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

Seyed Mohammad Farhad Vahidi 0 1 Ali Reza Tarang 0 1 Arif-un-Nisa Naqvi 1 Mohsen Falahati Anbaran 1 Paul Boettcher 1 4 Stephane Joost 1 3 Licia Colli 1 2 Jose Fernando Garcia 1 5 Paolo Ajmone-Marsan 1 2 0 Agricultural Biotechnology Research Institute of Iran (ABRII) , North branch, Rasht 41635-4115 , Iran 1 and Health Division, Food and Agriculture Organization of the United Nations , Rome 00153 , Italy 2 Istituto di Zootecnica and Biodiversity and Ancient DNA - BioDNA - Research Centre, Universita Cattolica del Sacro Cuore , Piacenza , Italy 3 Laboratory of Geographic Information Systems, School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Federale de Lausanne (EPFL) , 1015 Lausanne , Switzerland 4 Animal Production and Health Section, International Atomic Energy Agency , A-1400 Vienna , Austria 5 Departamento de Apoio, Producaoe Saude Animal, Laboratorio de Bioquimica e Biologia Molecular Animal, Rua Clovis Pestana, Universidade Estadual Paulista , Aracatuba , Brazil 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. - Background Goats are multi-purpose animals that produce milk, meat and fiber and also serve other beneficial roles. In particular, they contribute to the economy of farmers living in arid and semi-arid regions, including southern Iran [1]. Although goat products are often cheaper than sheep products in the market place, goats are favored in the most marginal areas of Iran, where they are easier to manage and better adapted to harsh climate and ecological conditions than sheep. According to the latest livestock census, conducted in 2008, the Iranian caprine population is around 25 300 000 animals (http://faostat. fao.org). Iranian goats are mainly reared in traditional systems by small holders. Since nomadic tribes are almost completely economically dependent on animal rearing, these stakeholders play an important role in the conservation of animal genetic resources, especially of small ruminants. Genetic diversity is an essential component for population survival, evolution, genetic improvement and adaptation to changing environmental conditions [2]. Information on genetic diversity is therefore necessary to optimize both conservation and strategies for the use of animal genetic resources, to meet future market demands and improved production systems. Molecular tools permit the characterization of genetic resources at the DNA level. Because of favorable characteristics, such as abundant number, high polymorphism and co-dominant inheritance, microsatellite DNA markers have been extensively used for a number of applications in livestock genetics, including parentage testing, breed classification, conservation genetics and also to assess genetic variation and structure within and among populations [3]. This study was undertaken to examine the pattern of microsatellite variation within and among seven Iranian goat breeds. The resulting information may be used in national plans for sustainable improvement and conservation of goat genetic resources. This research was carried out as part of the IAEA-FAO joint program Characterization of genetic resources in small ruminants in Asia (D3.10.25), which aimed at developing methodologies, generating information and formulating decision support systems to analyze phenotypic and molecular genetic diversity, develop microsatellite and related technologies, and enable the development and implementation of national and regional strategies for optimum use and conservation of small ruminants in Asia (http://www-naweb.iaea.org/ nafa/about-nafa/index.html). south of the Caspian Sea, to the far western border of Iran, in the northern Zagros Mountains, to southern Zagros, along the mountain range. Seven indigenous goat breeds were mainly distributed in six provinces: Gilan, Ardabil, Isfahan, Fars, Kurdistan and Khuzestan (Table 1). A maximum number of five samples per flock were collected from an average of 11 flocks per breed (min = 5, max = 18). Two Pakistani goat breeds, collected from the Punjab province, were also included in the dataset for comparison. The geographic distribution of Iranian breeds sampled in this study is depicted in Figure 1 and their typical phenotype in Figure 2. Microsatellite DNA analysis The salting-out method [4] was used to isolate genomic DNA from blood samples of 317 animals from the seven Iranian and two Pakistani goat breeds. Fourteen microsatellite markers were chosen from the list recommended by the FAO [5]. Forward primers were end-labeled with fluorescent dyes (6-FAM, VIC, NED and PET) [see Additional file 1]. Polymerase Chain Reaction (PCR) was carried out on 50-10 (...truncated)