Meta-assembly of selection signatures in four groups within European, Zebu, African and Composite breeds of cattle.

<p>Meta-assembly of selection signatures in four groups within European, Zebu, African and Composite breeds of cattle.</p

A list of selection tests used in published studies on Bovine selection signatures.

<p>A list of selection tests used in published studies on Bovine selection signatures.</p

Map of selection signature hotspots captured in the meta-assembly of cattle breeds and groups.

<p>Middle Panels labelled as “Cattle Breeds” and “Cattle Groups”, show the location of prominent regions in the cattle breeds and groups, respectively represented with the unique colours as shown in the legends. The clustered dots, within a locus, located on top of each other represent shared selection signatures across the breeds and groups, each of which has been validated in multiple investigations. Lower Panel labelled as “Gene density” shows distribution of bovine genes on each chromosome that ranges 0–80 genes/Mb (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153013#pone.0153013.s014" target="_blank">S7 Fig</a> shows high-resolution comparison of MSS and genes per Mb in European). Top Panel labelled as "Candidate Genes" shows genomic locations of a few major genes underlying the outstanding peaks representing classic selective sweep regions in the meta-assemblies. Complete list of prominent regions, localized top MSS and underlying genes within the groups and breeds of cattle are respectively shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153013#pone.0153013.s004" target="_blank">S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153013#pone.0153013.s005" target="_blank">S5</a> Tables.</p

Summary of genome-wide scans on Bovine selection signatures.

<p>Summary of genome-wide scans on Bovine selection signatures.</p

Plot of relationship matrix and DNA score (<i>d</i>_<i>i</i>) weighting computed from 46 studies that published selection signature using European cattle.

<p><b><i>n</i></b>_{<b><i>i</i></b>} shows total number of DNA samples from European breed(s) from a particular study. The relationship score was computed as proportion of common samples between each pair of studies and it range between 0 and 1.</p

Meta-assembly of selection signatures of Holstein, Brown Swiss, Jersey, Simmental (Fleckvieh), Angus, Charolais, Hanwoo, Hereford, Limousin, Piedmontese, Brahman, Gir and Nellore cattle.

<p>Meta-assembly of selection signatures of Holstein, Brown Swiss, Jersey, Simmental (Fleckvieh), Angus, Charolais, Hanwoo, Hereford, Limousin, Piedmontese, Brahman, Gir and Nellore cattle.</p

Meta-assembly of selection signatures of Belgian Blue, Braunvieh, Guernsey, Italian Brown, Marchigiana, Murray Grey, Norwegian Red, Romagnola, Shorthorn, Santa Gertrudis, NDama and Sheko.

<p>Meta-assembly of selection signatures of Belgian Blue, Braunvieh, Guernsey, Italian Brown, Marchigiana, Murray Grey, Norwegian Red, Romagnola, Shorthorn, Santa Gertrudis, NDama and Sheko.</p

Table6.XLSX

<p>Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (N_e) revealed a demographic trend of diminishing N_e over time and that recent estimated N_e values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (F_ROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.</p

DataSheet1.PDF

<p>Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (N_e) revealed a demographic trend of diminishing N_e over time and that recent estimated N_e values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (F_ROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.</p

Table1.XLSX

<p>Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (N_e) revealed a demographic trend of diminishing N_e over time and that recent estimated N_e values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (F_ROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.</p