Population Structure Analysis of Bull Genomes of European and Western Ancestry

Chung, Neo Christopher; Szyda, Joanna; Frąszczak, Magdalena; Genomes, Bull

doi:10.1038/srep40688

Cited by 12 publications

(12 citation statements)

References 35 publications

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“…2014) or whole‐genome sequencing (Chung et al . 2017; Hayes & Daetwyler 2019). Analysis of genetic diversity typically uses three complementary analysis tools: coordination analysis, genetic distances and model‐based clustering.…”

Section: Domestication Dispersal and Differentiation Of Breedsmentioning

confidence: 99%

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Evolution and domestication of the Bovini species

et al. 2020

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Summary Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species – taurine cattle, zebu and yak – and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y‐chromosomal DNA. The high diversity of European breeds has been shaped through isolation‐by‐distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.

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Section: Domestication Dispersal and Differentiation Of Breedsmentioning

confidence: 99%

“…2015; Chung et al . 2017) or breeds from the same region or country: central Europe (Kukučková et al . 2018), northern Europe (Stronen et al .…”

Section: Domestication Dispersal and Differentiation Of Breedsmentioning

confidence: 99%

Evolution and domestication of the Bovini species

et al. 2020

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“…This trend has provided us novel opportunities for large-scale population-level genome analysis. As a result, many population-level genome projects, such as the 1000 bull genomes project [2], Bird 10 K project [3], and 100,000 genomes project [4], have been launched. Recently, many population-level studies for various species have also been conducted to identify unique genomic features of a specific population of interest.…”

Section: Introductionmentioning

confidence: 99%

Population analysis of the Korean native duck using whole-genome sequencing data

Lee

Heo

et al. 2020

BMC Genomics

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Background: Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. The objective of this study is to perform population and functional analyses of Korean native duck, which has a distinct meat flavor and texture phenotype, using whole-genome sequencing data. To study the distinct genomic features of Korean native duck, we conducted population-level genomic analysis of 20 Korean native ducks together with 15 other duck breeds. Results: A total of 15.56 million single nucleotide polymorphisms were detected in Korean native duck. Based on the unique existence of non-synonymous single nucleotide polymorphisms in Korean native duck, a total of 103 genes related to the unique genomic characteristics of Korean native duck were identified in comparison with 15 other duck breeds, and their functions were investigated. The nucleotide diversity and population structures among the used duck breeds were then compared, and their phylogenetic relationship was analyzed. Finally, highly differentiated genomic regions among Korean native duck and other duck breeds were identified, and functions of genes in those regions were examined. Conclusions: This is the first study to compare the population of Korean native duck with those of other duck breeds by using whole-genome sequencing data. Our findings can be used to expand our knowledge of genomic characteristics of Korean native duck, and broaden our understanding of duck breeds.

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“…The authors however, analysed only a small number of individuals (68 goats and 59 sheep) with a restricted geographic range. Furthermore, selection signatures associated with meat and milk production traits have been reported mostly for breeds of sheep and cattle in the developed countries [8,9,10,11]. To advance our knowledge and understanding of the genome dynamics of indigenous goats vis a vis well-de ned commercial breeds, we analysed 52K SNP genotype data of breeds of goats from a sub-tropical arid environment in Egypt verses temperate European environment, and exposed to contrasting selection pressures, natural versus arti cial.…”

Section: Introductionmentioning

confidence: 99%

Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

Mwacharo¹,

Kim²,

Elbeltagy³

et al. 2019

Preprint

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Background : Goats are distributed worldwide and include many breeds with marked phenotypic variation. Both natural and human driven processes have shaped their genomes. Here, 52K genome-wide SNP genotypes were used to investigate signatures of divergent selection between indigenous goats from an arid hot environment in Egypt and breeds developed under temperate environments in Europe. Three selection signature approaches were used, the di derivative of F ST , iHS and Rsb. Results: Out of a total of 36 candidate regions that were detected to be under selection by the three approaches, the analysis detected nine regions with the strongest selection signatures spanning 134 genes of which 68 were the most significantly functionally enriched. In addition to well-known genes affecting dairy traits ( LAP3 , ABCG2 , MEPE , IBSP , MED28 ) and body weight and stature ( LCORL , NCAPG , CCSER1 , DCAF16 ) in several mammalian species, we found evidence for selection in regions spanning genes implicated in the regulation of fatty acid synthesis and metabolic pathways ( PI4K2B and PPARGC1A ), inflammatory gene expression and autoimmune response pathways ( CXCL8 , HERC5 , RGS18 , TROVE2 ) and spermatogenesis ( SPATA18 , LAP3 ). Other genes not reported before in goats included SLIT2 , PACRGL , GRP125 , DHX15 , SOD3 and KCNIP4 which have been associated with thermal nociception in mice. We also detected a paralog of TBC1D12 , namely TBC1D14 , in one of the candidate regions. TBC1D12 has been linked to environmental adaptation in sheep. Gene ontology analysis revealed the 68 candidate genes were highly enriched in two biological processes viz regulation of G protein-coupled receptor signaling pathway (GO:0045744) and cellular response to stress (GO:0033554). Conclusions: Our results provide evidence that goat genomes have evolved, in part, via diverse positive selection directed at breed formation, at past and recent genetic improvement and adaptation to environments. Based on their uniqueness, these breed-group specific signatures of selection can be considered to be footprints of divergence which may be useful in characterizing genome architecture and diversity in domestic animals and for targeted genetic improvement.

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Population Structure Analysis of Bull Genomes of European and Western Ancestry

Cited by 12 publications

References 35 publications

Evolution and domestication of the Bovini species

Evolution and domestication of the Bovini species

Population analysis of the Korean native duck using whole-genome sequencing data

Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

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