AFLP and RAPD Analysis of the Boer and Indigenous Breeds of the Goat in Jiangsu

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.