The approach of scanning the entire genome of animals with evenly spaced, highly informative, genetically linked single-locus markers in a segregating population to identify segments of the genome associated with differences in phenotypes has been successful in localizing genes that cause genetic defects (especially in humans). This approach has identified locations in the genome that affect quantitative traits (traits such as growth rate or body composition; quantitative trait loci, QTL). However, determining the causal gene and DNA variation for these phenotypic differences is much more difficult. Results of a genome scan are used to identify genes located in the region whose function is necessary for the phenotype being studied (positional candidate gene). Positional candidate genes are evaluated for variation in DNA sequence that causes the observed effect on performance. If the positional candidate gene approach does not yield the causative variation, then potentially, the entire region of the genome is sequenced and the sequence data are evaluated for putative causative variation. After the causative variation is identified, the function of the variation as well as any pleiotropic effects that the gene may possess can be determined.
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