Best Practices for Most Accurate Genetic Predictions and Genomic Testing

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Best Practices for Most Accurate Genetic Predictions and Genomic Testing

Best Practices to Receive the Most Accurate Genetic Predictions

1. Clearly defined breeding objectives With the ability to increase the rate of genetic change comes the possibility to make mistakes at a faster pace. Breeding goals need to be clearly identified to ensure selection at the nucleus level matches the needs (profit-oriented) of the commercial industry.

2. Whole herd reporting Inventory-based reporting captures more complete phenotypes on reproduction and longevity traits, and thus creates more accurate genetic selection tools. 

3. Proper contemporary groups It is important for the precision of the genetic evaluation to group animals treated uniformly. Proper reporting of contemporary groups reduces bias in EPDs.

4. Take data collection and reporting seriously Phenotypes are the fuel that drives the genetic evaluation.  Take pride in collecting accurate data.  If possible, collect additional phenotypes like mature cow weight, cow body condition score, udder scores, feed intake, and carcass data. 

5. Phenotypic data collection for economically relevant traits needs to improve in both quantity and quality. The quantity and quality of fertility traits, needs to dramatically improve.  Providing disposal codes to identify why females leave the herd is vital.  Commercial data resources, where the true economically relevant traits exist, are going to become more critical to capture. Breeders can help prove the genetics of their own seedstock by encouraging their commercial customers to join ASA’s Commercial THE option and add valuable data to the evaluation. 

6. Use index-based selection As the list of published EPDs continues to grow, using economic selection indices will become even more helpful to reduce the complexity of multiple trait selection. If the number of EPDs increase, tools to reduce the complexity of sire selection for commercial producers must continue to develop.  Breed associations and seedstock producers have the obligation to aid commercial clientele in making profitable bull selection decisions. 

7. Use genomics Genomic selection offers an opportunity to increase the rate of genetic change and break the antagonistic relationship between generation interval (the average age of the parents when the next generation is born) and the accuracy of selection (e.g., accuracy of EPD) — two components that determine the rate of genetic change. However, as with any tool, genomic information must be used correctly and to its fullest extent. What is proposed herein is a list of ‘best practices’ for producers and breed organizations relative to genomic testing. 


Best Practices for Genomic Testing

1. All animals within a contemporary group should be genotyped. If genomic data are meant to truly enable selection decisions, this information must be collected on animals before selection decisions are made.  The return on investment of this technology is substantially reduced if it is used after the decision is made. 

2. Both male and female animals should be genotyped. The promise of genomic selection has always suggested the largest impact is for lowly heritable and/or sex-limited (e.g., fertility) traits or those that are not routinely collected (e.g., disease). This is indeed true, but it necessitates that genotyped animals have phenotypes.  For sex-limited traits, this becomes a critical choke point given the vast majority of genotyped cattle are males.  If producers wish to have genomic enhanced EPDs for traits such as calving ease maternal and heifer pregnancy, they must begin or continue to genotype females.  The ASA has a unique program called the Cow Herd DNA Roundup (CHR) to help herds collect female genotypes (see pop-out box below for more information). Through the CHR, members of the ASA more than tripled the number of female genotypes in the evaluation in less than one year. 

3. Genotypes can provide useful information in addition to predictions of additive genetic merit. Do not forget the value in correcting parentage errors, tracking inbreeding levels, identifying unfavorable haplotypes, estimating breed composition, and estimating retained heterozygosity.  All of these can be garnered from populations that have a well-defined set of genotyping protocols. The beef industry should be congratulated for the rapid adoption of genomic technology, but there is a lot of work to do.  Of critical importance is the fact that genomic technology will continue to change and does not replace the need for phenotypes nor the fundamental understanding of traditional selection principles including EPD and accuracy. 




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