences  Wild lines, landraces, market classes, released varieties, breeding lines  Population often referred to as a diversity panel
• Arabidopsis o Collection of wild samples from throughout the world  25 lines, four populations each • PLoS Biology (2005) 3:e196
• Maize o 92 inbred lines  12 stiff stalk, 45 non-stiff stalk, 35 tropical + semitropical • Nature Genetics (2001) 28:286
• Major benefit of AM o Samples many more recombination events than other populations  Greater resolution than F2 or RI populations
• Resolution depends upon the linkage disequilibrium in the population o But the disadvantage is  You need many markers to find meaningful associations
• Population size used today for plant AM experiments o 200-300 to 400-500 lines