Dairy Genetic Evaluation Glossary

A

Animal Genomics and Improvement Laboratory (AGIL)

The Animal Genomics and Improvement Laboratory is an agency of the United States Department of Agriculture (USDA) that performs world-renowned research to develop and test new genetic and genomic methodologies. This research supports top-quality evaluations, data integrity and implementation of technology and new scientific learnings.

B

Base of evaluation

The U.S. dairy genetic evaluation publishes PTAs on six different bases. There is a base for each of the six breeds – Holstein, Jersey, Brown Swiss, Guernsey, Milking Shorthorn, Ayrshire. Any dairy animal that goes through the U.S. genetic evaluation process will have its PTAs published on one of the six bases. Animals of dairy breeds that differ from the breeds mentioned above will have PTAs published on one of the six main bases. PTAs for crossbred animals are published on the base that is most appropriate given their  Breed Base Representation (BBR). The breed of evaluation is published with the PTAs on industry lists and should be published alongside the PTAs on published marketing material

Beta Casein (A2A2)

One of the caseins in milk protein that occurs in two variants: A1 and A2. Also, the name of the gene that regulates whether an animal produces milk of the A1, A2 or mixed A1 and A2 variety. The A2 casein has one more amino acid in its structure compared to the A1 casein. Beta Casein does not affect lactose or lactose intolerance.

Beta Lactoglobulin

One of the genes affecting whey content in milk protein. Animals can have one of three possible genotypes for beta lactoglobulin: AA, AB, or BB.

Breed Base Representation (BBR) 

BBR was introduced in 2016 as an estimate of the percentage of DNA contributed to an individual animal by each of the five dairy breeds evaluated in the U.S.: Holstein, Jersey, Ayrshire, Brown Swiss, and Guernsey. BBR values are used to determine the breed base for which the individual animal’s evaluation will be reported. Crossbred animals are reported on the breed base with the highest BBR value.

Breed Base Representation (BBR) reference population

For each breed, the reference population is comprised of bulls that are genotyped and progeny-tested (at least 10 daughters), enrolled with an NAAB status code (status C and N bulls excluded) and purebred (four generations of complete breed pedigree).

C

Council on Dairy Cattle Breeding (CDCB)

A non-profit organization that manages the world’s largest database of genotypes and phenotypes for dairy animals, calculates and distributes the U.S. genetic evaluations and genomic predictions, and analyzes dairy performance data

Crossbred evaluation

Genomic predictions for animals that have ancestors of more than one of the five main U.S. breeds are calculated as a blended average of the respective single-breed marker effects. The predictions are weighted by the estimated portion of the animal’s DNA that came from each of the five breeds (Holstein, Jersey, Ayrshire, Brown Swiss, and Guernsey).

D

Dairy Record Processing Centers (DRPCs)

The U.S. organizations that aggregate, normalize and distribute milk testing data and provide herd management information. The data types submitted by DRPCs to the Council on Dairy Cattle Breeding (CDCB) include sire and dam identification, lactation records, reproduction, health, calving, herd, test day, and yearly average.

Dairy Record Providers (DRPs)

The field service organizations and milk testing laboratories that operate the U.S. national milk recording program. DRPs often cover a regional area, and they work together on national issues and data quality standards through National Dairy Herd Improvement Association (NDHIA). DRPs are represented in CDCB by National Dairy Herd Improvement Association (NDHIA).

E

Estimated Breeding Value (EBV)

Twice the Predicted Transmitting Ability (PTA) of an animal, above or below the genetic base. EBV = 2 x PTA

G

Genetic condition

A term to categorize traits that are not quantitatively evaluated but instead expressed by a single genetic variant. Examples are genetic defects and conditions such as polled and red factor. 

Genomic inbreeding

Measures the actual homozygosity and percentages of genes in common of an animal. The genomic inbreeding is obtained from the diagonal of the genomic relationship matrix and is related to the portion of an animal’s markers that are homozygous, which is more precise than calculating pedigree inbreeding.

Genomic nominator

Organizations responsible for collecting DNA samples from the animal owner, providing CDCB with information about the animals sampled, and transferring the DNA samples to the genotyping laboratory. Nominators must meet CDCB quality certification guidelines before they are permitted to participate in the system, and their performance is monitored routinely and audited annually.

Genotyping laboratory  

Laboratories that extract DNA from samples, prepare single nucleotide polymorphism (SNP) genotypes, provide summary information back to the genomic nominator, and transfer the genotypes to the CDCB. Laboratories must meet CDCB quality certification guidelines before they are permitted to participate in the system, and their performance is audited on an annual basis. 

Genomic Predicted Transmitting Ability, or GPTA

A genomic-enhanced PTA (Predicted Transmitting Ability)

Genomic selection

A form of marker-assisted selection in which genetic markers that cover the entire genome are used in combination with pedigree and performance information to evaluate the genetic merit of an animal

Genomic testing

Evaluation of an animal’s genetic merit through means of a biological sample, DNA extraction, genotyping and subsequent genomic evaluation.

Genotyping

Assessing the genetic constitution of an animal through means of DNA extraction and determination of allele status of genetic markers distributed across the genome

H

Haplotype

Sequence of DNA markers, most often SNPs. Currently used as a tool to analyze carrier status of a genetic condition, most often when the causal variant is unknown or not on a commercial genotyping chip.

I

Interbull

A permanent sub-committee of the International Committee for Animal Recording . Interbull is the worldwide network that provides genetic information services for improvement of livestock. Interbull is mostly known for across-country evaluations that provides evaluation of a foreign bull on a local scale. The Interbull Center is located in Uppsala, Sweden.

Intergenomics

Large international consortium that established and manages the international genomic evaluation for the Brown Swiss breed

International Committee for Animal Recording (ICAR)

An international non-governmental organization that aims to promote the development and improvement of animal identification, performance recording and evaluation of farm animals.

K

Kappa Casein

One of the genes affecting casein content in milk protein. Animals can have one of six possible genotypes for Kappa Casein: AA, AB, AE, BB, BE or EE. Animals with the BB genotype for Kappa Casein have a slightly higher Kappa Casein content in milk, which can be beneficial for cheese making.

M

Microsatellite

A sequence of repetitive DNA in which certain DNA motifs are repeated, which were previously used as genetic markers for parent verification

Monogenic traits

Used as a term to categorize traits that are not quantitatively evaluated but instead expressed by a single (mono) genetic variant.

Multiple Across Country Evaluation (MACE)

A scientifically-advanced method used by Interbull to calculate International Genetic Evaluations. International Genetic Evaluations are across-country measures of genetic merit of individual dairy traits.

N

NAAB Uniform Code

Also referred to as the “NAAB code.” This 10-digit code is owned and managed by the National Association of Animal Breeders (NAAB) to identify bull used for A.I. The code is printed on semen straws that are produced by Certified Semen Services (CSS) participants following CSS guidelines. NAAB Uniform Code consists of a three-digit marketing organization code, a two-digit breed code and a five-digit bull number. The Uniform Code is used to cross reference inseminations to alternative bull identification numbers for traceability purposes and for increasing the usable records in genetic evaluation. Learn more at www.usacattlegenetics.com

National Association of Animal Breeders (NAAB)

Trade association that represents the U.S. A.I. industry. NAAB manages the dairy cross reference database which links A.I. bulls to the genetic evaluations through their unique NAAB code identifier. NAAB also owns Certified Semen Services (CSS), the authority responsible for monitoring and auditing U.S. collection centers to ensure semen quality that provide for animal health and safety.

Net Merit Dollars (NM$)

A national selection index which combines information on about 40 traits, including yield, conformation, health and fitness, feed efficiency and fertility traits. Composite selection indices are valuable tools in modern dairy cattle breeding because they enable information from many traits to be combined into a single value for ranking animals and simplifying selection decisions. 

P

Predicted Transmitting Ability (PTA)

The predicted difference that an animal transmits to its offspring compared to the average base cow due to the genes provided. Each PTA is expressed in the units used to measure the trait. For example, the PTA for Milk is reported in pounds or kilograms, and the PTA for Productive Life is reported in months. EBV = 2 x PTA since a PTA describes the transmission from the parent which is 50% of the animal’s true genetic difference.

R

Recessive

Genetic conditions that are expressed in homozygous form. Recessives can be positive or negative; they are often referred in the context of a genetic defect.

S

Sequencing

Assessing the genetic constitution of an animal by DNA extraction and determination (‘reading’) of the animals’ entire genome (all 2.6 billion base pairs)

SNP, or Single Nucleotide Polymorphism

A substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of the population. Present in abundance and used as a genetic marker in genomic selection.

Standard Transmitting Abilities (STAs)

Genetic evaluations for linear type traits are expressed as STAs in the Holstein breed. Standardized values for linear traits are used because without this adjustment each trait has a different PTA range. As a result of the standardization, linear type traits have an average of 0. Both extremes for each trait are approximately 3 STA units from the average.