Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D‐loop sequences

Révay, Tamás; Bodzsár, N.; Mobegi, V.E.; Hanotte, Olivier; Hidas, A.

doi:10.1111/j.1365-2052.2010.02041.x

Cited by 30 publications

(39 citation statements)

References 9 publications

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“…In this paper, we conducted an mtDNA control region sequences polymorphism analysis in Jiangxi, China. Our analyses revealed there to be five lineages present in this area (Lineages A, B, C, E and G), a finding that is consistent with previous reports (Haunshi et al, 2009;Oka et al, 2007;Revay et al, 2010;Storey et al, 2012). Multiple maternal origins appear to be a general phenomenon among domestic livestock species.…”

Section: Discussionsupporting

confidence: 91%

Phylogeography and origin of Chinese domestic chicken

Huo

Xie

et al. 2013

Mitochondrial DNA

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The loss of local chicken breeds as result of replacement with cosmopolitan breeds indicates the need for conservation measures to protect the future of local genetic stocks. The aim of this study is to describe the patterns of polymorphism of the hypervariable control region of mitochondrial DNA (HVR1) in domestic chicken in China's Jiangxi province to investigate genetic diversity, genetic structure and phylo-dynamics. To this end, we sequenced the mtDNA HVR1 in 231 chickens including 22 individuals which belonged to previously published sequences. A neighbor-joining tree revealed that these samples clustered into five lineages (Lineages A, B, C, E and G). The highest haplotype diversity and nucleotide diversity were both found in Anyi tile-liked gray breed. We estimated that the most recent common ancestor of the local chicken existed approximately 16 million years ago. The mismatch distribution analysis showed two major peaks at positions 4 and 9, while the neutrality test (Tajima's D = -2.19, p < 0.05) and Fu's F-statistics (-8.59, p < 0.05) revealed a significant departure from the neutrality assumption. These results support the idea that domestication of chickens facilitated population increases. Results of a global AMOVA indicated that there was no obvious geographic structure among the local chicken breeds analyzed in this study. The data obtained in this study will assist future conservation management of local breeds and also reveals intriguing implications for the history of human population movements and commerce.

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Section: Discussionsupporting

confidence: 91%

Phylogeography and origin of Chinese domestic chicken

Huo

Xie

et al. 2013

Mitochondrial DNA

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“…The highest haplotype diversity (Hd), was found in VA chicken (0.8440±0.0800), whereas the lowest value (excluding the monomorphic AN) was observed in RO (0.3780±0.1810). Haplotype diversity estimates of all breeds investigated in this study were similar to what was observed in Hungarian breeds by Revay et al (2010). The lack of polymorphism in mitochondrial Dloop region of AN breed may be related to higher degree of inbreeding of this breed as also shown later by the microsatellite analysis.…”

Section: Resultssupporting

confidence: 86%

Phylogeny, Genetic Relationships and Population Structure of Five Italian Local Chicken Breeds

Ceccobelli¹,

Lorenzo²,

Lancioni³

et al. 2013

Italian Journal of Animal Science

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Number and population size of local chicken breeds in Italy is considered to be critical. Molecular data can be used to provide reliable insight into the diversity of chicken breeds. The first aim of this study was to investigate the maternal genetic origin of five Italian local chicken breeds (Ancona, Livorno, Modenese, Romagnola and Valdarnese bianca) based on mitochondrial DNA (mtDNA) information. Secondly, the extent of the genetic diversity, population structure and the genetic relationships among these chicken populations, by using 27 microsatellite markers, were assessed. To achieve these targets, a 506 bp fragment of the D-loop region was sequenced in 50 chickens of the five breeds. Eighteen variable sites were observed which defined 12 haplotypes. They were assigned to three clades and two maternal lineages. Results indicated that 90% of the haplotypes are related to clade E, which has been described to originate from the Indian subcontinent. For the microsatellite analysis, 137 individual blood samples from the five Italian breeds were included. A total of 147 alleles were detected at 27 microsatellite loci. The five Italian breeds showed a slightly higher degree of inbreeding (FIS=0.08) than the commercial populations that served as reference. Structure analysis showed a separation of the Italian breeds from the reference populations. A further sub-clustering allowed discriminating among the five different Italian breeds. This research provides insight into population structure, relatedness and variability of the five studied breeds.

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“…2. (A) Two pie charts showing differences in mtDNA haplogroup frequencies between ancient and modern European chickens. The ancient sample consists of specimens sequenced in this study (n = 38) and from a previous publication (n = 5) (34) and the modern data was compiled from (19,32,39) (Table S5). The colors in A correspond to haplogroups depicted in a phylogenetic tree in B.…”

Section: Resultsmentioning

confidence: 99%

Establishing the validity of domestication genes using DNA from ancient chickens

Flink

Allen²,

Barnett³

et al. 2014

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

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Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone.selective sweep | breed formation | animal domestication | Gallus gallus | cultural history

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Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D‐loop sequences

Cited by 30 publications

References 9 publications

Phylogeography and origin of Chinese domestic chicken

Phylogeography and origin of Chinese domestic chicken

Phylogeny, Genetic Relationships and Population Structure of Five Italian Local Chicken Breeds

Establishing the validity of domestication genes using DNA from ancient chickens

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