Genome-wide associations with longevity and reproductive traits in U.S. rangeland ewes

Authors: SMITCHGER, JAMIN - University Of Idaho; Taylor, Joshua - Bret; Mousel, Michelle; SCHAUB, DANIEL - University Of Idaho; THORNE, JACOB - Texas A&M Agricultural Experiment Station; BECKER, GABRIELLE - University Of Idaho; MURDOCH, BRENDA - University Of Idaho

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2024
Publication Date: 5/27/2024
Citation: Smitchger, J., Taylor, J.B., Mousel, M.R., Schaub, D., Thorne, J., Becker, G., Murdoch, B. 2024. Genome-wide associations with longevity and reproductive traits in U.S. rangeland ewes. Frontiers in Genetics. 15. Article 1398123. https://doi.org/10.3389/fgene.2024.1398123.
DOI: https://doi.org/10.3389/fgene.2024.1398123

Interpretive Summary: Improving longevity (productive life) of a ewe has the potential to provide economic benefits to the producer, as well as support favorable animal welfare and sustainable farming practices. Characterizing genetic factors influencing ewe longevity and related traits would improve lifetime production of sheep through early, informed selection of replacement ewes. Towards this aim, ewe longevity, lambing and weaning traits were evaluated through a genome-wide association study to identify potential associations with genetic markers. The genes implicated by our results are associated with immune function, dentition, and reproduction. The genetic associations we identified may be used to improve ewe longevity if prioritized during the application of genomic selection.

Technical Abstract: Improving ewe longevity is an important breeding and management goal, as death loss and culling of mature ewes can be an economic burden in the sheep industry. Ewe longevity can be improved by selecting for sheep with positive health and reproductive outcomes; however, identifying ewes with superior longevity cannot be accomplished until the end of their reproductive life, which is inconducive to early selection decisions. Characterizing genetic factors underpinning ewe longevity and related traits would improve the stayability of United States sheep through early, informed selection of replacement ewes. Towards this aim, ewe longevity, lambing and weaning traits were evaluated through genome-wide association study (GWAS) to identify potential associations with markers on a high-density SNP array. Traits evaluated included longevity, parity and the lifetime and average number of lambs born, lambs born alive, lambs weaned and weight of lambs weaned. Flock records of Rambouillet (n = 480), Polypay (n = 404), Suffolk (n = 182) and Columbia (n = 64) ewes (N = 1,130) were analyzed against 503,617 SNPs in across-breed and within-breed GWAS conducted with the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model in R. Flock longevity ranged from 1.59 to 9.08 years, with Suffolk having the shortest mean longevity (5.31 ± 1.91 years) and Rambouillet ewes having the greatest (6.34 ± 1.56 years). Additionally, Rambouillet ewes achieved the highest average parity and Polypay ewes had the greatest average lambing and weaning traits. Through Pearson correlation testing, longevity was significantly correlated with all other traits, and the strongest correlations were identified between longevity and ewe parity (r = 0.93, p-value =0.001) and longevity and lifetime weight of lambs weaned (r = 0.86, p-value =0.001). The across-breed GWAS identified 31 genome-wide significant SNPs and within-breed GWAS for Rambouillet, Polypay, and Suffolk ewes identified an additional 22 significant SNPs. The most significant results were rs411309094 associated with longevity in across-breed GWAS (P-value = 8.3E-13) and rs429525276 associated with both longevity (P-value = 6.4E-15) and parity (P-value = 4.8E-15) in Rambouillet GWAS. Significant SNPs were identified within or in proximity (± 50 kb) of genes with known or proposed roles in the immune system, dentition, and reproduction. Genes containing significant SNPs included ALPL, ANOS1, ARHGEF26, ASIC2, ASTN2, ATP8A2, CAMK2D, CEP89, DISC1, ITGB6, KCNH8, MBNL3, MINDY4, MTSS1, NRXN3, PLEKHA7, PRIM2, RNF43, ROBO2, SLCO1A2, TMEM266, TNFRSF21, UNC13C, ZNF804B. This study proposes multiple SNPs as candidates for use in selection indices and suggests genes for further research towards improving understanding of the genetic factors contributing to longevity and production traits of ewes.