Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes

Abstract

BackgroundGoat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats.ResultsA high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows.ConclusionsAfter domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0422-x) contains supplementary material, which is available to authorized users.

The origin of domestication genes in goats

“…This geographic structure is also supported by TreeMix and haplotype-based statistics ( figs. S11 and S12 ), in agreement with the scenario that the ancestors of present-day domestic goat populations followed distinct dispersal routes along the east-west axis of Afro-Eurasia ( 4 ) ( Fig. 2A, figs.…”

“…Domestication presents an extreme shift of physiological and behavioral stress for free-living animals ( 1 ) to a high-density and disease-prone anthropogenic environment, especially for herbivores. The goat ( Capra hircus ) was one of the first domesticated livestock species, demonstrating remarkable adaptability and versatility ( 2, 3 ), and has been intimately associated with human dispersal ( 4 ). Recent studies have identified candidate targets of selection during goat domestication, including loci related to pigmentation, xenobiotic metabolism and milk production ( 5, 6 ); however, the evolutionary dynamics of key genes involved in adaptation during the early phase of domestication remains unclear.…”

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

“…Geographic plots of haplogroup frequencies show a considerable spatial differentiation, which resonates the strong phylogeography displayed by autosomal SNPs (Colli et al, 2018), but is in clear contrast with the phylogenetic structure displayed by mtDNA haplogroups (Luikart et al, 2001; Naderi et al, 2007, 2008; Zhao et al, 2014b, 2014a). Most likely, by a series of bottlenecks in the male lineage subcontinents have different major haplogroups, while none has a global-wide coverage: - Haplogroup Y2B is absent in Europe, Africa and west Asia, but became a major haplotype in east Asia and southeast Asian, where Y2A is not represented.…”

“…We differentiating the major Y-chromosomal haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B for 1720 domestic goats from 132 breeds by combining data from several sources as detailed per breed in Table 4: From the goat panel collected for the Econogene project, DNA samples of 353 male goats from 38 European or southwestern Asian breeds were analyzed by PCR amplification and dideoxy-sequencing of segments within the DBY, SRY and ZFY genes (Lenstra and Econogene Consortium, 2005) as described previously for bovine samples (Nijman et al, 2008; Edwards et al, 2011) and using the primers listed in Table 5. We used published data for 90 goats from 5 Portuguese breeds or from Morocco (Pereira et al, 2009), for 211 goats from 10 Asian breeds (Waki et al, 2015), for 181 goats from 8 Turkish breeds (Cinar Kul et al, 2015) and for 270 goats from 26 Spanish or Swiss breeds (Vidal et al, 2017). 362 DNA samples (57 breeds) from several sources, including the AdaptMap panel (Colli et al, 2018) were genotyped by the KASP assay (Table 4). For 90 goats from 15 breeds genotypes were obtained by B last searching of the ShortRead Archive (SRA). …”

“…362 DNA samples (57 breeds) from several sources, including the AdaptMap panel (Colli et al, 2018) were genotyped by the KASP assay (Table 4).…”