How Alta BLUE LINK Genetic Planning Works

Which genetic data are used for genetic planning?

Alta BLUE LINK incorporates multiple inputs and analyzes genetic trait and mating data using the following:

Current herd's genetic data, which is based on:
The Data Integrity report is a useful tool to improve plan accuracy. To quickly identify missing or incomplete animal data, download the Data Integrity Report from the Genetic Dashboard.
- Sire (SID Sire identifier)
- Dam (DID Dam identifier)
- Maternal grandsire (MGS)
- Maternal great-grandsire (MGGS)
This data is used to assess the herd's genomic profile and is the basis of calculations made for specific animal traits and potential improvements.
Breed averages for traits. The breed average is used as a benchmark and for calculating trait deviations for the current herd and potential genetic improvement in the next generation.
Sire proof, which includes detailed genetic trait data based on individual bull codes. UDS matches the bull data with sires, sires of conception, grandsires, and great-grandsires. The genetic planning tool currently supports Holstein and Jersey bulls.
Female proof, which includes detailed genetic trait data based on the female's registration number (RegNum or IntRegNum). UDS matches the female proof match to any female, focusing on females included in the herd's data. If females or bulls match, we have can use their genomic data for more accurate planning.
Alta Marketing list, which includes the latest listing of available semen doses by product line. This listing is imported and presented as part of sire selection in the genetic planning process.

When a new plan is started, PULSE pulls genomic data from the latest proofs for new animals. If proofs are not available for a new animal, PULSE finds the animal's sire records, then uses the one-generation parent (sire and dam) trait averages to construct the animal's genomic data.

Then, as you proceed through the steps of building a genetic plan, the sire, dam, and marketing list are included in the analysis of potential herd improvements and as part of the mating plan. Depending on the options you set for mating, specific sires are recommended for different animals in the herd based on the plan goals and other criteria set in mating options.

How are trait averages evaluated?

Most trait averages are evaluated using three-generation parent averages, but some trait averages are evaluated using one-generation parent average or a breed average. The use of parent or breed averages depends on the type of animal that is being evaluated:

Three-generation parent average: If a proof is not available for a female, trait data is used from three previous sire generations (sire, maternal grandsire, and maternal great-grandsire) to calculate the female's trait averages. Alta BLUE LINK calculates the trait values using weighted percentages of the three-generation parent averages and the breed average:
- 50% sire
- 25% maternal grandsire
- 12.5% maternal great-grandsire
- 12.5% breed average
One-generation parent average: To calculate a potential progeny's trait averages, trait data is used from the progeny's parents (sire and dam).
Breed average: When parent data is unavailable, a progeny's trait averages are based on the breed average.

How are genetic values projected for future progeny?

During genetic planning, we collect the genetic values for all females and calculate the average of the collected female data. During Step 4: Create Your Strategy, we collect the genetic values for all bulls and calculate the average of the collected bull data. We then use the average female value and the average bull value to project the progeny's genetic values. After mating, we use the bull’s actual genetic values to predict the progeny’s genetic values.

How is inbreeding evaluated and prevented?

Evaluation: To ensure that inbreeding information is accurate, inbreeding values are evaluated using seven generations of the progeny's pedigree.
Prevention: The mating plan always performs a check to ensure the animal's sire is not her assigned mating sire. Additionally, you can set additional restrictions and protections to prevent inbreeding in Step 4: Create Your Strategy, such as customizing the maximum allowed inbreeding percentage.

How is trait data used to match bulls to females in the mating list?

The plan's individual females' traits are analyzed and Alta BLUE LINK identifies their three traits that are furthest from the plan goals. Then, bulls are matched to each female to improve the identified traits in their potential progeny. Before selection, Alta BLUE LINK prohibits any bull and female match that would result in recessive traits, inbreeding, or negative haplotypes (see the full list below). In these calculations, trait data is based on one-generation parent (sire and dam) trait averages.