Genomic analysis of feed efficiency traits in beef cattle using random regression models

Area of Science:

• Animal Genetics and Breeding
• Quantitative Genetics
• Beef Cattle Production

Background:

• Feed efficiency is crucial for beef cattle profitability and sustainability, impacting input demand and methane emissions.
• Traditional feed efficiency calculations use average daily intake and weight gain.
• Longitudinal analysis via random regression models (RRMs) accounts for genetic and environmental effects over time.

Purpose of the Study:

• To propose genomic evaluations for dry matter intake (DMI), body weight gain (BWG), residual feed intake (RFI), and residual weight gain (RWG) using RRMs.
• To compare the goodness-of-fit of RRMs using Legendre polynomials (LP) and B-spline functions.
• To evaluate genetic parameters and inform new selection strategies for feed efficiency traits.

Main Methods:

• Genomic breeding values (GEBVs) were estimated using RRMs under ssGBLUP for Nellore cattle.
• Orthogonal LPs and B-spline functions were employed, with model comparison based on the deviance information criterion (DIC).
• Rankings of weekly and overall GEBVs were compared using Spearman correlation and percentage of common individuals.

Main Results:

• Linear B-spline functions with heterogeneous residual variance showed the best goodness-of-fit.
• Heritability estimates across the 84-day test ranged from 0.03 to 0.30 for DMI, BWG, RFI, and RWG.
• High genetic correlations were observed for DMI and RFI, while BWG and RWG showed negative correlations early in the test.
• GEBV rankings for DMI and RFI at week 8 closely matched overall rankings (Spearman correlation 0.95-1.00).
• BWG and RWG rankings at week 11 showed high correlation with overall rankings (Spearman correlation 0.94-0.98).

Conclusions:

• Random regression models using linear B-splines are a viable method for genomic evaluation of feed efficiency.
• Sufficient additive genetic variance exists for DMI, RFI, BWG, and RWG, supporting moderate selection response.
• Performance testing can be shortened to 56 days for DMI/RFI selection and 77 days for BWG/RWG selection.