PORCINE (CT)(N) SEQUENCES - STRUCTURE AND ASSOCIATION WITH DISPERSED AND TANDEM REPEATS

Loci containing (GT)(n) repeats were isolated from three different pla smid libraries with inserts of porcine genomic DNA between 140 and 200 , 200 and 300, and 350 and 400 bp. Sequencing showed that the average repeat length and the fraction of perfect repeats were increased in th e libraries containing longer inserts (greater than or equal to 200 bp ). The polymorphism of (GT)(n) loci containing at least 10 repeat unit s was analyzed using the polymerase chain reaction and an automated DN A sequencer. Nearly all tested loci are polymorphic and can therefore be used as marker loci for gene mapping and for other applications. Th e (GT)(n) loci were categorized into three classes: (1) loci containin g the (GT)(n) repeats associated with a SINE element, (2) loci contain ing the (GT)(n) repeats associated with one or more other simple repea ts, and (3) loci containing (GT)(n) as the only detected repetitive el ement. At most loci of the first class, the (GT)(n) repeat was in a fi xed configuration adjacent to the 3' end of the SINE. The findings sup port the notion of clustering of different repeat types in the mammali an genome. (C) 1994 Academic Press, Inc.