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Genetic evaluation of beef cattle has evolved from strictly visual evaluation to weights and ratios to the first expected progeny differences (EPDs) to the current system in which the Angus breed evaluates 18 traits. The next innovation to be incorporated into genetic evaluation systems may be gene- or marker-test results.
Although few genes or markers for traits of economic importance in beef cattle have been discovered to date, the pace of progress is increasing. The first few tests are now being marketed to cattlemen worldwide, but for quantitative traits, such as growth or carcass traits, the results are of limited use unless they are included in calculations for EPDs.
Incorporation of such tests into genetic evaluations is not difficult once the effect of the gene is well-documented. Genetic evaluations using gene or marker tests will provide more-accurate evaluation of animals at a younger age and allow more cost-effective evaluation of traits that are difficult or expensive to measure.

Genetic terminology
A review of terminology may be in order before proceeding. Key terms are chromosome, DNA and gene.
Chromosomes are structures in the nucleus of cells that store genetic information in the form of DNA.
Deoxyribonucleic acid, or DNA, is a molecule made up of a chain of bases (A, T, G and C). Although much of the DNA sequence within any chromosome is believed to be meaningless, certain sections of chromosomes (genes) control the synthesis of proteins in cells. Protein synthesis determines the characteristics of an organism.
Thus, a gene is a sequence of DNA bases on a chromosome that causes an organism to have a certain characteristic. Animals and plants have many chromosomes, and each chromosome contains many genes. The precise locations of most genes are unknown, especially in livestock.
The number of chromosomes that several species of animals possess is listed in Table 1. As chromosomes vary in size and number of genes, the number of chromosomes is not related to the complexity of the animal.
Chromosomes are arranged into homologous pairs. These chromosome pairs have similar size and structure and contain genes for the same traits. For example, humans have 46 chromosomes, or 23 homologous pairs. The sex chromosomes that determine gender (XX for female or XY for male) are one of the homologous pairs. With 60 chromosomes, cattle have 30 homologous pairs, or two each of 30 different types of chromosomes.
Each gene can take on two or more different forms, called alleles, which result in different characteristics. For example, all cattle have two genes for either red or black coat color, one on each member of a homologous pair of chromosomes.
A parent will contribute one randomly chosen chromosome from each homologous pair to its offspring. When an individual has two identical alleles for the same trait, they are homozygous (homo = same). When the two alleles for a trait are different, they are heterozygous (hetero = different).
An example of this is the red/black coat color in cattle. In this system, the gene for black color (B) is dominant to red color (b). Animals that have genes for black color on both members of the homologous pair of chromosomes (BB), like most Angus, are called homozygous black and always will pass a black gene to their offspring. Those with one black gene and one red gene (Bb) are heterozygous, but they are also black in color.
However, these heterozygous, or red-carrier, animals will pass on a gene for black color half the time and a gene for red color the balance of the time. Because red color is recessive, all red animals are homozygous red (bb), and they always pass on the gene for red color.

Qualitative vs. quantitative traits
Traits can be classified as either qualitative (having a quality) or quantitative (having a quantity). Traits like red or black color, diluted or nondiluted color (red or yellow), and horned or polled are examples of qualitative traits. One or a few genes determine these traits, and they fall into distinct classes.
Quantitative traits are those that show a continuous, usually bell-shaped distribution. All performance traits of cattle are quantitative traits. These traits are influenced by many, possibly hundreds, of genes. Each gene is assumed to have a relatively small effect, although “major genes” that control a greater portion of the variation in a trait are theoretically possible.
Quantitative traits are the result of genes for factors that control growth, development, reproduction, lactation and other biological processes. Genes that influence weaning weight might actually control production or recognition of hormones and other factors affecting growth. Most economically important traits in beef cattle are quantitative traits. Genes that have a measurable effect on quantitative traits are called quantitative trait loci (QTL).

Mapping genes
Genes can be found by either direct mapping in the species of interest, such as cattle, or by comparative mapping from other species, such as humans or mice. Considerably more money has been invested in mapping the human and mouse genomes than in livestock genetics. Livestock species are more difficult to manipulate genetically than mice, and the generation interval is much longer. Many genetic sequences are common across species due to the evolutionary relationships they share. Most discoveries of QTL in livestock originated from research on humans or mice.
An example of comparative mapping benefiting livestock producers is the discovery of the red/black gene in cattle, formally known as the melatonin receptor gene. The red/black coat color gene was first mapped in mice. Researchers interested in cattle observed the discovery and noted that the location of the gene in mice corresponds with a region on Chromosome 18 in cattle. Once researchers focused on that specific region, they were able to map the red/black gene in cattle in a short period of time. Similar efforts resulted in the mapping of the double-muscling (myostatin) gene in cattle.
Currently, only a few genes have been mapped fully in cattle. The gene test for red/black coat color is commercially available, and the double-muscling test could be if demand warranted. However, finding the exact genes that cause an effect, while difficult for qualitative traits, is even more difficult for quantitative traits.
At this writing, one gene test for a qualitative trait, called GeneStar Marbling, is being marketed to beef cattle producers. This gene was discovered by Australian government researchers and is now commercially available in many countries, including the United States. It tests for the presence of a gene influencing production of thyroglobulin, which is involved in fat synthesis.
Although the effects of the marker have not been peer-reviewed, the company selling the test claims significant increases in marbling for animals that have two copies of the favorable gene. The effect of the gene on subcutaneous (sub-Q) fat or kidney, pelvic and heart (KPH) fat has not been reported. The reported frequencies of the GeneStar Marbling marker in Angus, Wagyu and other breeds are listed in Table 2. The cost of the test is currently $80/sample.
Marker-assisted selection
A genetic marker is a known DNA sequence that is believed to be located physically near a QTL. These markers have a statistical association with a particular trait because the marker and the actual gene will be inherited together most of the time. Markers are a step toward finding the actual genes for a trait; but, in some cases, producers could use marker tests for selection before the precise location of the gene is known.
Markers often work well for selection within families, but unrelated animals may or may not have the same association between the marker and the gene. The effect of the marker becomes more consistent as the marker gets physically closer to the actual gene. It is plausible that marker tests might be useful for all animals of a species, only several breeds or only some families within breeds.
Both the swine and dairy industries are using marker-assisted selection to a limited extent. In Holsteins, at least two markers affecting milk production and one affecting protein yield have been identified. Among others, major swine genetic companies are testing for genes believed to convey resistance to common diseases, such as porcine reproductive and respiratory syndrome (PRRS).

EPDs with markers, genes
Several research projects are underway that may find markers or actual genes that influence economically important traits. One example is the National Cattlemen’s Beef Association (NCBA) Carcass Merit Project, which is testing proposed markers for tenderness, marbling and ribeye area (REA) in 14 beef breeds.
Other notable studies include tenderness genes, which are being studied at the Meat Animal Research Center (MARC) in Clay Center, Neb., and genes for marbling and other carcass traits studied by researchers at Ohio State University with support from Certified Angus Beef LLC (CAB). Several agricultural conglomerates, such as Continental Grain, are also conducting beef cattle genomics research.
Potential benefits from gene mapping are greatest for traits that are difficult or expensive to measure. Tenderness is an example of a trait that is expensive to measure but has economic importance. Traits where the maximum is ideal, such as disease resistance, are better candidates for gene tests than those where an intermediate level is ideal, such as growth rate. It should be noted that, if genes exist that have major effects on traits currently selected for, the unfavorable allele should be mostly eliminated in the population through traditional selection methods.
Marker or gene tests enhance traditional genetic evaluation systems because the tests can be run early in the animal’s life and do not require the actual trait to be measured in every animal. Males can be tested for genes affecting female fertility, live animals can be tested for carcass traits, and disease resistance might be evaluated without subjecting the animal to the disease.
Because an animal’s progeny inherit a random 50% of a parent’s chromosomes, traditional genetic evaluation systems make assumptions that may not be fully true. For example, full siblings will have similar EPDs until they can be measured for a trait of interest. If an accurate gene or marker test for a major growth gene were available, it might be possible to test flushmates at birth or before then to determine which received the more favorable genes from each parent, enhancing the accuracy of their EPDs.

Issues, strategies
Marker-assisted selection or gene selection would be used most effectively if the marker or gene data were incorporated into the calculation of EPDs. However, before such tests can be used, the effects of the gene or marker need to be known for each breed, as well as how consistent the effect is across families in the breed. Results of all tests should be reported to the breed association directly rather than through the breeder. To use marker or gene tests in EPD calculation, the results of all tests must enter the evaluation database, not just those with a favorable result.
Deciding which marker tests to use in genetic evaluation will be a difficult process. Breeders will not want to spend money on testing unless the results will be used in genetic evaluation, but the breed association needs independently validated results before committing to the use of a test. Because the location of markers being tested is proprietary information, and therefore confidential, it is possible that two companies could discover and market the same test independently under different names.
Seedstock producers might consider collecting and storing blood samples, hair follicles or an ear-tissue punch on artificial insemination (AI) sires or cows used as donors for embryo transfer (ET) so the animals can be tested beyond their life span. Frozen semen is a convenient way to store DNA from bulls. Having DNA samples from cows that leave many daughters and granddaughters in the herd may reduce the cost of testing animals in the future.
Although gene and marker tests can enhance current genetic evaluation systems, they will not replace EPDs — only improve their accuracy. Regardless of how many gene or marker tests eventually become available, they will most likely never eliminate the need to take weights and measurements, but they may reduce the number of animals that need to be measured for certain traits.

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