Investigating inbreeding in the turkey (Meleagris gallopavo) genome

Sarah M Adams; Martijn F L Derks; Bayode O Makanjuola; Gabriele Marras; Ben J Wood; Christine F Baes

doi:10.1016/j.psj.2021.101366

Investigating inbreeding in the turkey (Meleagris gallopavo) genome

Poult Sci. 2021 Nov;100(11):101366. doi: 10.1016/j.psj.2021.101366. Epub 2021 Jun 29.

Authors

Sarah M Adams¹, Martijn F L Derks², Bayode O Makanjuola¹, Gabriele Marras³, Ben J Wood⁴, Christine F Baes⁵

Affiliations

¹ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
² Animal Breeding and Genomics, Wageningen University and Research, Wageningen 6700 AH, The Netherlands.
³ Semex Alliance, Guelph, Ontario N1H 6J2, Canada.
⁴ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Hybrid Turkeys, A Hendrix Genetics Company, Kitchener, Ontario N2K 3S2, Canada; School of Veterinary Science, The University of Queensland, Brisbane, Queensland 4072, Australia.
⁵ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland. Electronic address: cbaes@uoguelph.ca.

Abstract

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.

Keywords: genomic relationship matrix; inbreeding coefficient; pedigree; runs of homozygosity; turkey.

MeSH terms

Animals
Genome
Genotype
Homozygote
Inbreeding*
Polymorphism, Single Nucleotide
Turkeys