Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information

Authors: SUMREDDEE, PATTARAPOL - University Of Georgia; TOGHIANI, SAJJAD - University Of Georgia; Hay, El Hamidi; Roberts, Andrew; AGGREY, SAMUEL - University Of Georgia; REKAYA, ROMDHANE - University Of Georgia

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2018
Publication Date: 10/10/2018
Publication URL: http://handle.nal.usda.gov/10113/6471092
Citation: Sumreddee, P., Toghiani, S., Hay, E.A., Roberts, A.J., Aggrey, S., Rekaya, R. 2018. Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information. Journal of Animal Science. 97(1):1-18. https://doi.org/10.1093/jas/sky385.
DOI: https://doi.org/10.1093/jas/sky385

Interpretive Summary: Line 1 Hereford is an important line of cattle that has been developed and maintained as a closed population since 1934. This population provides a unique opportunity to study inbreeding with a relatively complete pedigree. Increase in inbreeding leads to a negative impact on economically important traits. This occurs largely due to the accumulation of deleterious mutations. Furthermore, most of breeding animals in the Line 1 population are highly inbred providing the opportunity to assess the effect of parental inbreeding on progeny performance and fitness. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), average daily gain (ADG), and age at first calving (AFC). The objectives of this study were to: 1) assess inbreeding using pedigree and genomic information 2) determine the effects of global and chromosome specific inbreeding on growth and fertility traits and 3) evaluate the effects of parental inbreeding on progeny performance. Inbreeding depression analyses showed that an increase of 1% in animal inbreeding resulted in a decrease of 1.20 kg, 2.03 kg and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 days for each 1% increase in inbreeding of the cow and her dam, respectively. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected which may be attributed to the ability of animals to adapt to a relatively old inbreeding.

Technical Abstract: This study aimed at assessing inbreeding and its effect on growth and fertility traits using the longtime closed line 1 Hereford cattle population. Inbreeding was estimated based on pedigree (FPED) and genomic information. For the latter, three estimates were derived based on the diagonal elements of the genomic relationship matrix (FGRM) or fixed (at 0.5) minor allele frequencies (FGRM0.5), or runs of homozygosity (ROH) (FROH). The 10,186 animal pedigree was used to calculate FPED. Genomic inbreeding was evaluated using 785 animals genotyped for 30,810 single nucleotide polymorphisms. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), average daily gain (ADG), and age at first calving (AFC). The number of ROH per animal ranged between 6 and 119 segments with an average of 83. The shortest and longest segments were 1.36 and 64.86 Mb long, respectively, reflecting both ancient and recent inbreeding occurring in the last 30 to 40 generations. The percentage average inbreeding was 29.2, 16.1, 30.2, and 22.9 for FPED, FGRM, FGRM0.5, and FROH, respectively. FROH provided the highest correlations with FPED (r = 0.66). Across paternal half-sib families, with minimal variation in FPED, there were substantial variations in their genomic inbreeding. Inbreeding depression analyses showed that an increase of 1% in animal FPED resulted in a decrease of 1.20 kg, 2.03 kg and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 days for each 1% increase in FPED of the cow and her dam, respectively. Using genomic inbreeding, similar impact on growth traits was observed although the magnitude of the effect varied between methods. Across all genomic measures, WWT, YWT, and ADG decreased by 0.21 to 0.53 kg, 0.46 to 1.13 kg, and 0.002 to 0.006 kg/d for each 1% increase in genomic inbreeding, respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity (FROH-CHR) and growth traits. Variability in genomic inbreeding could be useful when deciding between full and half sib selection candidates. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected which may be attributed to the ability of animals to adapt to a relatively old inbreeding.