Analyses of pig genomes provide insight into porcine demography and evolution

By M. Groenen, A. Archibald, H. Uenishi, C. Tuggle, Y. Takeuchi, Max F. Rothschild, C. Rogel-Gaillard, Chankyu Park, D. Milan, H. Megens and 126 more. Nature, 2012

1,345 citations recorded by the source corpus.

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 European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/924ec095bdb0ecd5eb3fea209a841995d6999891

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In Genetics

1. Carissa A. Park
2. Zhi-Liang Hu
3. James M. Reecy
4. Haja N. Kadarmideen
5. Kerstin Howe
6. Paul Flicek

Citations in the corpus

• Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB (2018, background): “Whole-genome assemblies for cattle ((1,2), chicken (3), pig (4), sheep (5), horse (6), catfish (7), rainbow trout (8) and other agricultural species have become available within the last 15 years.”
• Genomics to systems biology in animal and veterinary sciences: Progress, lessons and opportunities☆ (2014, background): “…like cattle (The Bovine Genome Sequencing and Analysis Consortium et al., 2009), sheep (The International Sheep Genomics et al., 2010) and pig (Groenen et al., 2012) have led to a paradigm shift in availability of highthroughput genetic markers ranging from 10,000 to 50,000, 100,000 and up to…”
• The Genome 10K Project: A Way Forward (2015, neutral): “Polypteriformes Polyodontidae Acipenseriformes Hagfishes (71, 0) Lampreys (43, 2) Sharks, rays (1,199, 2) Gars (7, 1) Bowfins (1, 1) Teleosts (30,195, 60) Sturgeons (26, 1) Paddlefish (2, 0) Bichirs (12, 1) Coelacanths (2, 2) Lungfishes (6, 0) Amphibians (6,570, 12) Reptiles, birds, mammals (24,141,”
• The Ensembl gene annotation system (2016, background): “4 67 May 2012 (45) Zebra finch Taeniopygia guttata taeGut3.”
• gEVAL — a web-based browser for evaluating genome assemblies (2016, background): “There are chromosomal, regional overview, detailed region and comparative browser views, in addition to lists of anomalies.”