Genomic Evaluation Guidelines

DNA technology has developed rapidly in the past decade and now has a variety of applications. For beef cattle genetic improvement, the primary areas of application are pedigree validation, parentage determination, and gene-based (genotypic) selection. Individual and parentage verifications are now routine practices, and genomic data is now routinely used in EPD production. This chapter describes current uses of DNA technology and provides an overview of applications currently under development.

Types of DNA Markers

Analytical techniques to differentiate DNA of individuals or populations require genetic markers, which are defined as identifiable DNA segments that differ in nucleotide sequence from one individual to the next. Two types of markers may be used: microsatellites and single nucleotide polymorphisms (SNPs). Both create uniquely identifiable DNA patterns that may be used to follow the transmission of specific chromosomal regions from parents to progeny.

Microsatellite markers are segments of chromosomal DNA that include a variable number of repeated two to six nucleotide base sequences. Such markers are interspersed throughout the genome and are generally found in non-coding regions. These repetitive regions are subject to additions and subtractions in the number of tandem repeats of basic two to six nucleotide segments, and this creates uniquely identifiable alleles at each site within the genome where the particular microsatellite is found. Microsatellites routinely have been used in parentage analysis, because multiple alleles generally found at each locus make them highly informative. They have provided the basis for individual and parentage identification in humans, dogs, cattle, and many other species.

Single nucleotide polymorphisms are the other type of marker. As the name implies, they are a change (mutation) from the specific nucleotide originally present in a particular location in an individual to a different nucleotide at that same site and are transmitted from parent to offspring, just like any other gene. Across evolutionary time, thousands of SNPs have been created by mutation. They now can be found every 100 to 300 bases throughout the 3 billion base pairs in the genome. Because SNPs are widely distributed, it is likely that any gene of economic importance is located closely adjacent to several SNPs that can be used to mark its presence. SNP markers promise to be increasingly useful in the future for developing high- resolution maps because of their high throughput capability and potentially low cost in generating data. With the availability of whole genome sequences, SNPs that are dispersed across all chromosomes present important advantages as markers for genome analysis.

Some SNPs are located within the coding region of a gene and can affect the structure and function of a protein. This type of variation may be directly responsible for differences among individuals in phenotypic merit for economically important traits. Other SNPs occur either “upstream” or “downstream” of the coding region of a gene and may influence the regulation of gene expression. Others occur in locations that do not interfere with the structure or production of a protein. SNPs have the advantage that they are less likely to undergo spontaneous mutation than microsatellites; thus they are inherited with greater stability.

DNA Collection

DNA is found in every nucleated cell in the body. It can be extracted from semen, muscle, fat, white blood cells found in blood and milk, skin, and epithelial cells collected from saliva. Minute amounts of tissue, such as a single drop of blood or several mucosal cells, are all that are required for routine DNA analysis. Common collection methods include a drop of blood blotted on a paper that is dried, covered, and stored at room temperature, ear tag systems that deposit a tissue sample in an enclosed container with bar code identification, and hair follicles. Techniques have been developed that allow for rapid release of DNA from cells and immediate analysis of the samples.

Combining Molecular and Quantitative Approaches in Genetic Evaluation

Research into the molecular basis of inheritance is progressing at a rapid pace. Technologies that permit identification of molecular genetic differences in deoxyribonucleic acid (DNA) sequence among animals are also evolving very rapidly. Several DNA-based tools are being marketed in the beef industry, with some as selection tools. These tools are known by a variety of names in the academic community and within the beef industry (e.g., genomic tests, DNA markers, molecular tests or markers). DNA-based selection tools present opportunities and challenges to the U.S. beef industry. Accurate DNA-based selection tools will give beef cattle breeders opportunity to identify animals with superior breeding value (BV) as soon as a tissue sample can be collected and analyzed, potentially leading to significant savings in time and money associated with performance testing and genetic evaluation. However, as currently marketed, the BV information provided by DNA-based tools is not uniformly reported and the proportion of variation in true BV accounted for by the tools is unknown. Further, the BV information provided by competing DNA-based tools overlaps and is not independent of information provided by current national cattle evaluation (NCE) systems.[THIS PARAGRAPH NEEDS UPDATING]

Performance testing and genetic evaluation are being conducted on an increasing number of traits. Types of information available (i.e., available from a practical and economical view) vary among traits. Types of information include pedigree relationships, performance measurements (i.e., phenotypes), and DNA test results. Phenotypes may include direct and indirect measurements on the same trait.

Some traits are difficult to measure for which there are currently no DNA tests available. These traits will likely be the focus of future research. In a second category are traits for which phenotypes are regularly measured in the field, systematically data-based, and for which EPDs are computed. The emergence of DNA tests now permits estimation of BV on animals for which little or no phenotypic information is available (a third category). A current example would be tenderness. Tenderness phenotypes are difficult and expensive to measure, but DNA tests are available. In a fourth category are traits where both phenotypes and DNA tests are available. A current example would be carcass marbling.

Guiding Philosophy

BIF believes that information from DNA tests only has value in selection when incorporated with all other available forms of performance information for economically important traits in NCE, and when communicated in the form of an EPD with corresponding BIF accuracy. For some economically important traits information other than DNA tests may not be available. Selection tools based on these tests should still be expressed as EPD within the normal parameters of NCE.

Types of Current DNA Technologies

There are a variety of DNA-based tools available to the beef industry today. The number of DNA-based technologies marketed will likely increase rapidly over time. Following is a list of the broad types available based on their applications. All are based on identifying differences in DNA base-pair sequence among animals. The number of base pairs involved, and the lab techniques employed vary greatly. Parentage Identification/Validation tests are used to identify or validate identification of sires and dams of calves. The calf and at least one parent are tested.

'Identification/Traceability tests are used to track animals and tissues through the food production chain as animals and their products change ownership and move from location to location. Variation in DNA is used to identify individual animals. Each animal being tracked must be tested.

Management tests are used to predict the future phenotypes of animals in specific production/marketing systems. They are based on identifying differences in total genetic merit among animals (i.e., additive and non-additive genetic merit).

Selection tests are used to estimate breeding value (i.e., distinguish among animals on the basis of their expected progeny performance). Traits may be qualitative or quantitative in nature. Qualitative traits are controlled by one or a few loci, and phenotypes generally fall into distinct classes (e.g., presence of horns, coat color, and certain genetic defects). Quantitative traits are controlled by many loci. Quantitative phenotypes may be measured on a continuous scale (e.g., weights) or in classes (e.g., pregnancy success). The focus of the guidelines presented here is on DNA tests for quantitative traits used for selection.

Validation

DNA tests are developed based on associations between variations in base-pair sequences at one or more loci with variations in phenotypes. The animal populations used to develop the test may or may not be representative of beef industry populations. Validation generally involves the confirmation or rejection of these associations in populations that are representative of the beef industry and different from those in which the tests were developed. Validation studies are considered to be more reliable if conducted by scientists who have no vested interest in the tests (e.g., development, commercialization, or marketing). To date, components of commercially available DNA tests have been validated by the National Beef Cattle Evaluation Consortium (NBCEC) serving as an independent third party. Validation serves to reduce risk for breeders using DNA tests for selection.

BIF recommends that breeders who use DNA tests should, whenever possible, choose DNA tests that have been validated in populations that are representative of the beef cattle industry by scientists independent of the organization that developed or will market the test.

Assessment

Assessment involves determining how specific DNA tests are associated with each other and with non-target phenotypes. Assessment seeks to determine how competing DNA tests overlap and how non-target traits will be influenced by selection based on these tests. For example, it is important to know if selection based on a DNA test for tenderness has any desirable or adverse effects on other economically important traits (growth, feed intake, fertility, etc.). As with validation, assessment studies are considered to be more reliable if conducted by scientists who have no vested interest in the tests.

BIF recommends that assessment studies should be conducted in populations that are representative of the beef cattle industry by scientists independent of the organization that developed or will market the test.

Reference Populations

As used here, reference populations are: 1) pedigreed herds that are representative of and genetically linked to commercial populations in the beef industry, 2) managed in production/marketing systems representative of the beef industry, 3) measured for economically relevant traits and (or) important indicator traits, and 4) from which tissue samples are available.

Ownership may be public or private; however, as envisioned here the most useful on- going reference populations are likely to be federally owned and managed. BIF recognizes the critical importance of pedigreed reference populations for the successful implementation of DNA-based selection tools in the beef industry. BIF considers the partnerships of USDA-ARS and Agriculture Canada in the establishment and maintenance of reference populations to be vital to the successful implementation of DNA-based selection tools in the beef industry.

Inclusion of DNA Test Information in NCE Programs

Statistical procedures for incorporating DNA test information into NCE and the computation of EPD and associated accuracies are described in Single-step Hybrid Marker Effects Models and Single-step Genomic BLUP. Results of the evaluation of a DNA test will also provide estimated genetic correlations among competing DNA tests, genetic correlations between DNA tests and non-target traits, and the fraction of the additive genetic variance of the target trait accounted for by the DNA test.

Results of the evaluation phase (described above) will provide all the statistical parameters needed for NCE. The decision to include a DNA test in a NCE system should be made by the organization responsible for computing the EPD. Consideration should be given to heritability of the trait, availability of producer-collected phenotypes, and increase in accuracy provided by the addition of the DNA test information. BIF recommends that a DNA test should be considered for inclusion in the NCE system when after estimating the covariances and running the NCE system, use of the DNA test results in more accurate EPD at a young age.

Reporting of DNA Test Results by Genomic Companies It is important the DNA test results be reported to the beef industry in a consistent, understandable format. Further, the format should be compatible with NCE methods. It’s possible that a single DNA test (i.e., genotypes from a single panel of markers) may yield information useful for both management and selection. Predictors based on these tests should be clearly identified with respect to their uses – i.e., future phenotypes versus breeding value.

BIF recommends that DNA test results be reported in the form of an EPD, in units of the trait, on a continuous scale, and with a corresponding BIF accuracy. It is likely that research will develop new DNA tests for traits that have no industry-collected phenotypes. If the target trait is measured in the reference populations, evaluation of the DNA test as a selection tool should be as described above.

Novel Traits

It’s conceivable that the target traits for some new DNA tests may not be measured in reference populations. In such cases precise definition of the target trait will be important.

An independent organization such as NBCEC should conduct or coordinate the validation studies of novel DNA tests. Validation may be approximated by review and (or) re-analysis of data used to develop the test. Such data should include DNA test results, phenotypes, and pedigree relationships. Data used to develop such new tests should be of sufficient quality and quantity to allow the estimation of the additive genetic variance of the target trait and the covariance between the DNA test score and the target trait.

BIF recommends that, for DNA tests targeting traits that have no industry-collected phenotypes and for which no phenotypes are collected in reference populations, results should be reported in the form of an EPD, in the units of the trait, on a continuous scale, and with a corresponding BIF accuracy.

Attribution

Information in this article was derived from Chapter 4 of the 9th edition of the BIF Guidelines. The attribution in that chapter was to: M. W. Tess and the BIF Commission on DNA Markers. Commission members: Bill Bowman, Ronnie Green, Ronnie Silcox, Darrell Wilkes, and Jim Wilton.