Pedigree diversity and implications for genomic selection of Katahdin sheep

Authors: NILSON, SARA - University Of Nebraska; Burke, Joan; MURDOCH, BRENDA - University Of Idaho; MORGAN, JAMES - Round Mountain Consulting; LEWIS, RON - University Of Nebraska

Submitted to: Genetic Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2023
Publication Date: 12/18/2023
Citation: Nilson, S., Burke, J.M., Murdoch, B., Morgan, J.L., Lewis, R.M. 2023. Pedigree diversity and implications for genomic selection of Katahdin sheep. Genetic Selection Evolution. https://doi.org/10.1111/jbg.12842.
DOI: https://doi.org/10.1111/jbg.12842

Interpretive Summary: Sheep producers using genetic/genomic selection through programs such as the National Sheep Improvement Program strive to improve traits such as parasite resistance and increased lamb growth. It is important to understand and maintain genetic diversity within a breed which can be compromised with intense selection. The objective of collaborators from University of Nebraska, USDA-ARS, and University of Idaho was to use pedigree records (up to 92,030) from 1984 to 2019 to estimate the quality and diversity of the pedigree in light of selection using genomic estimated breeding values introduced in 2021. It was determined that the effective population size is sufficient to maintain diversity while achieving progress with selection. Low rates of inbreeding and relatedness were uncovered suggesting that diverse genetic conservation is a low priority, and high levels of accuracy for genomic prediction can be achieved, but intense selection has the potential to cause loss of genetic diversity. These results are important to the U.S. sheep industry, the producers and consultants, geneticists and other scientists involved in improving sheep production.

Technical Abstract: The Katahdin breed gained popularity in the United States as low-input due its medium-size, prolificacy, shedding ability, and propensity to express parasite resistance. Even with increasing registration numbers, the genetic diversity of this breed has yet to be fully explored. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining selection strategies that preserve diversity become pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 provided by the National Sheep Improvement Program (NSIP), our objectives were to 1) estimate the completeness and quality of the pedigree, 2) calculate complimentary diversity statistics for the whole pedigree and relevant reference sub-populations, and 3) assess the impact of current diversity on genomic selection. Statistics were estimated for the whole pedigree, and two reference subpopulations born from 2017 to 2019 defined as: all Katahdins (n = 23,494), and Katahdins with at least three generations of known Katahdin ancestry (n = 9,327). The completeness of the whole pedigree, reference 1, and reference 2 were above 50% through the 4th, 5th, and 7th generation of ancestors, respectively. Effective population size (Ne) estimates ranged from 42 to 450 depending on the method used with an average of 111 animals. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. When only progeny that were selected as replacements were considered, the average generation interval decreased to 2.8 years for the whole pedigree and reference 1, and 2.7 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90%, and 2.94% and 1.46% for the full pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders identified for the whole pedigree and reference 1, with 169 for reference 2. Estimates of the effective number of ancestors were over 150 for the whole pedigree and reference 1 while there were 67 for reference 2. Accuracy of prediction was estimated for genomic reference population sizes from 1k to 25k. Across heritabilities of 0.1, 0.3, and 0.5, prediction accuracies increased as the reference population grew, and plateaued as the reference exceeded 15k animals. The largest differences in accuracy were due to the size of Ne for the population. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. While current Ne estimates suggest that with limited resources (genotyping) high levels of accuracy for genomic prediction can be achieved, intense selection on GEBV has the potential to cause loss of genetic diversity long term.