Genetic parameters and genome-wide association studies for fertility and reproduction traits in U.S. Katahdin sheep based on the single-step GBLUP methodology

Authors: OSPINA, ALEJANDRA TORO - Purdue University; LEWIS, RONALD - University Of Nebraska; Freking, Bradley; Burke, Joan; Murphy Jr, Thomas; Wilson, Carrie; BRITO, LUIZ - Purdue University

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/13/2026
Publication Date: 3/30/2026
Citation: Ospina, A.T., Lewis, R.M., Freking, B.A., Burke, J.M., Murphy, T.W., Wilson, C.S., Brito, L.F. 2026. Genetic parameters and genome-wide association studies for fertility and reproduction traits in U.S. Katahdin sheep based on the single-step GBLUP methodology. Journal of Animal Breeding and Genetics. Article 70048. https://doi.org/10.1111/jbg.70048.
DOI: https://doi.org/10.1111/jbg.70048

Interpretive Summary: Katahdin is one of the fastest-growing sheep breeds in the United States and the first to have genomic selection implemented in its national breeding program. Two reproductive performance traits are currently reported in the Katahdin genetic evaluation: number of lambs born (NLB), and number of lambs weaned (NLW), as indicators of ewe prolificacy, ewe rearing ability, and lamb survival. The genetic basis of these reproductive traits are complex and typically influenced by a large number of genes each with small effects. A search for genomic associations with these reproductive traits in Katahdins has not been previously reported but those results would provide substantial benefits to breeders utilizing genomic information for selection. We report results from the largest genome wide association study conducted in the U.S. Katahdin breed. Associations with four indicator traits (NLB, NLW, age at first lambing, and interval from first to second lambing) of reproduction were identified using datasets provided by the National Sheep Improvement Program (NSIP). A total of 24,067 Katahdin ewe records and genomic data from 10,032 animals were evaluated. We identified 14 significant associations on eight different sheep chromosomes for the four reproductive traits. The candidate genes near these locations have been previously associated with fertility, embryonic development, growth, disease resistance, and climatic adaptation traits. Our findings indicate that fertility and reproduction traits can be improved through direct selection in Katahdin sheep, and genomic selection is likely to play a major role in obtaining more accurate breeding values in younger animals. A better understanding of the biology underlying the genetic control of reproduction in Katahdin sheep has been revealed and will improve ability of breeders to make genetic progress by selection.

Technical Abstract: Sheep production contributes to a secure and diverse food and fiber supply in the United States, with growing ethnic diversity strengthening demand. Katahdin is a composite hair-type sheep breed developed in the United States that has become the most popular breed in many regions of the country and the first one to have genomic selection implemented in its breeding program. Therefore, the main objectives of this study were to estimate variance components of reproductive traits, including number of lambs born (NLB), number of lambs weaned (NLW), age at first lambing (AFL), and interval from first to second lambing (LI), in Katahdin sheep using the single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) methodology, and to identify genomic regions and candidate genes associated with these traits. The datasets used consisted of 127,536 animals in the pedigree, phenotypic records of 56,128 parities from 24,067 ewes, and genomic data from 10,032 animals with 30,308 single-nucleotide polymorphisms (SNP) after quality control. Analyses were performed using the BLUPF90 family of programs. We observed low heritability estimates for all studied traits (0.098 ± 0.004 for NLB, 0.087 ± 0.003 for NLW, 0.091 ± 0.013 for AFL, and 0.083 ± 0.012 for LI). The genetic correlations between the traits ranged from 0.79 ± 0.02 (NLB and NLW) to 0.17 ± 0.02 (AFL and LI). All traits were found to be highly polygenic; however, we identified 14 significant SNP on eight Ovis aries (OAR) chromosomes (3, 6, 7, 8, 9, 12, 13, and 15). These SNP were located near or within a total of 18 candidate genes: four genes associated with NLB (AAK1, GFPT1, SLC23A2, and GDAP1), four with NLW (ARHGAP18, TTLL2, UNC93A, and GPR31), six with AFL (NAP1L5, FAM13A, HS3ST1, CCDC181, NME7, and BLZF1), and four with LI (TAF4, CDH4, CADM1, and SEL1L). These candidate genes have been previously associated with fertility, embryonic development, growth, disease resistance, and climatic adaptation traits. Our findings indicate that fertility and reproduction traits can be improved through direct selection in Katahdin sheep, and genomic selection is likely to play a major role in obtaining more accurate breeding values at a younger age of selection candidates due to the low heritability and high polygenicity of these traits. Although the studied traits are highly polygenic, the candidate genes’ associations enable a better understanding of the biological mechanisms underlying reproductive performance in Katahdin sheep.