Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran

Abstract

Background: Iran is an area of particular interest for investigating goat diversity. Archaeological remains indicate early goat domestication (about 10,000 years ago) in the Iranian Zagros Mountains as well as in the high Euphrates valley and southeastern Anatolia. In addition, mitochondrial DNA data of domestic goats and wild ancestors (C. aegagrusor bezoar) suggest a pre-domestication management of wild populations in southern Zagros and central Iranian Plateau. In this study genetic diversity was assessed in seven Iranian native goat breeds, namely Markhoz, Najdi, Taleshi, Khalkhali, Naini, native Abadeh and Turki-Ghashghaei. A total of 317 animals were characterized using 14 microsatellite loci. Two Pakistani goat populations, Pahari and Teddy, were genotyped for comparison.

Results: Iranian goats possess a remarkable genetic diversity (average expected heterozygosity of 0.671 across loci, 10.7 alleles per locus) mainly accounted for by the within-breed component (GST = 5.9%). Positive and highly significant FIS values in the Naini, Turki-Ghashghaei, Abadeh and Markhoz breeds indicate some level of inbreeding in these populations. Multivariate analyses cluster Iranian goats into northern, central and western groups, with the western breeds relatively distinct from the others. Pakistani breeds show some relationship with Iranian populations, even if their position is not consistent across analyses. Gene flow was higher within regions (west, north, central) compared to between regions but particularly low between the western and the other two regions, probably due to the isolating topography of the Zagros mountain range. The Turki-Ghashghaei, Najdi and Abadeh breeds are reared in geographic areas where mtDNA provided evidence of early domestication. These breeds are highly variable, located on basal short branches in the neighbor-joining tree, close to the origin of the principal component analysis plot and, although highly admixed, they are quite distinct from those reared on the western side of the Zagros mountain range.

Conclusions: These observations call for further investigation of the nuclear DNA diversity of these breeds within a much wider geographic context to confirm or re-discuss the current hypothesis (based on maternal lineage data) of an almost exclusive contribution of the eastern Anatolian bezoar to the domestic goat gene pool.

Figure 1

Distribution of Iranian goat populations surveyed in this study.

Figure 2

Morphologies of animals from the different Iranian goat breeds analyzed. Breed ID, age of animal in years (yrs) and age are shown in the white boxes.

Figure 3

Graphical output from LOSITAN. Outliers are tagged with labels.

Figure 4

Neighbor-Joining tree based on D_A genetic distances for nine populations. Numbers at the nodes are bootstrap values based on 1000 permutations.

Figure 5

Principal component analysis. The principal components were extracted by correlation coefficients of Pearson, based on allele frequencies. A) PCA analysis of seven Iranian breeds. B) PCA analysis of nine goat breeds (Iran and Pakistan).

Figure 6

Clustering assignments of the nine goat breeds obtained by STRUCTURE analyses. Each of the 317 animals is represented by a thin vertical line that is divided into segments the size and color of which correspond to the relative proportion of the animal genome assigned to a particular cluster; breeds are separated by thin black lines. A) Estimated population structure displayed with individual Q-scores. B) Estimated population structure displayed with population average Q-scores.