A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

Kijas, James W.; Townley, David; Dalrymple, Brian P.; Heaton, Michael P.; Maddox, J F; McGrath, Annette; Wilson, Peter; Ingersoll, Roxann; McCulloch, Russell; McWilliam, Sean; Tang, Dave; McEwan, John C.; Cockett, Noelle E.; Oddy, V. H.; Nicholas, F. W.; Raadsma, Herman W.

doi:10.1371/journal.pone.0004668

Cited by 301 publications

(299 citation statements)

References 55 publications

Supporting

Mentioning

256

Contrasting

Unclassified

Order By: Relevance

“…The strategy used in the development of the chips included divergent breeds in the discovery panel, and prior to their release, they were tested and validated on a large panel of divergent breeds and populations Tosser-Klopp et al, 2014). Ascertainment bias has also not been reported as an issue in studies that have used the two chips (for example, Kijas et al, 2009;Lv et al, 2014;Lashmar et al, 2015), and results from these studies and ours show that the two chips are highly polymorphic.…”

Section: Discussionmentioning

confidence: 93%

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

et al. 2015

View full text Add to dashboard Cite

Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

show abstract

Section: Discussionmentioning

confidence: 93%

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

et al. 2015

View full text Add to dashboard Cite

show abstract

“…By examining modern genetic diversity and its global distribution, it is possible to gain insight into the domestication process, because, in the absence of recurrent introgression, populations close to the putative domestication centers are assumed to retain higher levels of ancestral polymorphism (20). Such distribution of genetic diversity has been suggested to explain the frequently observed negative correlation between genetic diversity and the geographic distance from the place of origin in numerous livestock species (20)(21)(22)(23)(24)(25). In the case of the dromedary, before the introduction of the domestic form, there had been no representatives of Camelus on the African continent since the Late Pleistocene, and the Holocene native distribution of wild dromedaries seems to have been restricted to the Arabian Peninsula (6, 7).…”

Section: Resultsmentioning

confidence: 99%

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Almathen

Charruau

Mohandesan

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

117

135

View full text Add to dashboard Cite

Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.anthropogenic admixture | Camelus dromedarius | demographic history | paleogenetics | wild dromedary T he dromedary (Camelus dromedarius) is one of the largest domestic ungulates and one of the most recent additions to livestock. Known as the "ship of the desert" (1), it enabled the transportation of people and valuable goods (e.g., salt, incense, spices) over long distances connecting Arabia, the Near East, and North Africa. This multipurpose animal has outperformed all other domestic mammals, including the donkey, in arid environments and continues to provide basic commodities to millions of people inhabiting marginal agro-ecological zones. In the current context of advancing desertification and global climate change, there is renewed interest in the biology and production traits of the species (2), with the first annotated genome drafts having been recently released (3, 4). SignificanceThe dromedary is one of the largest domesticates, sustainably used in arid and hostile environments. It provides food and transport to millions of people in marginal agricultural areas. We show how important long-distance and back-and-forth movements in ancient caravan routes shaped the species' genetic diversity. Using a global sample set and ancient mitochondrial DNA analyses, we describe the population structure in modern dromedaries and their wild extinct ancestors. Phylogenetic analyses of ancient and modern dro...

show abstract

“…de found a similar density for effective across-breed Bos taurus GEBV predictions and estimated an average required spacing of about 12 kbp. The sheep breeds in this study have the advantage of being mostly of European origin (Kijas et al, 2009), which reduces their (across-breed) effective population size compared to more distantly related sheep breeds.…”

Section: Discussionmentioning

confidence: 99%

The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections

et al. 2011

View full text Add to dashboard Cite

SummaryGenetic resistance to gastrointestinal worms is a complex trait of great importance in both livestock and humans. In order to gain insights into the genetic architecture of this trait, a mixed breed population of sheep was artificially infected with Trichostrongylus colubriformis (n=3326) and then Haemonchus contortus (n=2669) to measure faecal worm egg count (WEC). The population was genotyped with the Illumina OvineSNP50 BeadChip and 48 640 single nucleotide polymorphism (SNP) markers passed the quality controls. An independent population of 316 sires of mixed breeds with accurate estimated breeding values for WEC were genotyped for the same SNP to assess the results obtained from the first population. We used principal components from the genomic relationship matrix among genotyped individuals to account for population stratification, and a novel approach to directly account for the sampling error associated with each SNP marker regression. The largest marker effects were estimated to explain an average of 0 . 48% (T. colubriformis) or 0 . 08 % (H. contortus) of the phenotypic variance in WEC. These effects are small but consistent with results from other complex traits. We also demonstrated that methods which use all markers simultaneously can successfully predict genetic merit for resistance to worms, despite the small effects of individual markers. Correlations of genomic predictions with breeding values of the industry sires reached a maximum of 0 . 32. We estimate that effective across-breed predictions of genetic merit with multi-breed populations will require an average marker spacing of approximately 10 kbp.

show abstract

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

Cited by 301 publications

References 55 publications

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections

Contact Info

Product

Resources

About