Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

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.

Genome‐wide scan for signatures of selection in the Brangus cattle genome

“…The local ancestry results showed that BTA5 has a candidate region almost completely selected towards Zebuine. This is concordant with previous results that reported higher Zebuine proportions than expected in BTA5 (Crum et al, 2021; Paim et al, 2020b; Porto‐Neto et al, 2014). Furthermore, a signature of selection in this region was previously identified by Porto‐Neto et al (2014), who reported a region of 20 Mb under selection in Tropical Composite cattle from Australia that affects several productive traits (parasite resistance, yearling weight, body condition score, coat colour, etc.).…”

“…Our results are quite similar to those reported by Goszczynski et al (2018) in a smaller sample size, where the average Angus fraction was 63.7%. This also agrees with those reported by Paim et al (2020b) and Crum et al (2021), who observed a higher proportion of Angus (74.19% and 72.40%, respectively) in the USA compared with expectations. However, the initial difference in Taurine composition between USA and Argentinean Brangus (resulting from the selection criteria applied by the USA and Argentinean associations) could have been maintained in time due to the low percentage (<5%) of foreign semen (mostly from the US) in the Argentinean breed.…”

“…Results from local ancestry analysis demonstrated that some chromosomes possessed a higher Zebuine genetic proportion than expected, such as BTA5, while others (i.e., BTA26) showed an overrepresentation of Taurine genome. This result matches with previous analyses in the same breed (Crum et al, 2021; Paim et al, 2020b). Not only does the breed composition at the chromosome level diverge from the genome‐wide values, but also varied along the chromosomes.…”

“…This is concordant with values reported by Paim et al (2020b), who estimated a 96.5% probability of this region coming from Angus. Crum et al (2021) confirmed the strong selection in POLLED locus in the same breed, detecting a high Angus genetic proportion of the same region. As POLLED locus possesses dominant inheritance, it was expected that the composite Brangus would show a POLLED phenotype with the mentioned locus in a homozygote or heterozygote status.…”

“…In the present work, several genes were identified within this region that influence different traits, such as growth ( IGF1 ), reproduction ( AMDHD1 ) and immunity ( HAL ). Furthermore, several QTLs were reported in studies for Zebuine or Zebuine x Taurine cattle for traits known to be under strong selection in beef cattle (Crum et al, 2021).…”