Abstract
Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.
Highlights
Indicine cattle were first imported into the United States from India in 1906 and from Brazil in the 1920’s and were used via crossbreeding with taurine cattle and backcrossing to develop the Bos taurus indicus Brahman (Sanders, 1980) which has very little residual Bos taurus taurus within its genome (Chan et al, 2010)
For each of the American Breeds, the ANCESTRAL reference panel contained at least twice the number of animals from the ancestral populations than the CRUMBLER reference panel and ancestry estimates produced using the two panels were similar
Statistical power was limited when comparing the Brahman content of the genomes of early- and advancedgeneration animals due to the use of only ∼10% of the animals from each breed in each tail of the haplotype number distribution, these analyses clearly revealed that the Brahman proportion of the genome of these American breeds has increased with generation number and that this increase has occurred almost genome-wide
Summary
Indicine cattle were first imported into the United States from India in 1906 and from Brazil in the 1920’s and were used via crossbreeding with taurine cattle and backcrossing to develop the Bos taurus indicus Brahman (Sanders, 1980) which has very little residual Bos taurus taurus within its genome (Chan et al, 2010). Breed Associations for the American Breeds began to be formed in the 1940’s and advanced generation composite animals exist for the older Brangus, Beefmaster, and Santa Gertrudis breeds. Taurus) and Brahman cattle in Oklahoma, Mississippi, Texas, and Louisiana in the 1930’s and have been stabilized at an expected genome content of 3⁄8 Brahman and 5⁄8 Angus (http://afs.okstate.edu/breeds/cattle/brangus/index.html/). Santa Gertrudis was recognized as a breed by the United States Department of Agriculture in 1940. Beefmaster was recognized as a beef breed by the United States Department of Agriculture in 1954 These American Breeds of cattle provide an interesting opportunity to study the genomic architectures of advanced generation composites with a priori known expected genomic breed proportions based on pedigree that have been exposed to natural selection for adaptation and artificial selection for beef performance traits
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