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

Investigating inbreeding in the turkey (Meleagris gallopavo) genome

Sarah M Adams  1 , Martijn F L Derks  2 , Bayode O Makanjuola  1 , Gabriele Marras  3 , Ben J Wood  4 , Christine F Baes  5
Affiliations

Investigating inbreeding in the turkey (Meleagris gallopavo) genome

Sarah M Adams et al. Poult Sci. 2021 Nov.

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 (FPED) with genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). 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 (FROH = 0.27; FGRM = 0.32) were higher than coefficients estimated from pedigree records (FPED = 0.14). Correlations between FROH and FPED, FROH and FGRM, and FPED and FGRM ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between FROH from different lengths and FPED 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.

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Figures

Figure 1
Figure 1
Number of runs of homozygosity (ROH) per individual and the length of the genome covered by ROH in megabase pairs (Mb) for lines A, B, and C.
Figure 2
Figure 2
Mean percent coverage of runs of homozygosity per chromosome along the turkey genome (calculated standard errors for each bar ranged from 0.00 to 0.01).
Figure 3
Figure 3
Distribution of inbreeding coefficients based on pedigree information (FPED), runs of homozygosity (FROH), and the genomic relationship matrix (FGRM) for each turkey line.
See this image and copyright information in PMC

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