On the efficiency of marker-assisted introgression

The efficiency of marker-assisted introgression programmes, expressed as ge netic lag relative to a commercial population under continuous selection, w as investigated using analytical methods. A genetic model was assumed for w hich the genetic variance in the introgression population was a function of the within-breed genetic variance and the initial breed difference. It was found that most of the genetic lag occurs in the latter stages of an intro gression programme, when males and females which are heterozygous for the a llele to be introgressed are mated to produce homozygous individuals. Reduc ing genetic lag through selection on genomic proportion by using genetic ma rkers throughout the genome, i.e. by selecting heterozygous individuals whi ch resemble the recipient (commercial) population most, was effective if th e initial breed difference was very large (e.g. 20 within-breed phenotypic standard deviations). In that case, selection solely on genetic markers cou ld be practised to speed up genome recovery of the commercial line. If the initial breed difference is small, phenotypic or best linear unbiased predi ction (BLUP) selection is superior in reducing genetic lag under the assume d genetic model.