Blood and tissue samples were collected from 105 goats including 60 Boer goats (30 for eachsex), 30 Xuhuai goats (15 for each sex) and 15 Haimen goats (7 stud and 8 does). DNA was extracted andDNA pools were constructed on the basis of goat breeds. In 36 selective primer combinations, 29 combinationsamplified totally 3 253 markers including 92 polymorphic markers by amplified fragment length polymor-phism (AFLP). On average, 3.17 polymorphic markers were amplified per combination, with a polymorphicfrequency of 2.8%. The primer combinations amplifying more polymorphic markers (showed in brackets)were involved in E00+ACG/M00+CAA (13), E00+ACG/M00+CAG (10), E00+AAC/M00+CAC (8)and E00+AAC/M00+ACT (7). A total of 183 markers including 60 polymorphic markers were amplified byRAPD from the pooled DNA of three breeds using 22 primers with strong polymorphism and high reproduc-ibility selected from 93 RAPD primers. On average, 2.73 polymorphic markers were amplified per primer,with a polymorphic frequency of 32.8%. The results of AFLP and RAPD coincidently suggested that the ge-netic distance is the closest between Xuhuai and Haimen goat, next between Xuhuai and Boer goat, and the far-thest between Haimen and Boer goat. According to the UPGMA method, Haimen and Xuhuai goats can begathered together as a cluster, then Boer goat. Both methods can be used to implicate the genetic difference ofthese three breeds, in particular AFLP has more polymorphic markers.
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