Advanced Intercross Lines

The first step in the identification of a gene that causes genetic variation in a phenotype, without any prior hypothesis, consists of mapping the gene to a defined chromosomal location and searching the databases for appropriate candidate genes. Often, standard mapping procedures lack the necessary mapping resolution to limit the number of candidates. Advanced intercross lines (AILs) are an experimental population designed to increase the actual recombination proportion across the genome, providing higher mapping resolution. The higher proportion of recombination in an AIL is achieved by a series of intercrosses carried out over successive generations in a single population. With the higher rate of recombination, only markers closely linked to the gene of interest will still exhibit linkage, allowing a more precise location of the gene. With AIL only generations used for mapping are genotyped and phenotyped, but intervening generations are not. Nevertheless, producing an AIL is quite laborious but efficient when a large number of traits are analyzed. Alternatively, variations to the AIL design can be used so that the built resource can be maintained for future use as a set of recombinant inbred strains.