ESTIMATION OF GENETIC DIVERSITY IN SOME SUDANESE (AUTOCHTHONOUS) CATTLE USING DNA MARKERS

Abstract

Two different types of molecular markers (RAPD and AFLP) were used to measure genetic diversity and fingerprint 4 local breeds of Sudanese cattle namely Western Baggara (Nialawy), Nilotic (Majock), Butana and Kenana. The level of polymorphism revealed by RAPD and AFLP among the four breeds was 51.5% and 91.5% respectively. While RAPD techniques recorded 22.9%, 36.8%, 24.4% and 41.4% within the 4 local breeds, respectively. Only 8 out of 22 primers (36%) used in the RAPD analysis and 11 primers combinations used in the AFLP techniques gave unique markers that singularly identified specific breeds. The RAPD and AFLP data matrix was utilized to estimate the genetic similarity using Jaccard’s coefficient. It ranged from 78.4% to 84.8% with an average of 81.6% and from 46.9 to 80.3% with an average of 63.6% respectively. While it ranged from 98.9% to 92.9% with an average of 95.9%; from 96.3% to 88.2% with an average of 92.2%, from 98.7% to 88% with an average of 93.3% and from 97.2% to 80.3% with an average of 88.7% within the above four local breeds, respectively using RAPD markers. Cluster analysis based on similarity matrices using UPGMA from RAPD data distinguished two groups, Kenana and Butana the first encompassed and second included Western Baggara and Nilotic with a genetic relationship of 80%. The genetic relationship within iv each of the two groups were 82% and 85%, respectively. Within the local breeds the dendrogram distinguished two main groups within each of Western Baggara, Nilotic and Butana breeds. It also distinguished three groups within Kenana cattle, with a degree of genetic relationship ranging from 86% to 95% between the various strains within breeds. The AFLP dendrogram constructed from UPGMA cluster analysis resolved three main clusters with a genetic relationship of 53%, 57% and 66% between Western Baggara and Nilotic; between Western Baggara and Butana; and between Butana and Kenana cattle, respectively. Within the 4 local breeds the genetic relationships were 61%, 67% 80% and 72% for Nilotic, Western Baggara, Butana and Kenana cattle respectively.