Detection of quantitative trait loci for carcass traits in the pig by using AFLP

For evaluation of the suitability of Amplified Fragment Length Polymorphism (AFLP) for detection of quantitative trait loci in farm animals, a combination of AFLP and selective genotyping has been applied as a rapid screening method for marker–QTL associations. Focusing on loci affecting eye muscle area, six extreme discordant sib pairs were selected from a Duroc × Berlin Miniature Pig F₂ experimental cross and examined by using 48 AFLP primer combinations. Two prominent AFLP markers were converted into simple codominant PCR markers (STS-Bo1 and STS-Bo3) and assigned to Sscr4 by physical and linkage mapping. Single marker analysis indicated association of the STS markers with a putative QTL influencing eye muscle area. Interval mapping confirmed the presence of a significant QTL for eye muscle area (P_genomewide < 0.01) on the Sscr4, with STS-Bo1 being the closer marker. At the same location, significant effects (P_genomewide < 0.01) on carcass length and backfat thickness were also detected. Our results demonstrate the capability of the combination of AFLP analysis and selective genotyping as a method for detection of genome regions containing QTL in livestock.