Genetic architecture of a composite beef cattle population

Area of Science:

• Animal Genetics and Breeding
• Genomic Analysis in Livestock

Background:

• Composite breeds are crucial in the beef industry for combining desirable traits and simplifying herd management.
• Understanding the genetic dynamics of composite populations is essential for effective breeding strategies.

Purpose of the Study:

• To evaluate the genetic composition and characteristics of a three-breed beef cattle composite (CGC) using genomic information.
• To assess changes in breed proportions and identify selection signatures within the CGC population over generations.

Main Methods:

• Genotyping of 248 animals (CGC, Red Angus, Charolais, Tarentaise) using a 777k HD panel.
• Principal component and ADMIXTURE analyses to determine genetic structure.
• Runs of homozygosity (ROH), Fst, and HapFlk analyses to evaluate genomic composition and selection signatures.

Main Results:

• ADMIXTURE analysis showed Tarentaise proportion increased to ~57%, Charolais decreased to ~5%, and Red Angus to ~38% across generations.
• Red Angus had the highest mean ROH length (349.92 Mb), while CGC had the lowest (141.10 Mb).
• New haplotypes formed in CGC around the sixth generation; selection sweeps identified on chromosomes 5 and 14.

Conclusions:

• Progenitor proportions in the CGC composite are not stable across generations, influenced by direct or natural selection.
• Tarentaise contributed valuable traits in a cool, semi-arid environment, suggesting further investigation into its role.
• Genomic analysis provides insights into the evolutionary trajectory of composite breeds.