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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #422068
Research Project: Genomes to Phenomes in Beef Cattle Research

Location: Genetics and Animal Breeding

Title: Genomic heterozygosity in stable beef cattle populations

Author
item Snelling, Warren
item McDaneld, Tara
item Kuehn, Larry

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/20/2024
Publication Date: 2/17/2025
Citation: Snelling, W.M., McDaneld, T.G., Kuehn, L.A. 2025. Genomic heterozygosity in stable beef cattle populations [abstract]. In: Plant and Animal Genome Conference Proceedings, January 10-15, 2025, San Diego, California. Paper No. 59528.

Interpretive Summary:

Technical Abstract: The advantages of heterozygosity in beef cattle are well established. The phenomenon observed as hybrid vigor in crossbred cattle may also affect performance of cattle with stable breed composition, although parental breed composition is not informative to assess heterozygosity in these populations. This study was conducted to evaluate genomic measures of heterozygosity in stable composite and straight-breed cattle and determine relationships with cow productivity. The cattle in this study were either Angus or one of three stable composites developed in the 1970s. Genotypes on calves and their parents were obtained using commercial assays from 2016 to 2019, and with imputation from low-coverage (~0.5x) sequence in 2020 and later. Pedigree imputation was used to fill low-confidence low-pass calls and impute sequence variants to individuals with assay genotypes. Genotypes of assay SNP and variants occurring in protein-coding sequence, untranslated regions and non-coding RNA features were extracted, filtered for MAF (> 0.005) and pruned for LD (r < 0.98), leaving 203,412 variants for analysis. Overall, 24.8% of genotypes were heterozygous (Het) with Angus having the lowest % Het and the 5-breed composite having higher % Het than the four-breed composites. Ranks were reversed for percent of the genome covered by runs of homozygosity (ROH), with Angus having the highest % ROH and the 5-breed composite the lowest. A smaller percentage of the genome (1.7%) was in heterozygosity-rich regions (HRR) than the 11.9% covered by ROH. The HRR metric and inbreeding from the diagonal of the genomic relationship matrix (Fg) were not consistent with heterozygosity indicated by Het and ROH. While Het and ROH suggested Angus was less heterozygous than composites, Angus also had higher HRR than composites, and the 5-breed composite had higher Fg than Angus or the other composites. Cumulative weight weaned by females in these populations was used as a measure of cow productivity. A random regression model with random additive and dominance effects was employed to project total weight weaned by 8-year-old cows. All measures of heterozygosity were associated with 8-year weight weaned. Increased Het and decreased ROH are associated with increased weight weaned (p < 0.01) and explain meaningful variation in projected weight weaned (r2 > 0.18). The HRR and Fg measures both have negative associations (p<0.01) with weight weaned but explain little variation in projected productivity (r2 < 0.03). For each measure, Het, ROH, HRR and Fg, sire measures were moderately correlated with progeny means (0.45 < r < 0.62), indicating selection could influence heterozygosity. Manipulating genomic measures of heterozygosity in populations with stable breed composition may provide an opportunity to improve traits that are affected by heterosis.