quantitative trait mapping

Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C & Mott R 2009 A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5:e1000551.

• synthetic populations include F2, backcrosses, recombinant inbred lines and advanced intercross lines, all created from a cross between two accessions that differ for the trait of interest
• their two advantages are that the power to detect a QTL segregating in a two-allele system is high, and that synthetic populations usually have no population substructure

• the main disadvantage is poor mapping resolution
• QTL identified using these designs typically have confidence intervals of 5 to 20 cM

• the use of heterogeneous stocks improves the power to detect and localise QTL
• a disadvantage is that each individual's genome is unique and heterozygous
• the population must be genotyped at high density each time it is phenotyped

• a related strategy, that avoids the need to re-genotype, is to generate RILs from multiple parents
• MAGIC (for multiparent advanced generation intercross)
• an intermediate niche between naturally occurring accessions and existing synthetic populations

• an advanced intercross of Arabidopsis thaliana produced by intermating 19 natural accessions for four generations and then inbreeding for 6 generations