DNA Technology for Seedstock Producers By Jennifer Minick Bormann Kansas State University We are in the middle of perhaps the most exciting time in beef cattle genetics since the development of EPD 30 years ago. Information directly from DNA has long had the potential to revolutionize cattle breeding, but only very recently has it begun to be incorporated in a way that can influence selection decisions on a large scale. To understand the contribution of genomics information, it’s important to review. Any data we collect on an animal (birth E weight, marbling score, scrotal G circumference, etc.) is made up M of two main components: genetics and environment (G and E in Figure 1). In other words, some of what makes an animal Figure 1. Proportion of phenotypic variation made up good or bad for a given trait is of environmental variance (E), due to the animal’s genetics and additive genetic variance (G), some is due to its environment. and molecular information (M) The environmental portion is for early genomic tests. not passed on, so our goal is to determine how much of that animal’s ‘goodness’ or ‘badness’ for the trait is due to its additive genetics. As breeders, we really only care about the purple part of the chart in Figure 1. Unfortunately, we can never know exactly an animal’s genetic merit. We have to estimate it based on all the data available. The EPD is our best estimate of an animal’s genetic merit and it is based on performance data collected on the animal itself, its relatives and its progeny. The accuracy associated with the EPD is determined by the amount and type of data available. If there are hundreds of progeny records on a bull, his EPD will be estimated with very high accuracy. In other words, we are confident that his EPD is very close to his actual genetic merit. If there is very little information available on a bull, the EPD is still our best estimate of his genetic merit, but we are not as confident that it is very close to his actual genetic merit. That is reflected in his lower accuracy value. A high accuracy EPD is the gold standard as a prediction of genetic merit. There is no better way to know what kind of progeny a bull will produce. Phenotype
The biggest limitation to obtaining high accuracy EPD is the amount of progeny needed to get there. Depending on the trait, this can be very costly. If you have scales, the cost of collecting birth or weaning weights may be negligible. However, some data (carcass, ultrasound, feed intake, etc.) can be very expensive. From a genetic improvement standpoint, the time lag is costly as well. It takes many years for a bull to get high accuracy EPD, which slows the rate of genetic improvement. The billion dollar question posed by developing DNA technology is: Can we bypass the time and expense of collecting a lot of data and go directly to the DNA to learn about an animal’s genetic merit? Early efforts to use DNA in beef cattle selection involved tests for one or two genes. The amount of genetic variation explained by the gene test is represented by the red circle in Figure 1. The first generation of genetic tests explained very little of an animal’s genetic merit for the trait; the red circle was very small. Whether an animal had the correct genotype for a trait as determined by the gene test really had very little
20
to do with his overall genetic merit for that trait (which is predicted by the EPD). This also led to the confusing situation where bulls had gene test results as well as EPD. Over the last fifteen years, scientists have identified thousands of single nucleotide polymorphisms (SNPs) in the bovine genome. These are places in the DNA that are different between animals. Some of these SNPs are in genes and cause differences in the traits we care about. Many of them are in parts of the genome that don’t have any function, but they may be close to genes that have important effects. High density SNP chips were developed that can test for tens of thousands of SNPs at one time. One commonly used bovine SNP chip tests for over 50,000 SNPs at once. By comparing animals’ genotypes at the SNPs with their phenotypes or EPD for important traits, we can figure out which SNPs are related to which traits, and how much variation they control. Then future animals can be genotyped for the important SNPs (usually not all of them) and equations developed from the previous data can be used to predict those animals’ genetic merit. Figuring out the relationships between the SNPs and the important traits and developing the equations takes very large data sets of animals that have both genotypes on the chip and phenotypes or high accuracy breeding values. Both Igenity® and Pfizer offer tests that use panels of SNPs to predict an animal’s genomic or molecular breeding value. Igenity® calls this value the Profile, and Pfizer uses Molecular Value Prediction (MVP®). These panels are only predicting part of the animal’s genetic merit. Depending on the panel and the trait, the molecular breeding values are explaining between about 5-35% of the genetic variation. Figure 2 shows the current scenario, where some of genomic tests are predicting over Phenotype a third of the genetic variation in Angus cattle. Remember, the EPD is predicting 100% of the geE netic variation, with variable accuracy. These marker panels that G result in a molecular breeding M value represent a large improvement over single or a few gene tests, as shown in Figures 1 and Figure 2. Proportion of 2. However, until recently, we phenotypic variation made up of environmental variance were still in the situation where (E), additive genetic variance some animals had EPD and mo(G), and molecular informalecular breeding values. tion (M) for some current genomic tests.
The academic community has agreed for many years that the best way to use genomic information was to incorporate it into existing national genetic evaluation. The statistical methodology to do that was developed in the past 3-4 years. In 2009, the American Angus Association incorporated Igenity ® Profile results into its carcass evaluation (CW, Marb, RE, and Fat). They have since added Profile information to evaluations of CED, the growth traits (BW, WW, YW, Milk), docility, RADG, SC, YH, and MW, as well as included Pfizer information into the above evaluations. This is a huge milestone, because all possible information on an animal (pedigree, own records, sibs, progeny, genomics) is being used to get the most accurate EPD. The DNA panels and the equations to incorporate the results into genetic evaluation are breed-dependent and need to be developed within breeds. Large numbers of animals with DNA information and phenotypes or high accuracy EPD are needed. At this point, no other breeds have genomic information incorporated into their genetic evaluations, but