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Estimates of autozygosity through runs of homozygosity in farmed coho salmon

Grazyella M. Yoshida, Pablo Cáceres, Rodrigo Marín-Nahuelpi, Ben F. Koop, José M. Yáñez
doi: https://doi.org/10.1101/2020.02.01.930065
Grazyella M. Yoshida
1Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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Pablo Cáceres
1Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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Rodrigo Marín-Nahuelpi
1Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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Ben F. Koop
2Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
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José M. Yáñez
1Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
3Nucleo Milenio INVASAL, Concepción, Chile
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  • For correspondence: jmayanez@uchile.cl
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Abstract

The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon breeding nuclei, genotyped using a 200K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two “pure” lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.

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Posted February 02, 2020.
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Estimates of autozygosity through runs of homozygosity in farmed coho salmon
Grazyella M. Yoshida, Pablo Cáceres, Rodrigo Marín-Nahuelpi, Ben F. Koop, José M. Yáñez
bioRxiv 2020.02.01.930065; doi: https://doi.org/10.1101/2020.02.01.930065
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Estimates of autozygosity through runs of homozygosity in farmed coho salmon
Grazyella M. Yoshida, Pablo Cáceres, Rodrigo Marín-Nahuelpi, Ben F. Koop, José M. Yáñez
bioRxiv 2020.02.01.930065; doi: https://doi.org/10.1101/2020.02.01.930065

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