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Open AccessArticle

Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon

1
Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8820808, Chile
2
Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC V8W 2Y2, Canada
3
Nucleo Milenio INVASAL, Concepción 4030000, Chile
*
Author to whom correspondence should be addressed.
Genes 2020, 11(5), 490; https://doi.org/10.3390/genes11050490
Received: 3 April 2020 / Revised: 23 April 2020 / Accepted: 24 April 2020 / Published: 30 April 2020
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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 (Oncorhynchus kisutch) breeding nuclei, genotyped using a 200 K 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. View Full-Text
Keywords: admixture; autozygosity; inbreeding; run of homozygosity; Oncorhynchus kisutch; runs of homozygosity; pedigree admixture; autozygosity; inbreeding; run of homozygosity; Oncorhynchus kisutch; runs of homozygosity; pedigree
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MDPI and ACS Style

Yoshida, G.M.; Cáceres, P.; Marín-Nahuelpi, R.; Koop, B.F.; Yáñez, J.M. Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon. Genes 2020, 11, 490. https://doi.org/10.3390/genes11050490

AMA Style

Yoshida GM, Cáceres P, Marín-Nahuelpi R, Koop BF, Yáñez JM. Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon. Genes. 2020; 11(5):490. https://doi.org/10.3390/genes11050490

Chicago/Turabian Style

Yoshida, Grazyella M.; Cáceres, Pablo; Marín-Nahuelpi, Rodrigo; Koop, Ben F.; Yáñez, José M. 2020. "Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon" Genes 11, no. 5: 490. https://doi.org/10.3390/genes11050490

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