147 Determining Status of Five Genetic Conditions in U.S. Sheep with a Medium-Density Ovine Bead Array
Authors: Lewis Ronald M , Freking Bradley A , Heaton Michael P , Gore Klint , Burke Joan M , Pejsar Benjamin G , Burgett Russell L , Brown Daniel J 
Published: November 2023

Abstract
Using molecular information in genetic evaluation has become routine in most livestock species. Small ruminants, however, are lagging in use of this technology, partly due to the higher cost of genotyping versus the value of the individual animal. Using a single genotyping platform to simultaneously obtain information for making genomic predictions, identifying genetic condition status, and verifying parentage avoids costs of running multiple DNA tests. Our objective was to develop and validate a process to obtain accurate genotypes for genetic conditions using a medium-density array, and to estimate their frequencies in U.S. sheep breeds. Samples (DNA) from 10,569 sheep from 9 breeds in the National Sheep Improvement Program, primarily Katahdin (8,657), Rambouillet (886), and Polypay (584), were genotyped with a commercial 50k single nucleotide polymorphism (SNP) bead chip. Genotypes for 5 genetic conditions, ovine progressive pneumonia (OPP) susceptibility (TMEM154), scrapie susceptibility (PRNP), double muscle (MSTN), callipyge (CLPG), and booroola FecB (BMPR1B), were determined using 66 SNP genotypes extracted from the bead chip. Targeted SNP markers were replicated 2 to 8 times on the array. The TMEM154 diplotypes were obtained by combining genotypes at 10 SNP markers. Variants for PRNP codon 136 and 171 were determined using 6 markers. The accuracy of assigning genetic status was validated using 15 reference DNA with known genotypes submitted blindly to the commercial laboratory. Consistency of replicated calls for an SNP was also evaluated. Following in-house laboratory-based quality control of the assay, acceptance of a genotype involved two steps. First, at least 60% of the replicated SNP on an animal needed to be assigned a genotype. Second, amongst those SNP genotyped, at least 60% needed to detect the same nucleotide. This strategy resulted in 98.4% and 90.9% of the animals having genetic status scored for PRNP and TMEM154, respectively. Where genotypes were accepted, OPP and scrapie susceptibility was assigned based on TMEM154 diplotypes and PRNP codons 136 and 171 genotypes, respectively. As shown in Table 1, genetic condition status differed appreciably among Katahdin, Polypay, and Rambouillet. Nearly 60% of Katahdins were characterized as highly susceptible to OPP while such was so in less than 15% Polypay and Rambouillet. Most (93.3%) Polypay were deemed scrapie resistant, with a majority of Katahdin (93.1%) and Rambouillet (80.6%) either resistant or rarely susceptible to this disease. However, 18.6% of Rambouillet were characterized as highly susceptible to scrapie. No animals carried the callipyge or FecB mutation. The double muscle mutation also was rare; in Katahdins, 2.7 and 0.2% of animals carried one or two copies, respectively. The approach developed accounted for genotyping inaccuracies, with full validation of genetic status. Furthermore, considerable variation in susceptibilities to OPP and scrapie was detected among breeds, which can be used in defining breeding objectives.