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Investigating inbreeding in the turkey (Meleagris gallopavo) genome

The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an i...

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Autores principales: Adams, Sarah M., Derks, Martijn F.L., Makanjuola, Bayode O., Marras, Gabriele, Wood, Ben J., Baes, Christine F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8445901/
https://www.ncbi.nlm.nih.gov/pubmed/34525446
http://dx.doi.org/10.1016/j.psj.2021.101366
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author Adams, Sarah M.
Derks, Martijn F.L.
Makanjuola, Bayode O.
Marras, Gabriele
Wood, Ben J.
Baes, Christine F.
author_facet Adams, Sarah M.
Derks, Martijn F.L.
Makanjuola, Bayode O.
Marras, Gabriele
Wood, Ben J.
Baes, Christine F.
author_sort Adams, Sarah M.
collection PubMed
description The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an individual. The estimation of inbreeding coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of pedigree-based inbreeding coefficients (F(PED)) with genomic-based inbreeding coefficients estimated from ROH (F(ROH)) and the genomic relationship matrix (F(GRM)). A total of 2,616,890 pedigree records were available. Of these records, 6,371 genotyped animals from three purebred turkey (Meleagris gallopavo) lines between 2013 and 2019 were available, and these were obtained using a dense single nucleotide polymorphism array (56,452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a mean number of 84.87 ± 8.79 ROH per animal. Short ROH with lengths of 1 to 2 Mb long were the most abundant throughout the genome. Mean ROH coverage differed greatly between chromosomes and lines. Considering inbreeding coefficient means across all lines, genomic derived inbreeding coefficients (F(ROH) = 0.27; F(GRM) = 0.32) were higher than coefficients estimated from pedigree records (F(PED) = 0.14). Correlations between F(ROH) and F(PED), F(ROH) and F(GRM), and F(PED) and F(GRM) ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between F(ROH) from different lengths and F(PED) substantially increased with ROH length from -0.06 to 0.33. Results of the current research, including the distribution of ROH throughout the genome and ROH-derived inbreeding estimates, can provide a more comprehensive description of inbreeding in the turkey genome. This knowledge can be used to evaluate genetic diversity, a requirement for genetic improvement, and develop methods to minimize inbreeding in turkey breeding programs.
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spelling pubmed-84459012021-09-22 Investigating inbreeding in the turkey (Meleagris gallopavo) genome Adams, Sarah M. Derks, Martijn F.L. Makanjuola, Bayode O. Marras, Gabriele Wood, Ben J. Baes, Christine F. Poult Sci GENETICS AND MOLECULAR BIOLOGY The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an individual. The estimation of inbreeding coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of pedigree-based inbreeding coefficients (F(PED)) with genomic-based inbreeding coefficients estimated from ROH (F(ROH)) and the genomic relationship matrix (F(GRM)). A total of 2,616,890 pedigree records were available. Of these records, 6,371 genotyped animals from three purebred turkey (Meleagris gallopavo) lines between 2013 and 2019 were available, and these were obtained using a dense single nucleotide polymorphism array (56,452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a mean number of 84.87 ± 8.79 ROH per animal. Short ROH with lengths of 1 to 2 Mb long were the most abundant throughout the genome. Mean ROH coverage differed greatly between chromosomes and lines. Considering inbreeding coefficient means across all lines, genomic derived inbreeding coefficients (F(ROH) = 0.27; F(GRM) = 0.32) were higher than coefficients estimated from pedigree records (F(PED) = 0.14). Correlations between F(ROH) and F(PED), F(ROH) and F(GRM), and F(PED) and F(GRM) ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between F(ROH) from different lengths and F(PED) substantially increased with ROH length from -0.06 to 0.33. Results of the current research, including the distribution of ROH throughout the genome and ROH-derived inbreeding estimates, can provide a more comprehensive description of inbreeding in the turkey genome. This knowledge can be used to evaluate genetic diversity, a requirement for genetic improvement, and develop methods to minimize inbreeding in turkey breeding programs. Elsevier 2021-06-29 /pmc/articles/PMC8445901/ /pubmed/34525446 http://dx.doi.org/10.1016/j.psj.2021.101366 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle GENETICS AND MOLECULAR BIOLOGY
Adams, Sarah M.
Derks, Martijn F.L.
Makanjuola, Bayode O.
Marras, Gabriele
Wood, Ben J.
Baes, Christine F.
Investigating inbreeding in the turkey (Meleagris gallopavo) genome
title Investigating inbreeding in the turkey (Meleagris gallopavo) genome
title_full Investigating inbreeding in the turkey (Meleagris gallopavo) genome
title_fullStr Investigating inbreeding in the turkey (Meleagris gallopavo) genome
title_full_unstemmed Investigating inbreeding in the turkey (Meleagris gallopavo) genome
title_short Investigating inbreeding in the turkey (Meleagris gallopavo) genome
title_sort investigating inbreeding in the turkey (meleagris gallopavo) genome
topic GENETICS AND MOLECULAR BIOLOGY
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8445901/
https://www.ncbi.nlm.nih.gov/pubmed/34525446
http://dx.doi.org/10.1016/j.psj.2021.101366
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