Abstract
BackgroundSudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Using the 50 K SNP chip, 24 animals of each breed were genotyped.ResultsMore than 96% of high quality SNPs were polymorphic with an average minor allele frequency of 0.3. In all breeds, no significant difference between observed (0.4) and expected (0.4) heterozygosity was found and the inbreeding coefficients (FIS) did not differ from zero. Fst coefficients for the genetic distance between breeds also did not significantly deviate from zero. In addition, the analysis of molecular variance revealed that 93% of the total variance in the examined population can be explained by differences among individuals, while only 7% result from differences between the breeds. These findings provide evidence for high genetic diversity and little inbreeding within breeds on one hand, and low diversity between breeds on the other hand. Further examinations using Nei’s genetic distance and STRUCTURE analysis clustered Taggar goats distinct from the other breeds. In a principal component (PC) analysis, PC1 could separate Taggar, Nilotic and a mix of Nubian and Desert goats into three groups. The SNPs that contributed strongly to PC1 showed high Fst values in Taggar goat versus the other goat breeds. PCA allowed us to identify target genomic regions which contain genes known to influence growth, development, bone formation and the immune system.ConclusionsThe information on the genetic variability and diversity in this study confirmed that Taggar goat is genetically different from the other goat breeds in Sudan. The SNPs identified by the first principal components show high Fst values in Taggar goat and allowed to identify candidate genes which can be used in the development of breed selection programs to improve local breeds and find genetic factors contributing to the adaptation to harsh environments.
Highlights
Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment
principle component 1 (PC1) could separate three out of four different subpopulations, namely Taggar, Nilotic and a mix of Desert and Nubian goats, this is seen in Fig. 2b where the Taggar goats are colored green, the Nilotic goats are mostly yellow, and the other 2 breeds have a low contribution to the first principal component
Among the genes in the vicinity of the Single Nucleotide Polymorphism (SNP) contributing to PC1, we identified genes which might be interesting candidates when looking at breed characteristics and adaptation differences between Sudanese breeds studied here
Summary
Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Goats in Sudan have an important contribution to food security by producing milk and meat. Goats constitute an important source of livelihood, social security and rural economy. The improvement of the productivity of local breeds contributes to rural development. Even under the harsh environments, selection of favorable genome variants could sustainably improve productivity. Systematic genetic diversity studies of indigenous adapted breeds would be necessary to understand the acquired unique features of these breeds
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