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    The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds

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    Author
    Purfield, Deirdre C
    McParland, Sinead
    Wall, E.
    Berry, Donagh cc
    Keyword
    runs of homozygosity (ROH)
    sheep
    genetic diversity
    breed effective population size
    pedigree inbreeding coefficient
    Date
    2017-05-02
    
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    URI
    http://hdl.handle.net/11019/1511
    Citation
    Purfield DC, McParland S, Wall E, Berry DP (2017) The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS ONE 12(5): e0176780. https://doi.org/10.1371/journal.pone.0176780
    Abstract
    Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.
    Funder
    Department of Agriculture, Food and the Marine, Ireland
    Grant Number
    11/S/112; 14/S/849
    ae974a485f413a2113503eed53cd6c53
    https://doi.org/10.1371/journal.pone.0176780
    Scopus Count
    Collections
    Livestock Systems
    Animal & Bioscience

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