Sheep GEMS provides project update

Authors: Freking, Bradley - Brad

Submitted to: Sheep Industry News
Publication Type: Trade Journal
Publication Acceptance Date: 9/27/2024
Publication Date: 10/4/2024
Citation: Freking, B.A. 2024. Sheep GEMS provides project update. Sheep Industry News. ASI Weekly Newsletter. October 4, 2024. p.4-5.

Interpretive Summary:

Technical Abstract: The Sheep GEMS project has enabled producers to capture genetic information from their animals with the intent to simultaneously make genomic predictions of breeding values, verifying parentage, and identifying genetic condition status. Such multiple uses of a single genotyping platform will help avoid the extra costs of running DNA tests separately for these different purposes. Our objective was to develop and validate a process to accurately obtain genetic conditions as one outcome of genotyping with a common medium-density (50K markers) single nucleotide polymorphism platform (assay), and to estimate frequencies of those genetic conditions in American sheep breeds. The first of those genetic conditions -TMEM154- was covered in a prior Sheep GEMS update, which explained favorable and unfavorable genetic effects on susceptibility to ovine progressive pneumonia. Samples (DNA) from 15,586 sheep were genotyped from four breeds in the National Sheep Improvement Program: Katahdin (12,495), Rambouillet (1276), Polypay (1292), and Suffolk (523). Genotypes for five genetic conditions, namely: OPP susceptibility (TMEM154), scrapie susceptibility (PRNP), double muscle (MSTN), callipyge (CLPG), and booroola fecundity (FecB) were determined using 66 SNP extracted from the 50K platform. Each targeted SNP marker was replicated 2 to 8 times each on the assay. A total of 11 SNP were used to determine the TMEM154 variants present. Variants for PRNP codons 136 and 171 were determined by combining information from 6 SNP markers. The accuracy of assigning genetic status was validated using 15 reference DNA with known genotypes submitted blindly to a commercial laboratory. The consistency of the genotypes for repeats of a SNP on the array also was evaluated. Following in-house laboratory-based quality control of the assay, the acceptance of a genotype for reporting to a producer involved two steps. First, at least 60% of the replicated marker SNP on an animal needed to be assigned a genotype. Second, amongst those SNP, at least 60% needed to detect the same genotype. This strategy resulted in 98.8% of the animals having genetic status scored for PRNP. Where genotypes were accepted, scrapie susceptibility was assigned based on PRNP codons 136 and 171 genotypes. Genetic conditions for MSTN, CLPG, and FecB were based on the allele present at a single SNP marker. It is not surprising that there were no animals from any of the four breeds in this dataset that contained the CLPG or FecB mutations. The CLPG mutation originated in the Dorset breed. Its detrimental impact on tenderness of loin muscle has led to a strong push for its removal from American populations. The use of the booroola fecundity mutation has mostly been limited to intensive accelerated lambing production systems, with minimal implementation in the United States. The frequency of the MSTN mutation, which originated in the Texel breed, was also small. In Katahdins, 4.3 and 0.4% of animals carried one or two copies, respectively. In Suffolks, those equivalent values were 6.2 and 0.2%. The MSTN variant was not detected in either of the Rambouillet or Polypay breeds. Lines within breeds that are targeted for use as terminal sires would benefit the most from increased selection for MSTN. Genetic condition status of PRNP differed appreciably among Katahdin, Polypay, Rambouillet, and Suffolk breeds. Most Polypay(92.0%) were deemed scrapie resistant, with a majority of Katahdin (93.3%), Suffolk (92.5%) and Rambouillet (83.5%) either resistant or rarely susceptible to this disease. However, 15.8% of Rambouillet were characterized as highly susceptible to scrapie. Selection to increase the amount of scrapie resistant genotypes is considered a key part of the National Scrapie Eradication effort in the U.S. An evaluation of any unintended consequences of selection for scrapie resistance o