Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia

Wu, Guisheng; Yao, Yong-Gang; Qu, Kaixing; Ding, Zijing; Li, Hui; Palanichamy, Malliya Gounder; Duan, Ziyuan; Li, Ning; Chen, Yaosheng; Zhang, Yaping

doi:10.1186/gb-2007-8-11-r245

Cited by 136 publications

(185 citation statements)

References 58 publications

Supporting

Mentioning

161

Contrasting

Unclassified

Order By: Relevance

“…In addition to the p value, Watterson's estimator (y w ) was calculated from the observed number of polymorphic sites in samples, and this also suggested that the level of diversity in the MC1R-coding region was low in Chinese domestic pigs (y w ¼ 0.00049), comprising 14% of the diversity found in Chinese wild boars (y w ¼ 0.00356). Together, our findings show low levels of MC1R-coding region diversity in Chinese domestic pigs, which is in contrast to previous observations of higher levels of genetic diversity in domesticated pigs (Wu et al, 2007;Ojeda et al, 2006Ojeda et al, , 2008a. Our findings are consistent, however, with the logical theory of domestication events in that genetic diversity is generally thought to become lower after domestication.…”

Section: Genetic Diversitycontrasting

confidence: 57%

“…In contrast, 16 unique haplotypes were observed in the Chinese wild boar samples, including two previously described haplotypes, MC1R*1 and MC1R*5 (Giuffra et al, 2000;Kijas et al, 1998Kijas et al, , 2001. The frequency of haplotypes in Chinese wild boars ranged from 1.25 to 13.75%, indicating that many rare haplotypes were present in Chinese wild boars and possibly reflecting recent population growth as described by Wu et al (2007). In the Chinese wild boar samples, B87.5% of the haplotypes differed only at synonymous sites, which possibly suggests that a strong functional constraint was acting on wild boars to maintain a camouflaging coat colour for survival enhancement in the wild.…”

Section: Sequence Variationmentioning

confidence: 95%

“…However, in Chinese domestic pigs, the p value was significantly smaller in the flanking 'MC1R whole' denotes the 1552 bp region, including the 5 0 untranslated region (5 0 UTR), the coding region and 3 0 UTR. The glucose phosphate isomerase pseudogene (GPIP) and melanocortin receptor 1 (MC1R) data are from this study, and the other data are from previous reports: FABP4 (Ojeda et al, 2006), mitochondrial DNA (Wu et al, 2007), FABP5 (Ojeda et al, 2008a) and IGF2 (Ojeda et al, 2008b).…”

Section: Test For Selectionmentioning

confidence: 99%

“…As one of the first domesticated animals in China, the presence of domesticated pigs can be traced back to B8000 years (Yuan and Rowan, 2002). Our previous research on mitochondrial DNA showed that Chinese domestic pigs were separately domesticated from wild boars in the Mekong region and in the middle and downstream regions of the Yangtze River (Wu et al, 2007). Since the initial domestication, more than 48 indigenous breeds have been domesticated so far (Zhang, 1986).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication

Yang

et al. 2010

Heredity

View full text Add to dashboard Cite

Black coat colour is common in Chinese indigenous domestic pigs, but not among their wild ancestors, and it is thus presumed to be a 'domestication trait.' To determine whether artificial interference contributes to morphological diversification, we examined nucleotide variation from 157 Chinese domestic pigs and 40 wild boars in the melanocortin receptor 1 (MC1R) gene, which has a key role in the coat pigmentation of Sus scrofa. Compared with a pseudogene GPIP, our results showed that the joint effects of demography and selection have resulted in markedly low genetic diversity of MC1R in Chinese domestic pigs. Coalescent simulation and selection tests further suggest that the fixation of two non-synonymous substitutions associated with black colour is the result of artificial selection. In contrast, a much higher genetic diversity and only a single non-synonymous substitution were found among the wild boars, suggesting a strong functional constraint. Moreover, our conclusion is consistent with the preference for black colour in the ancient Chinese sacrificial culture. This case provides an interesting example of a molecular evaluation of artificial livestock selection and its associated cultural impact in ancient China.

show abstract

Section: Genetic Diversitycontrasting

confidence: 57%

Section: Sequence Variationmentioning

confidence: 95%

Section: Test For Selectionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication

Yang

et al. 2010

Heredity

View full text Add to dashboard Cite

show abstract

“…It is widely accepted that within and between populations genetic diversity is essential for effective management practices and to develop sustainable conservation strategies. Most studies of chicken mtDNA rely on sequences of partial control region (Muchadeyi et al, 2008;Razafindraibe et al, 2008) but recent researches used the complete mtDNA genome to reconstruct the history of animal domestication, such as in cattle (Achilli et al, 2008;Bonfiglio et al, 2010), pigs (Wu et al, 2007), chicken (Miao et al, 2013) and sheep . As already alluded two different hypotheses are discernible about the origin of domestic chickens.…”

mentioning

confidence: 99%

The role of mitochondrial DNA to determine the origin of domestic chicken

Lorenzo

Ceccobelli

Panella

et al. 2015

World's Poultry Science Journal

View full text Add to dashboard Cite

Mitochondrial DNA (mtDNA) is has recently lost relevance especially when utilised to study species that are characterised with a history of several migrations. Nonetheless, mtDNA can still represents a useful additional tool in the study of molecular genetic diversity. The reason for the adoption of mtDNA is that it is easy to amplify because it appears in multiple copies in the cells and the mitochondrial gene content is strongly conserved across generations. Thousands of published studies have reached conclusions about population history, patterns of gene flow, genetic structure, and species limits, on the basis of mtDNA sequence variation. MtDNA has been used to study phylo-geographic structure of avian species, and to identify the number of maternal lineages and their geographic origins. Most studies of chicken mtDNA rely on sequences of partial control region but recent researches used the complete mtDNA genome to reconstruct the history of animal domestication. The first genetic study on mtDNA suggests that the Indochinese Red Junglefowl subspecies Gallus gallus gallus is the primary ancestor of the domestic chicken (Gallus gallus domesticus). Other studies showed that at least three subspecies of Gallus gallus were enrolled in the origin of domestic chicken breeds, and that there may be at least two domestication centres: one in Southeast Asia and one in the Indian subcontinent. The authors suggested nine highly divergent clades (named clade A-I) related to geographical distribution in a wide range of domestic chickens and Red Junglefowls across Eurasian regions. Understanding when chickens were transported out of domestication centres and the directions in which they were moved provides information about prehistoric human migration, trade routes and cultural diffusion. MtDNA has been used to infer regions of domestication and to identify the number of maternal lineages and their geographic origins in macroevolution studies. IntroductionThe chicken has a long history of anthropomorphic usage in Southeast and East Asia, where it has been bred for entertainment and show (Macdonald and Blench, 2000). The origin and domestication of chickens has been of interest to people since at least Roman times (Storey et al., 2012). Based on archaeological and historical evidence the domestication of the fowl is thought to have occurred in multiple, independent centres. Archaeological research has identified centres of chicken domestication in India and China; both within the natural range of wild Junglefowl (Crawford, 1990). Chickens were likely domesticated from wild Red Junglefowl, though some have suggested possible genetic contributions from other Junglefowl species (Eriksson et al., 2008;Nishibori et al., 2005). Darwin (1896) was the first to propose that all domestic fowls descended directly from one common ancestor; the Gallus Bankiva, or wild Junglefowl breed that originated in Eastern and Southern Asia. He came to this conclusion based on comparisons of morphology and progeny produced from crosses between vari...

show abstract

Origin and Genetic Diversity of Pig Breeds

Amills

Clop

Ramírez

et al. 2010

Encyclopedia of Life Sciences

View full text Add to dashboard Cite

Genetic and archaeological findings suggest that pig domestication began about 9000–10 000 YBP at multiple sites across Eurasia, followed by their subsequent spread at a worldwide scale. Development of local types throughout the centuries led to the foundation, mostly during the nineteenth century, of current modern breeds with defined phenotypes and production abilities. Extensive intercrossing markedly increased the gene pool of these founder populations. For instance, it is well known that many European pig breeds carry Far Eastern haplotypes at high frequencies because of an ancient introgression with Chinese swine. Since then, artificial selection, genetic bottlenecks and inbreeding have significantly modified the allelic diversity of pig breeds. In the next future, state‐of‐the‐art scientific advances as well as conservation programmes will be fundamental to preserve the genetic reservoir of pig breeds as well as to exploit it in the context of artificial selection schemes. Key Concepts: Pigs were domesticated at multiple locations across Eurasia. Exploratory and commercial journeys favoured the dissemination of European and Far Eastern pigs into Africa and America. England, United States and China were the main centres of breed development during the eighteenth to nineteenth centuries. Genetic variation of pigs has been shaped by the complex interplay of artificial selection, population admixture, inbreeding and genetic drift. Artificial selection is evolution but an accelerated pace; therefore, by comparing breeds that have undergone distinct selective pressures we can glimpse the molecular basis of adaptation. Approximately 20% of local pig breeds face extinction because of dramatic decreases in their census or extensive intercrossing with foreign populations. New genotyping and sequencing technologies will revolutionise knowledge on patterns of diversity in livestock species, including pigs.

show abstract

Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia

Abstract: Background: Previously reported evidence indicates that pigs were independently domesticated in multiple places throughout the world. However, a detailed picture of the origin and dispersal of domestic pigs in East Asia has not yet been reported.

Cited by 136 publications

References 58 publications

Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication

Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication

The role of mitochondrial DNA to determine the origin of domestic chicken

Origin and Genetic Diversity of Pig Breeds

Contact Info

Product

Resources

About