Multiple Asian pig origins revealed through genomic analyses

Luetkemeier, Erin S.; Sodhi, Monika; Schook, Lawrence B.; Malhi, Ripan S.

doi:10.1016/j.ympev.2009.11.004

Cited by 42 publications

(44 citation statements)

References 24 publications

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“…Observations such as these suggest that it would not be necessary for polymorphisms in proteins of the electron transport chain to cause dramatic changes in protein function, as subtle differences in proton motive force could meaningfully impact feed efficiency. Despite low bootstrap values for the fine structure of the tree, our data illustrate a phylogenic relationship that is consistent with features of trees reported previously and show that Mangalica swine are most closely related to European breeds (22,23,26,27). The grouping of Turopolje and Mangalica breeds with European swine is unsurprising.…”

Section: Discussionsupporting

confidence: 89%

“…It was noted that haplotypes observed within a single herd indeed vary (32). Previously published swine phylogenies often support the relationship of Yorkshire breeds with other European breeds, and it may be important to consider nuclear loci in any phylogeny of swine in addition to mtDNA sequences in order to obtain an accurate evolutionary lineage (22)(23)(24)(25)(26)(27)(28). The observation that both Asian and European haplotypes still exist may suggest that none of the haplotypes studied were associated with more optimal production or metabolic characteristics.…”

Section: Discussionmentioning

confidence: 99%

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Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically DisparateSus scrofaBreeds

Cannon

Brandebourg

Köhn

et al. 2014

Animal Biotechnology

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Next generation sequencing of mitochondrial DNA (mtDNA) facilitates studies into the metabolic characteristics of production animals and their relation to production traits. Sequence analysis of mtDNA from pure-bred swine with highly disparate production characteristics (Mangalica Blonde, Mangalica Swallow-bellied, Meishan, Turopolje, and Yorkshire) was initiated to evaluate the influence of mtDNA polymorphisms on mitochondrial function. Herein, we report the complete mtDNA sequences of five Sus scrofa breeds and evaluate their position within the phylogeny of domestic swine. Phenotypic traits of Yorkshire, Mangalica Blonde, and Swallow-belly swine are presented to demonstrate their metabolic characteristics. Our data support the division of European and Asian breeds noted previously and confirm European ancestry of Mangalica and Turopolje breeds. Furthermore, mtDNA differences between breeds suggest function-altering changes in proteins involved in oxidative phosphorylation such as ATP synthase 6 (MT-ATP6), cytochrome oxidase I (MT-CO1), cytochrome oxidase III (MT-CO3), and cytochrome b (MT-CYB), supporting the hypothesis that mtDNA polymorphisms contribute to differences in metabolic traits between swine breeds. Our sequence data form the basis for future research into the roles of mtDNA in determining production traits in domestic animals. Additionally, such studies should provide insight into how mtDNA haplotype influences the extreme adiposity observed in Mangalica breeds.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically DisparateSus scrofaBreeds

Cannon

Brandebourg

Köhn

et al. 2014

Animal Biotechnology

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“…Observed heterozygosity ranged from 0.35 to 0.60, with an average ~ 0.5 across 17 autosomal chromosomes in 11 European pig breeds [25]. These values were similar to those in Chinese populations, ranging from 0.429 to 0.677 [19-20]. The expected heterozygosity was much higher than the observed heterozygosity in many reports.…”

Section: Pig Genomic Diversity Within Sitesmentioning

confidence: 75%

Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock

Plastow¹

2011

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We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (FIS), population differentiation (FST), and Nei’s genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher FIS, and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies.

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“…Further east, a genetic survey of pigs originally found on the island of Lanyu off the east coast of Taiwan discovered a highly unusual haplotype (31,50) that, despite its genetic distance, still clusters alongside other East Asian signatures. There are currently no wild boar on Lanyu, suggesting either that the wild ancestor of these pigs was endemic to Lanyu and has since been exterminated, or that Lanyu domestic pigs were derived from an as-yet-undiscovered population of wild boar whose genetic differentiation may be explained by rising and falling sea levels discussed previously.…”

Section: Cryptic Pig Domestication In Southeast Asia and The East Chimentioning

confidence: 99%

Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA

Larson

Liu

Zhao

et al. 2010

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

286

188

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The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.Asian colonization | mtDNA | phylogeography

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Multiple Asian pig origins revealed through genomic analyses

Cited by 42 publications

References 24 publications

Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically DisparateSus scrofaBreeds

Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically DisparateSus scrofaBreeds

Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock

Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA

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