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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Animal Health Genomics » Research » Publications at this Location » Publication #404059
Research Project: Strategies to Control Respiratory Diseases of Cattle

Location: Animal Health Genomics

Title: Evaluating the efficiency and accuracy of a commercial test for estimating genetic risk of bovine congestive heart failure

Author
item CARLSON, JADEN - University Of Nebraska
item Heaton, Michael
item Allison, Nathan
item HANGMAN, ALYSSA - Matmacorp
item PETRIK, DUSTIN - Matmacorp
item PISCATELLI, HEATHER - Matmacorp
item VANDER LEY, BRIAN - University Of Nebraska

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 4/24/2023
Publication Date: 4/24/2023
Citation: Carlson, J.M., Heaton, M.P., Allison, N.J., Hangman, A., Petrik, D., Piscatelli, H., Vander Ley, B.L. 2023. Evaluating the efficiency and accuracy of a commercial test for estimating genetic risk of bovine congestive heart failure. bioRxiv. Article 536588. https://doi.org/10.1101/2023.04.24.536588.
DOI: https://doi.org/10.1101/2023.04.24.536588

Interpretive Summary: Bovine congestive heart failure (BCHF) is a significant cause of death in feedlot cattle in the Western Great Plains of North America. Genetic markers have been discovered to be associated with this disease. This discovery prompts the need for efficient and accurate genetic tests so cattle producers can manage their severely affected herds. Ultimately, the genetic test evaluated here was efficient and accurate in most instances and can be a useful tool for producers to select cattle with reduced BCHF risk.

Technical Abstract: Background: Bovine congestive heart failure (BCHF) is a significant cause of death in feedlot cattle in the Western Great Plains of North America. Single nucleotide polymorphisms (SNPs) in the ARRDC3 and NFIA genes have been previously associated with BCHF and genetic tests can classify animals by their risk for disease. Here, our aims were to evaluate the efficiency (genotypes obtained / samples tested) of a rapid DNA extraction kit and the accuracy of a 2-SNP assay for BCHF risk. Methods: Skin biopsies from 100 cattle were randomized and extracted with a proprietary rapid DNA extraction kit. A custom duplex, combined sequence amplification and nucleotide detection (C-SAND) assay was developed and run once on a commercial thermocycling machine to determine the genotypes. Both the rapidly extracted DNA and highly purified reference DNA from the same individuals were genotyped with the 2-SNP assay by operators blinded to the sample identity. The C-SAND genotypes were compared to known genotypes derived from a bead array assay. A priori standards for missing and incorrect genotypes were set at less than 3% and 1%, respectively. Results: When using reference DNA samples, there were no missing and no incorrect C-SAND-derived genotypes, meeting the a priori standards. When DNA samples from the rapid extraction kit were used, genotypes were not determined for 5% of the samples. Of the 95 samples successfully extracted, there were 0% and 3% incorrect genotypes for the respective ARRDC3 and NFIA SNPs. Conclusions: This duplex C-SAND assay and thermocycling machine combination were efficient and accurate when reference DNA was used, meeting a priori standards. Although the reduced efficiency of the rapid extraction kit can be overcome by repeated testing, increased genotype errors present an important issue. Despite these challenges, this rapid extraction kit and assay can be a reasonable tool for producers to select animals with reduced BCHF risk.