Dr. Calhoun's Research Group

Research Project Introduction

During the 1800s, the American Bison population was hunted to near extinction by trappers and settlers moving westward through the Great Plains.  Estimates suggest that nearly 200,000 animals were killed annually until around only around 300-500 animals remained dispersed in small, sheltered herds.  

As bison were found to be more resistant to temperature extremes and tended to have easier calvings due to smaller calf sizes, ranchers intentionally began crossing bison with domestic cattle to produce hybrids with these preferred characteristics but retained the temperament of domesticated animals.  In many cases, however, the crosses were considered unsuccessful as male 50/50 hybrids were usually sterile, among other difficulties.  Not until the hybrid fraction reaches around 3/8 bison, do many of these concerns disappear.  Thus the "Beefalo" was born (Figure 1). 

Today to qualify as "Beefalo” for meat production purposes, an animal must contain between 37.5% - 17% bison DNA. This percentage is calculated mainly through breeding parentage and not by direct DNA analysis. As a result, favorable bison characteristics are often variably expressed between two beefalo animals, despite BOTH animals being 3/8 bison.  Current Bison DNA genetic testing is inadequate for this analysis as at most 18 genetic markers are used to evaluate the 30 individual chromosome pairs.  Our research attempts to identify DNA sequences (i.e., segregation sites) that can be used to more efficiently track Bison DNA in beefalo hybrids and to help predict the inheritance of favorable Bison characteristics in bred offspring.  Comparing publicly available genomic sequences, numerous segregation single nucleotide polymorphisms (i.e., sSNPs) between Bison and domestic cattle can be identified across all 30 chromosomal pairs and are the targets for our studies.  

Our recent work with DNA-based blood-typing (Calhoun 2020) and Eye Color prediction (Grey 2024), suggest that a technique known as allele-specific PCR (as-PCR) could be used to interrogate sSNPs within Cattle, Bison and Beefalo genomic samples.  This technique exploits the need for DNA polymerases to have a relatively stable 3' end of a primer annealed to a template before copying that strand (Figure 2).  By intentionally positioning a primer so that the 3' terminal  nucleotide rests right at the sSNP position, we create a situation that allows amplification when only one of the sSNPs alleles are present.  Thus, we should be able to determine the presence of bison specific alleles without the need for sequencing by using this technique.      

RESS participant experiences 

This project will allow RESS participants to 1) become adept at polymerase chain reaction and horizontal gel electrophoresis, 2) learn how to optimize reaction conditions that balance amplification efficiency and specificity, 3) gain experience in comparative genomics by visualizing/manipulating genetic sequences in silico, 4) learn how to create primers that facilitate allele-specific amplification, and 5) learn to communicate and collaborate with other peer researchers in a laboratory setting. 

References

Calhoun ES, Jungling P, Prillwitz KB, Khan I, Susan S, Papciak J, Martin MP. 2020. Using allele-specific primer PCR to determine ABO blood type genotypes. Article 26. In: McMahon K, editor. Advances in biology laboratory education. Volume 41. Publication of the 41st Conference of the Association for Biology Laboratory Education (ABLE). https://doi.org/10.37590/able.v41.art26

Gray AR, Dech SR, Plath TM and Calhoun ES. 2024. Using allele-specific PCR to genotype single nucleotide polymorphisms associated with eye color prediction. Article 25 In: Boone E and Thuecks S, eds. Advances in biology laboratory education. Volume 44. Publication of the 44th Conference of the Association for Biology Laboratory Education (ABLE). DOI: https://doi.org/10.37590/able.v44.art25