Genetic characterisation of indigenous goat populations of sub-saharan Africa using microsatellite dna markers
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Date
2002
Authors
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Publisher
Sokoine University of Agriculture.
Abstract
Two studies were carried out to genetically characterize the sub-Saharan African goats
using 19 microsatellite markers. The aims were to understand the genetic uniqueness
and relationships among breeds and to quantify the level of genetic diversity within
each breed. The first study investigated the genetic relationships among the major goat
types in sub-Saharan Africa. Ten African breeds were sampled from eastern Africa
(Maasai. Kigezi, Mubende, North West Highland, Arsi-Bale), southern Africa (Ndebele,
Pafuri) and West Africa (West African Dwarf, Maure, Djallonke). Two European
breeds (Grisons Striped, Toggenburg). two Asian breeds (Mongolian Cashmere,
Bandipur) and one Middle East breed (Arab) were included as reference breeds. Twenty
to forty eight animals per breed
breed genetic diversity was determined as the mean number of alleles per locus and
average gene diversity. Two measures of population differentiation, Gst and 0 were
computed to measure the genetic differentiation among the breeds. Breed assignment
test was performed to identify the source populations of individual animals. Three
measures of genetic distances, Ds, DA, and (bp.)2 were used to estimate the genetic
distances between pairs of breeds. These distances were used to construct neighbour joining (NJ) trees to assess the relationships among breeds. The genetic relationships
among breeds were further assessed using principal component analysis (PCA) and
multidimensional scaling (MS).
were genotyped at the 19 microsatellite loci. Within
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In total, 263 alleles were detected across all the breeds. Among the sub-Saharan African
breeds, the mean number of alleles per locus ranged from 5.26 ± 0.464 (Djallonke) to
7.05 ±0.516 (Mubende). The lowest and highest average gene diversities were observed
in Pafuri (0.542 ± 0.036) and Ndebele (0.672 ± 0.031), respectively. For all the breeds,
the within breed genetic diversities of European breeds were slightly less than those of
African and Asian breeds. Between 14.6% (0) and 15.7% (Gst) of the total genetic
variation was due to differences between breeds. In the assignment test, 92.1% of all
animals were correctly assigned to their original population. The three measures of
genetic distances indicated that the largest genetic distances were observed between
West African and southern African breeds and the lowest genetic distances were found
between the pairs of breeds within the same country. The (5p)2 distances were found
less effective in revealing the true genetic relationships among the breeds compared to
differences, however, both grouped the breeds according to their geographic origins.
The PCA and MS supported the grouping of the breeds according to their geographic
origins. Unlike the NJ trees, the PCA and MS clearly separated the European breeds
from the Asian breeds. Furthermore, the MS separated the Arab breed from the other
breeds more clearly.
Ds, and Da distances. The NJ trees constructed from Ds, and Da showed some
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The second study examined the genetic diversity and structure of Small short-eared
eastern African goats as a case study. The same 19 microsatellite markers were used to
genotype 13 populations. The populations sampled were Afar, North East Highland,
Boran, Galla, Kenyan Small East African, Maasai, Ugogo, Sukuma, Ujiji, Tanzanian
Coastal, Newala, Mbeya and Landim. The reference breeds were Tswana, Venda, West
African Dwarf, Red Sokoto and Toggenburg. The Galla had the lowest (5.53 ± 0.599)
mean number of alleles per locus while Afar had the highest (6.53 ± 0.646). The level of
gene diversity ranged from 0.667 ± 0.035 (Afar) to 0.553 ± 0.036 (Newala). Between
11% (0) and 12% (Gst) of the total genetic variability could be attributed to differences
among the populations. In the assignment test, 79.1% of the individuals were correctly
assigned to their source populations. NJ tree using individual animals as the taxonomic
units was constructed to study the structure of eastern African goats. Among the
Tanzanian populations, only the Newala appeared to be tightly clustered together, the
rest of the populations were mixed together. Among the Kenyan and Ethiopian
populations, only the Afar and Kenyan Small East African featured in their distinct
clusters, the rest of the populations showed unclear pattern of clustering. The NJ trees
based on Ds, and Da distances, though differed in their topology, clearly marked the
separation of the Tanzanian populations from the Ethiopian and Kenyan populations.
The Landim was grouped together with the Tswana and Venda goats from southern
Africa. The MS supported the separation of the Tanzanian populations from the
Ethiopian-Kenyan populations. However, the PCA indicated that the eastern African
goat populations are genetically close to each other
Description
Phd Thesis
Keywords
Genetic characterisation, indigenous goat, microsatellite, dna