By Bob Weaber, Ph.D.
State Extension Specialist-Beef Genetics
University of Missouri
Beef cattle genetics researchers across the country have recently been armed with a new tool to aid in the search for new DNA markers that describe variation in economically important beef production traits. This new tool is a rapid, high-volume genotyping platform that produces nearly 50,000 genotypes per animal genotyped and genotypes 12 animals at a time on a single chip or glass slide. The system, called the Illumina BovineSNP50 platform, uses single base pair variant markers called single nucleotide polymorphisms (SNPs), called ‘snips’ for short. A base pair is the smallest unit in a DNA sequence represented by the letters A, C, G, and T. Combinations of these four letters form the language or genetic sequence for genes. Genes encode specific protein products produced by cells and influence the phenotype of an animal via expression of a specific gene.
The BovineSNP50 platform represents a step-change in the discovery tools available to beef researchers as it provides much higher density marker saturation across the bovine genome compared to any other tool ever created. The technology behind the BovineSNP50 platform was originally developed for use in human medical research and is now being applied to important agricultural species. Dr. Jerry Taylor at MU was one of the collaborators that helped discover and configure the SNPs for the chip.
Researchers will use BovineSNP50 DNA chip in conjunction with a wide variety of performance records and pedigrees to identify variation at locations in the genome sequence associated with variation in the performance record. These locations are called quantitative trait loci or QTL. One of the overarching goals of much of the research using the BovineSNP50 chip is to describe a large portion of the genetic variation in a trait. It turns out that in cattle and many other species there are a large number of genes that affect any given quantitative trait like weaning weight or marbling or heifer pregnancy rate. Recent discoveries at MU suggest there are greater than 60 genes that affect marbling in cattle. It is estimated that cattle have more than 20,000 genes. Therefore, variation in each of these genes results in small changes in a trait. One advantage of the BovineSNP50 platform is its ability score a very large number of SNP markers across the entire genome.
While research is underway to identify markers associated with traditional traits like growth, calving ease and carcass merit, research projects around the US have been undertaken to identify markers for a variety of traits that are difficult and/or expensive to measure. These include traits like heifer pregnancy, birth weight, feed intake, feed efficiency, disease resistance and the fatty acid profile of beef products. These traits offer significant opportunity to change the cost of production or profitability of beef production systems yet have been difficult to improve using traditional tools like EPDs. These features make such traits good candidates for genetic improvement via marker assisted selection systems. Work also is underway to develop methods for inclusion of DNA marker results in genetic evaluation systems that concurrently leverage the large legacy databases of performance records. Eventually, the expected progeny differences (EPD) that producers are accustomed to utilizing will include data from both DNA marker tests and performance records. Such methods will improve the utility and accuracy of both systems of genetic improvement.
