Genomic details explained

With the influx and importance of genetic information available in the form of EPDs and genetic tests for traits, CSU Extension Beef Specialist Jack Whittier says understanding the available information, how it can be used and how it is collected is important for producers.
    “Back in 2003, there was a lot of funding and effort put toward understanding the bovine genome,” says Whittier. “A line one cow, with a very well known pedigree, was the first candidate for identifying the genome of a cow.”
    He continued that, utilizing a host of new tools, the gene map of a cow was determined and the industry continually makes great strides based on that information.
A look at the biology
    DNA is made of a sugar phosphate backbone with side chains, which vary, explains Whittier. Four primary bases compose the side chains of DNA, called adenine, thymine, cytosine and guanine, and they pair specifically.
    “The sequence of the bases becomes the genetic code, and code for various amino acids and proteins,” explains Whittier. “The sequences and how they are arranged becomes a driving factor.”
    Whittier adds that, in the DNA, a series of genes code for specific physical aspects of cattle, including hair coat color and the presence of horns, for example.
    “Cattle have 30 chromosomes,” he says. “The chromosomes contain various base pairs, and they create different proteins. They control the output and the phenotype of the animal itself.”
    As scientists delve further into the realm of genomics, it is at the base pair level that differences can be seen between animals.
    “Along the coding areas, there are specific places called single nucleotide polymorphisms, or SNPs,” continues Whittier. “In simple terms, that is a flag along the chain of information that indicates or has been referenced to more information to specific genes about how the animal behaves, grows or reproduces.”
    The SNPs represent differences in the genetic code from that of the general population and become the key to referencing information for genomic tools.
Using SNPs
    Utilizing chemical and electrical engineering techniques, a tool has been developed to recognize SNPs, called SNP chips.
    “They are a chip that is available to detect the genetic variation among cattle,” he says. “The SNP chip has a specific receptor with an affinity for those sequences, and, as that happens, the SNP chip ‘lights’ up.”
    Whittier also mentions that the technology has continued to improve as more SNPs have been discovered and more information has become available.
    He notes, “The more beads and the more SNPs that are discovered, and how they relate to particular characteristics, the higher chance I have of finding the associated genes that allow a decision.”
Genetics in selection
    “We all understand certainly that the main driver has been, and will continue to be, EPDs,” says Whittier of the utilization of genomic information. “We’ve made a lot of progress in understanding that independent of any DNA information, but the challenge is that the process becomes fairly slow and meticulous because it involves proving progeny.”
    He continues that cost-prohibitive progeny testing, at around $25,000 per bull, combined with the statistic that only one in eight bulls becomes an active bull, has made marker assisted selection (EPDs) attractive in industry.
    One additional benefit is that tests can be done at an earlier age to save money, as well.
    “This doesn’t mean we don’t need to continue to do the conventional comparisons,” Whittier cautions. “DNA is based on relationships with phenotypes, but the number of bulls that are progeny-tested may be less.”
    “As we have more information, and as more of that information is understood and quantified, our ability to make good decisions improves,” he notes.
    “A word of caution: we need to not go too far, but we have the opportunity for continued growth,” Whittier adds. “Good genetics will not overcome a poor environment and poor management. This is not a silver bullet. There is a learning curve, and we will see that in the industry.”
    Jack Whittier addressed attendees of the 2011 Range Beef Cow Symposium in Mitchell, Neb. in late 2011. Saige Albert is editor of the Wyoming Livestock Roundup and can be reached at saige@wylr.net.