AFLP and RAPD Analysis on the Boer and Native Breed of Goats in Jiangsu

Blood and tissue samples were taken from 105 goats including 60 Boer goats (30 for each sex), 30 Xuhuai goats (15 for each sex) and 15 Haimen goats (7 stud and 8 does). DNA was abstracted and DNA pools were constructed on the basis of goat breed. In 36 selective primer combinations, 29 combinations amplified totally 3 253 markers, including 92 polymorphic markers by amplified fragment length polymorphism (AFLP). On average, 3.17 polymorphic markers were amplified per combination, with a polymorphic frequency of 2.8%. The primer combinations by which more polymorphic markers (showed in brackets) were obtained 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 by RAPD from the pooled DNA of three breeds using 22 primer with strong polymorphism and high repeatability selected from 93 arbitrary 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 genetic distance is the closest between the Xuhuai and the Haimen goat, next between the Xuhuai and Boer goat, and the farthest between the Haimen and the Boer goat. According to the UPGMA method, Haimen and Xuhuai goats can be gathered together as a cluster, then the Boer. Both methods can implicate the genetic difference of these three breeds, in particularly AFLP has more polymorphic markers.