Swine Global Genomic Resources: Insights into Wild and Domesticated Populations

Overview

Journal Mamm Genome

Specialty Genetics

Date 2023 Oct 7

PMID 37805667

Authors

Neal R Benjamin

Richard P M A Crooijmans

Luke R Jordan

Courtni R Bolt

Lawrence B Schook

Kyle M Schachtschneider

Martien A M Groenen

Alfred L Roca

Affiliations

Soon will be listed here.

Abstract

Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.

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References

Bosse M, Megens H, Madsen O, Crooijmans R, Ryder O, Austerlitz F . Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations. Genome Res. 2015; 25(7):970-81. PMC: 4484394. DOI: 10.1101/gr.187039.114. View

Elmore M, Burton M, Conrad M, Rytych J, Van Alstine W, Johnson R . Respiratory viral infection in neonatal piglets causes marked microglia activation in the hippocampus and deficits in spatial learning. J Neurosci. 2014; 34(6):2120-9. PMC: 3913866. DOI: 10.1523/JNEUROSCI.2180-13.2014. View

Frantz L, Madsen O, Megens H, Groenen M, Lohse K . Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations. Mol Ecol. 2014; 23(22):5566-74. PMC: 4245187. DOI: 10.1111/mec.12958. View

Frantz L, Schraiber J, Madsen O, Megens H, Cagan A, Bosse M . Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes. Nat Genet. 2015; 47(10):1141-8. DOI: 10.1038/ng.3394. View

Frantz L, Madsen O, Megens H, Schraiber J, Paudel Y, Bosse M . Evolution of Tibetan wild boars. Nat Genet. 2015; 47(3):188-9. PMC: 4455000. DOI: 10.1038/ng.3197. View

Frantz L, Meijaard E, Gongora J, Haile J, Groenen M, Larson G . The Evolution of Suidae. Annu Rev Anim Biosci. 2015; 4:61-85. DOI: 10.1146/annurev-animal-021815-111155. View

Frantz L, Rudzinski A, Nugraha A, Evin A, Burton J, Hulme-Beaman A . Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events. Proc Biol Sci. 2018; 285(1876). PMC: 5904307. DOI: 10.1098/rspb.2017.2566. View

Frantz L, Haile J, Lin A, Scheu A, Georg C, Benecke N . Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. Proc Natl Acad Sci U S A. 2019; 116(35):17231-17238. PMC: 6717267. DOI: 10.1073/pnas.1901169116. View

Gaba R, Elkhadragy L, Boas F, Chaki S, Chen H, El-Kebir M . Development and comprehensive characterization of porcine hepatocellular carcinoma for translational liver cancer investigation. Oncotarget. 2020; 11(28):2686-2701. PMC: 7367657. DOI: 10.18632/oncotarget.27647. View

10.

Giuffra E, Kijas J, Amarger V, Carlborg O, Jeon J, Andersson L . The origin of the domestic pig: independent domestication and subsequent introgression. Genetics. 2000; 154(4):1785-91. PMC: 1461048. DOI: 10.1093/genetics/154.4.1785. View

11.

Groenen M, Archibald A, Uenishi H, Tuggle C, Takeuchi Y, Rothschild M . Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 2012; 491(7424):393-8. PMC: 3566564. DOI: 10.1038/nature11622. View

12.

Hoss M, Kohn M, Paabo S, Knauer F, Schroder W . Excrement analysis by PCR. Nature. 1992; 359(6392):199. DOI: 10.1038/359199a0. View

13.

Larson G, Albarella U, Dobney K, Rowley-Conwy P, Schibler J, Tresset A . Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc Natl Acad Sci U S A. 2007; 104(39):15276-81. PMC: 1976408. DOI: 10.1073/pnas.0703411104. View

14.

Li H, Durbin R . Inference of human population history from individual whole-genome sequences. Nature. 2011; 475(7357):493-6. PMC: 3154645. DOI: 10.1038/nature10231. View

15.

MacLeod I, Larkin D, Lewin H, Hayes B, Goddard M . Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors. Mol Biol Evol. 2013; 30(9):2209-23. PMC: 3748359. DOI: 10.1093/molbev/mst125. View

16.

Meurens F, Summerfield A, Nauwynck H, Saif L, Gerdts V . The pig: a model for human infectious diseases. Trends Microbiol. 2011; 20(1):50-7. PMC: 7173122. DOI: 10.1016/j.tim.2011.11.002. View

17.

Ottoni C, Girdland Flink L, Evin A, Georg C, De Cupere B, Van Neer W . Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol Biol Evol. 2012; 30(4):824-32. PMC: 3603306. DOI: 10.1093/molbev/mss261. View

18.

Overgaard N, Principe D, Schachtschneider K, Jakobsen J, Rund L, Grippo P . Genetically Induced Tumors in the Oncopig Model Invoke an Antitumor Immune Response Dominated by Cytotoxic CD8β T Cells and Differentiated γδ T Cells Alongside a Regulatory Response Mediated by FOXP3 T Cells and Immunoregulatory Molecules. Front Immunol. 2018; 9:1301. PMC: 5999797. DOI: 10.3389/fimmu.2018.01301. View

19.

Pauli J, Whiteman J, Riley M, Middleton A . Defining noninvasive approaches for sampling of vertebrates. Conserv Biol. 2009; 24(1):349-52. DOI: 10.1111/j.1523-1739.2009.01298.x. View

20.

Rytych J, Elmore M, Burton M, Conrad M, Donovan S, Dilger R . Early life iron deficiency impairs spatial cognition in neonatal piglets. J Nutr. 2012; 142(11):2050-6. DOI: 10.3945/jn.112.165522. View