Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein‐coding loci

Abstract

Twenty-one microsatellite loci in 11 populations of Asian water buffalo (eight swamp, three river type) were analysed and, within and among populations, genetic variability was compared with results from 25 polymorphic protein-coding loci. Within-population mean heterozygosity ranged from 0.380-0.615, approximately twice that estimated from the protein-coding loci (0.184-0.346). Only eight significant departures from Hardy-Weinberg equilibrium (involving four loci) were detected; global tests showed significant heterozygote deficiencies for these four loci. Non-amplifying alleles are likely to be segregating in some or all populations for one of these loci, and probably for the other three. There was significant differentiation between the swamp and river types of water buffalo, and among populations within each buffalo type. Estimates of theta (measure of population differentiation) for each locus for the eight swamp populations were all highly significant (mean theta = 0.168 +/- 0.018). Mean theta for protein-coding loci was not significantly different (0.182 +/- 0.041). The variance among protein-coding loci was significantly higher than among microsatellite loci, suggesting balancing selection affecting allele frequencies at some protein-coding loci. Genetic distances show clear separation of the swamp and river types, which were estimated to have diverged at least 10,000-15,000 years ago. The topology of the swamp populations' microsatellite tree is consistent with their geographical distribution and their presumed spread through south-east Asia. By contrast, the tree based on the protein-coding loci distances is quite different, being clearly distorted by a bottleneck effect in one population, and possibly in at least two others. As many domestic livestock breeds are possibly descended from small numbers of founders, microsatellite-based trees are to be preferred in assessing breed genetic relationships.

Hierarchical analysis of genetic structure in Spanish donkey breeds using microsatellite markers

“…than 5% is due to differences among breeds. These values of total genetic differentiation (F ST ) among breeds are close to those found in other domestic species, for example: among river buffalo breeds (F ST = 0.038, Barker et al, 1997), among Spanish horse breeds (F ST = 0.078, Cañ on et al, 2000), though they are slightly lower than those found in Norwegian horse breeds (F ST = 0.12, Bjørnstad et al, 2000), in European cattle breeds (F ST = 0.11, MacHugh et al, 1998;Kantanen et al, 2000) and among Spanish dogs (F ST = 0.099, Jordana et al, 1992). The results from the hierarchical analysis further show that populations of Spanish donkeys are substructured at different levels ( Table 2).…”

Genetic diversity of eleven European pig breeds

“…An evaluation of buffalo genetic diversity along the same lines by Barker et al [3] is also to be mentioned. Once an agreement is reached on a common set of markers, the essential requirements for achieving comparability of allele sizing between different laboratories are (i) to include on the same gel a set of common control DNA samples previously distributed to the participants, and (ii) to preferably use primers derived from a single synthesis, as done in the present experiment.…”

Conformação Corporal De Equinos De Diferentes Grupos Genéticos

“…A subdivisão ou estruturação em espécies de animais domésticos é, geralmente, mais evidente do que em espécies selvagens, devido à separação após serem diferenciadas raças e/ou grupo genéticos geneticamente superiores para uso local, regional ou nacional (1) . Assim, compreender as diferenciações fenotípicas é fundamental para identificar as aptidões específicas entre os grupos genéticos, tendo em vista que, para praticar qualquer tipo de atividade equestre, são necessários equinos com perfil corporal compatível (2,3) .…”