Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds

Naval-Sánchez, Marina; Nguyen, Quan; McWilliam, Sean; Porto-Neto, Laércio R.; Tellam, Ross L.; Vuocolo, Tony; Reverter, Antônio; Pérez‐Enciso, Miguel; Bräuning, Rüdiger; Clarke, Shannon; McCulloch, Alan; Zamani, Wahid; Naderi, Saeid; Rezaei, Hamid Reza; Pompanon, François; Taberlet, Pierre; Worley, Kim C.; Gibbs, Richard A.; Muzny, Donna M.; Jhangiani, Shalini N.; Cockett, Noelle E.; Daetwyler, Hans D.; Kijas, James W.

doi:10.1038/s41467-017-02809-1

Cited by 106 publications

(106 citation statements)

References 77 publications

(112 reference statements)

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“…A private signature was observed in SAM on OAR9 (36.48 Mb) in proximity to the well‐described PLAG1 gene (Naval‐Sanchez et al . ). On OAR6 we identified a selection signature at 37.65 Mb (in VBS, SAM, SWA, ERS and SMS) and at 36.69 Mb (in SAM, VBS, ERS, SWA and BOS).…”

Section: Discussionmentioning

confidence: 97%

“…Recently, Naval‐Sanchez et al . () compared the nucleotide diversity between domestic sheep and mouflon based on sequence data and reported a selective sweep in the region of TBX3 . Selection against camouflage color is an important reason for changes in coat color during animal domestication (Fang et al .…”

Section: Discussionmentioning

confidence: 99%

“…; Naval‐Sanchez et al . ) are located in this region as are genes associated with milk production ( ABCG2 , MEPE , LAP3 , NCAPG and SPP1 ; Ruiz‐Larrañaga et al . ) and litter size ( SPP1 ; Xu et al .…”

Section: Discussionmentioning

confidence: 99%

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Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

Signer-Hasler

Burren

Ammann³

et al. 2019

Animal Genetics

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A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between F PED and F ROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean F ROH estimates from medium-density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make-up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

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Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

Signer-Hasler

Burren

Ammann³

et al. 2019

Animal Genetics

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“…One notable pattern involves the high levels of genetic heterogeneity in domestic sheep. This includes multiple distinct mitochondrial DNA haplogroups found in modern breeds 10 , as well as higher nuclear genetic diversity in sheep compared to that in some other domesticates, such as cattle or dog 11,12 . High diversity would be consistent with scenarios where domestication involved multiple centres and/or a large and heterogeneous wild population.…”

Section: Introductionmentioning

confidence: 99%

“…Genetic distinctions between Asian and European sheep also imply multiple domestication or wild admixture events. Indeed, present-day sheep cluster in two main groups based on genome-wide polymorphism data: east (Asian and African, including East Mediterranean islands) and west (European) 11,12 . Similarly, Asian and European sheep tend to carry distinct proportions of mitochondrial DNA haplogroups, A and B, respectively 13–15 , a pattern that may have been established already by the 2nd millennium BCE 16,17 .…”

Section: Introductionmentioning

confidence: 99%

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Yurtman

Özer

Yüncü

et al. 2020

Preprint

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22Sheep was among the first domesticated animals, but its demographic history is little 23 understood. Here we present combined analyses of mitochondrial and nuclear polymorphism 24 data from ancient central and west Anatolian sheep dating to the Late Glacial and early 25 Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the 26 early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, 27 mitochondrial haplogroup diversity increases, compatible with admixture from other 28 domestication centres and/or from wild populations. Analysing archaeogenomic data, we 29 further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day 30 European breeds, and especially those from central and north Europe. Our results indicate that 31 Asian contribution to south European breeds in the post-Neolithic era, possibly during the 32 Bronze Age, may explain this pattern.33 34 35 36 65 traits across the globe, especially within the last 5 millennia, as part of the secondary products 66 revolution 18,19 . Although the first domesticated sheep were likely used for their meat and 67 possibly their milk 20 , they started to be increasingly exploited for their wool in Bronze Age SW 68 Asia, during the 3rd millennium BCE 21 . Intriguingly, a comparison of DNA retroelements 69 across modern breeds implies an expansion of SW Asian lineages, estimated to date back to the 70 Bronze Age; according to this model, SW Asian sheep with desired traits, such as fine wool, 71 were introduced into local breeds across the globe 22 . A recent ancient DNA study reports 72 evidence consistent with novel breeds being introduced to Bronze Age Europe, coinciding with 73 archaeological evidence for the introduction of wool to this continent 21 . In later periods, export 74 and admixture of selected sheep breeds into local stocks continued 11 . Indeed, the most recent 75 common ancestor of domestic sheep breeds has been inferred to date back only 800 generations 76 ago 11 -an unexpectedly recent estimate. 77 4We currently lack a solid demographic history model to explain these observations: high 78 diversity, clear genetic structure, and recent coalescence times. What is missing is genetic data 79 on the initial steps of domestication and characterisation of the early domesticated sheep gene 80 pool. Here we present a first attempt to bridge this gap, studying ancient DNA from Neolithic 81 period sheep remains from Anatolia, one of the possible domestication centres. Analysing both 82 mitochondrial DNA (mtDNA) sequences and nuclear polymorphism data, we find support for 83 the notions that the present-day domestic sheep population has multiple origins, and also that 84 the sheep gene pool changed considerably since the Neolithic period. 85 86 Results 87 We analysed DNA from c.200 archaeological sheep bone and tooth samples from early 88 Holocene Anatolia, originating from six different sites from central and west Anatolia and 89spanning the Epipaleolithic, Neolithic, and Ch...

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Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs

Liu,

Yi,

Yao

et al. 2024

iMeta

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The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes—seven of which were newly generated, high‐quality de novo assembled genomes—and 1081 resequencing genomes, we built a pan‐genome and identified 134.24 Mb nonredundant nonreference sequences, 1099 novel protein‐coding genes, 187,927 structural variations (SVs) and 30,143,962 single‐nucleotide polymorphisms (SNPs). Analysis of selective domestication revealed BRCA1 associated with enhanced adipocyte growth and fat deposition, and ABCA3 linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptomes and 162 methylomes of skeletal muscle across 27 developmental stages revealed the regulatory mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection reshaped local DNA methylation status and imparted regulatory effects on the progression patterns of heterochronic genes such as GHSR and BDH1, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.

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Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds

Cited by 106 publications

References 77 publications

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs

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