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

Jamin A Smitchger; J Bret Taylor; Michelle R Mousel; Daniel Schaub; Jacob W Thorne; Gabrielle M Becker; Brenda M Murdoch

doi:10.3389/fgene.2024.1398123

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

Front Genet. 2024 May 27:15:1398123. doi: 10.3389/fgene.2024.1398123. eCollection 2024.

Authors

Jamin A Smitchger¹, J Bret Taylor², Michelle R Mousel³, Daniel Schaub¹, Jacob W Thorne^{1

4}, Gabrielle M Becker¹, Brenda M Murdoch¹

Affiliations

¹ Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States.
² USDA, Agriculture Research Service, Range Sheep Production Efficiency Research Unit, U.S. Sheep Experiment Station, Dubois, ID, United States.
³ Animal Diseases Research Unit, Agricultural Research Service, US Department of Agriculture, Pullman, WA, United States.
⁴ Texas A&M AgriLife Research and Extension, San Angelo, TX, United States.

Abstract

Introduction: Improving ewe longevity is an important breeding and management goal, as death loss and early culling of mature ewes are economic burdens in the sheep industry. Ewe longevity can be improved by selecting for positive reproductive outcomes. However, the breeding approaches for accomplishing this come with the challenge of recording a lifetime trait. Characterizing genetic factors underpinning ewe longevity and related traits could result in the development of genomic selection strategies to improve the stayability of sheep through early, informed selection of replacement ewes. Methods: Towards this aim, a genome-wide association study (GWAS) was performed to identify genetic markers associated with ewe longevity, reproductive, and production traits. Traits evaluated included longevity (i.e., length of time in the flock), parity and the lifetime number of lambs born, lambs born alive, lambs weaned, and weight of lambs weaned. Ewe records from previous studies were used. Specifically, Rambouillet (n = 480), Polypay (n = 404), Suffolk (n = 182), and Columbia (n = 64) breed 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. Results: The across-breed GWAS identified 25 significant SNPs and the within-breed GWAS for Rambouillet, Polypay, and Suffolk ewes identified an additional 19 significant SNPs. The most significant markers were rs411309094 (13:22,467,143) associated with longevity in across-breed GWAS (p-value = 8.3E-13) and rs429525276 (2:148,398,336) 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 reproduction, dentition, and the immune system. These genes include ALPL, ANOS1, ARHGEF26, ASIC2, ASTN2, ATP8A2, CAMK2D, CEP89, DISC1, ITGB6, KCNH8, MBNL3, MINDY4, MTSS1, PLEKHA7, PRIM2, RNF43, ROBO2, SLCO1A2, TMEM266, TNFRSF21, and ZNF804B. Discussion: 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, reproductive, and production traits of ewes.

Keywords: GWAS; lifetime lambs born; lifetime lambs weaned; litter size; premature culling; productive life; sheep; weaning weight.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. JT and MM received research funds USDA-ARS CWA No. 2056-31610-007-000-D and 2090-32000-036-00D (http://www.ars.usda.gov/main/main.htm). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.