Analyses of pig genomes provide insight into porcine demography and evolution

@article{Groenen2012AnalysesOP,
  title={Analyses of pig genomes provide insight into porcine demography and evolution},
  author={M. Groenen and A. Archibald and H. Uenishi and C. Tuggle and Y. Takeuchi and M. Rothschild and C. Rogel-Gaillard and Chankyu Park and D. Milan and H. Megens and S. Li and D. Larkin and Heebal Kim and Laurent A. F. Frantz and M. C{\'a}ccamo and Hyeonju Ahn and Bronwen L. Aken and A. Anselmo and C. Anthon and L. Auvil and B. Badaoui and C. Beattie and C. Bendixen and Daniel Berman and F. Blecha and J. Blomberg and L. Bolund and M. Bosse and S. Botti and Zhan Bujie and Megan Bystrom and Boris Capitanu and D. Carvalho-Silva and P. Chardon and Celine T Chen and Ryan Cheng and Sang-Haeng Choi and William Chow and Richard C. Clark and C. Clee and R. Crooijmans and H. Dawson and P. D{\'e}hais and Fioravante De Sapio and B. Dibbits and Nizar Drou and Z. Du and K. Eversole and J. Fadista and S. Fairley and T. Faraut and G. Faulkner and K. Fowler and M. Fredholm and E. Fritz and J. Gilbert and E. Giuffra and J. Gorodkin and D. Griffin and J. Harrow and A. Hayward and K. Howe and Zhi-Liang Hu and S. Humphray and T. Hunt and H. Hornsh{\o}j and J. Jeon and P. Jern and Matt Jones and J. Jurka and H. Kanamori and R. Kapetanovic and Jaebum Kim and Jae-Hwan Kim and Kyu-Won Kim and Tae-Hun Kim and G. Larson and Kyooyeol Lee and Kyung-Tai Lee and R. Leggett and H. Lewin and Yingrui Li and Wansheng Liu and J. Loveland and Yao Lu and J. Lunney and J. Ma and O. Madsen and Katherine M Mann and L. Matthews and S. McLaren and T. Morozumi and M. Murtaugh and Jitendra Narayan and Dinh Truong Nguyen and Peixiang Ni and Song-Jung Oh and S. Onteru and F. Panitz and E. Park and Hong-Seog Park and G. Pascal and Yogesh Paudel and M. P{\'e}rez-Enciso and Ricardo H Ram{\'i}rez-Gonz{\'a}lez and J. Reecy and S. Rodriguez-Zas and G. Rohrer and L. Rund and Y. Sang and K. Schachtschneider and J. Schraiber and J. Schwartz and L. Scobie and C. Scott and S. Searle and B. Servin and B. Southey and G. Sperber and P. Stadler and J. Sweedler and Hakim Tafer and B. Thomsen and R. Wali and Jian Wang and J. Wang and S. White and Xun Xu and M. Yerle and Guojie Zhang and Jianguo Zhang and J. Zhang and Shuhong Zhao and J. Rogers and C. Churcher and L. Schook},
  journal={Nature},
  year={2012},
  volume={491},
  pages={393 - 398}
}
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between… Expand
Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication
Domesticated organisms have experienced strong selective pressures directed at genes or genomic regions controlling traits of biological, agricultural or medical importance. The genome of native andExpand
A decade of pig genome sequencing: a window on pig domestication and evolution
  • M. Groenen
  • Medicine, Biology
  • Genetics Selection Evolution
  • 2016
TLDR
Recent whole-genome sequencing studies in the pig and closely-related species are reviewed that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals. Expand
A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia
TLDR
It is concluded that pathway analysis facilitates the biological interpretation of genome-wide studies, and Notably, in the case of pig, behavior played an important role, among other physiological and developmental processes. Expand
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Using pig as model, this chapter provides an in-depth overview of domestication-related events leading towards the genetic diversity in extant pig breeds, and identifies five events important for the genetic variation in modern pig genomes. Expand
Chapter 2 A Genomics Perspective on Pig Domestication
Land animal domestication has typically led to remarkable phenotypic diversity, stemming from a broad genetic background. The process of land animal domestication turns out to be a complex, long-termExpand
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Insight is provided about the demography and the feralization process in the pig species using genomewide polymorphisms and the analysis of feral pigs of Isla del Coco improves the knowledge on the dynamics of feralization, and serves as yardstick against which to compare modern breeds. Expand
Annotation of the Domestic Pig Genome by Quantitative Proteogenomics.
TLDR
Mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 and 39 days after gestation provides evidence for and improve the annotation of 8176 protein-coding genes including 588 novel and 321 refined gene models. Expand
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TLDR
Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Expand
Mining the pig genome to investigate the domestication process
TLDR
An outline of the current knowledge on pig domestication is provided by considering both archaeological and genetic data, and several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication are discussed. Expand
Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds
TLDR
The data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species, and show widespread evolution of proximal regulatory elements. Expand
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