UTILIZING GENOMICS TO IMPROVE THE ACCURACY OF BREEDING VALUES

 

Genomics. Speak the word and people “run for the hills.” While an abstract concept for many to grasp, the fundamentals behind the practicality and value for genomic technologies in genetic selection programs can really be quite simple… once a basic understanding of genomics is reached.

Consider a comparison,
A pig is to a book,
As a DNA chromosome is to a chapter in a book,
As a base pair is to a word within a chapter of a book,
As a nucleotide is to a letter within a word within a chapter of a book.

We have the capability with genomic technologies to identify variable letters within a word within a chapter of a book. These single letter variations, in genomic terms, are called single nucleotide polymorphisms (SNPs).

When we genotype an individual animal, we are capturing the SNPs (or spots in the pig’s DNA where we know single letter variations to exist). These SNPs are of interest because they can be indicators of performance traits that have created value for pig production. This allows us to determine the unique characteristics and eventual performance of every animal that is genotyped.

So, why do we use genomics in genetic selection?
The Hard Traits. Phenotypes are pertinent to any genetic selection program. Yet there are some phenotypes for traits of interest that are hard to measure. With genomics, we can utilize SNPs to improve the accuracy of predicting performance related traits without collecting actual phenotype data. Traits where this is extremely effective:

Sex limited traits. Traits that can only be collected on one sex. Ex. Total Born is only collected on females.

Aged traits. Traits that require the animal to be aged (or in some cases postmortem). Ex. older growth, mortality, disease resilience, and carcass traits.

Expensive traits. Carcass traits can be hard to measure and costly, as it often means you have to employ personnel to take measurements at the plant.
Better Relationships. Have you noticed differences in full-sibling performance? Without the use of genomics, we assume that the offspring inherits half of the genes from their mother and half from their father. In reality, due to mendelian sampling, we know that offspring do not inherit exactly half of each of their parents. With genomics, we can fine tune our pedigree relationships to quantify the exact relationship between each animal, a genomic relationship pedigree. Additionally, genotype data can be used as a tool to identify and correct pedigree errors and even validate population integrity.
The end of phenotypes? Not quite. Genomic selection is based on the use of a reference population that has BOTH performance data (phenotypes) and genomic data (genotypes). While genomics allows us to more accurately predict Breeding Values (BVs) for animals in situations where performance data is not collected, the basis of this accuracy stems from the underlying assumption that the animals in the reference population are closely related to the animals in the next generation. As such, continual collection of phenotypes will be pertinent to the applicability of the genetic evaluation in the future, as animal phenotypes and genotypes from subsequent generations will begin to feed the reference population in the future.
When we use genomics, we are capitalizing on known SNPs that serve as links and indicators to eventual production performance. By combining genomics with the relationships of the pedigree and phenotyped animals, we can observe an increase in accuracy for breeding values over those with only pedigree and phenotypes available. Perhaps the greatest value is generated in young animals – as we are subsequently able to make informed selection decisions on the future of young boars and females much sooner.
Technical Expert: Tamar Crum, Ph.D., Acuity Geneticist
Tamar is a Geneticist at Acuity based in Carlyle, IL. She is a graduate of Kansas State University (BS) and the University of Missouri-Columbia (Ph.D.). At Acuity, she is focused on advancing the genomic data pipeline, while developing genetic tools for on-farm personnel to ensure they are driving genetic progress.
Connect with Tamar
Acuity was created in response to a need for genetic improvement with a systems-based focus. For nearly a decade, our technical team has worked to develop a platform capable of delivering solutions that increase profitability throughout the supply chain. Our focus is different: commercially-derived data supports decisions that enable value realization.
Build on a better foundation at www.acuityswine.com.