Current Progressive Dairy digital edition

Take a proactive approach to inbreeding control

Jeff Ziegler Published on 29 October 2012

Inbreeding continues to receive increasing attention on progressive dairy operations – and appropriately so. As profit margins continue to narrow, dairy producers are looking for alternative ways to sustain maximum profits while minimizing their inputs.

Losses resulting from inbreeding have been known for several years but are often overlooked, sometimes even due to the delusion that management practices and genetic gain offset inbreeding influences. However, despite dairymen’s best efforts to overcome inbreeding losses, the inbreeding depression phenomenon is nearly impossible to defeat.



For this reason, a proactive approach to inbreeding management is a crucial element for a successful genetic plan. The “best” way to control inbreeding? The debate continues. Researchers, genetic organizations and dairy producers alike can all agree that certain approaches to curtail negative inbreeding effects are more effective than others.

Regardless of approach, striking a balance between minimizing inbreeding and maximizing genetic progress is paramount to a successful and sustainable inbreeding control program.

Laying the groundwork

All successful attempts to rein in inbreeding must begin with accurate and reliable identification. This includes identification of each individual in the herd and a record of parentage for that animal. If the parentage of an animal is unknown, inbreeding management can be even more complicated.

Service sire information should be carefully and accurately recorded at breeding, and parent identification should be a part of the records within hours of the birth of a heifer calf.


A look at traditional approaches to inbreeding control

Often viewed as the most effective way to manage inbreeding, planned mating programs utilizing the technologies of computerization have value in controlling inbreeding levels within herds and allowing for continued genetic improvement.

With the incorporation of accurate pedigree information, these mating programs have the capacity to reference several generations to determine the inbreeding coefficient for a planned mating. However, traditional computerized mating programs were built on individual animal mating, a trend that large-scale dairies are moving away from due to a lack of time, staff and other variables.

The use of “outcross” genetics is one other way dairies have proposed to take on their inbreeding challenges. Loosely defined, outcross genetics are those that share a low level of genes with the national population.

A caveat to using outcross genetics is that while inbreeding is lower, the genetic merit of these individuals is usually lower, so one would be controlling inbreeding at the expense of genetic progress. This option has been found on several occasions to not be a sustainable tool for consistent genetic improvement.

Trends in inbreeding management


Pedigree mating : Reliability of genetic information continues to rise. This increase in reliability creates an opportunity to utilize pedigrees for mating purposes and subsequent inbreeding control. With adequate pedigree information, heifers can successfully be mated through computerized mating programs with nearly as much confidence as cows with linear evaluation information.

Pedigree mating utilizes parent averages to determine specific genetic needs of a female, with the goal to achieve maximum genetic progress while also controlling inbreeding levels.

Genomic relationship matrices (GRM) : There is no doubt that genomic information has revolutionized the dairy industry and the impact genomics has had on inbreeding control is no exception. The use of genomic information has rapidly become more widespread, with many herds using a 3K SNP on a regular basis.

While traditionally used as a means to test parentage, a low-density SNP genomic test is also becoming a practical tool for whole-herd testing. In fact, a recent Australian study concluded that a 1 percent reduction in progeny inbreeding valued at $5 to $10 per cow can be made with very little compromise to achieving genetic objectives.

A GRM program takes pedigree mating to a higher level because, unlike pedigree mating, GRM uses the female’s actual genes to calculate inbreeding. Inbreeding calculations from pedigree mating assumes that 50 percent of an animal’s genes came from the sire and 50 percent came from the dam.

GRM is able to determine which specific genes were transmitted and can therefore control the homozygosity of specific genes (the underlying factor causing inbreeding depression).

Mating allocation : Breeders on larger dairy operations are under tremendous pressure to get as many cows inseminated as efficiently as possible. For this reason, larger dairies find it increasingly difficult to control inbreeding on an individual cow basis and are moving from an individual mating scheme to group mating.

Mating allocation programs are an extension of traditional computerized mating programs but have been built on the group mating trend. These programs work by utilizing genomic data to increase the frequency of specific favorable alleles in a genetic line. These specific alleles are known to share a common source (common ancestry).

When genomic insights are used to influence herd sire sequence choices, a reduction in inbreeding within that herd is known to occur. These breeding programs allow for sustainable and profitable inbreeding solutions.

As new research continues to evolve the inbreeding debate, all dairy operations (regardless of breeding objectives) can take action and benefit from a sustainable and consistent inbreeding management tool. New tools and program approaches to inbreeding management can be easily implemented on dairy operations.

With the right combination of strategic development and accurate selection, these programs make it simple for producers and herd managers to implement a breeding plan, resulting in greater genetic outcomes, a reduction in inbreeding challenges and a more simplistic approach to an aspect of the already complicated day of a progressive dairy operation. PD

References omitted due to space but are available upon request. Click here to email an editor.

Jay Shannon
  • Jeff Ziegler

  • Genomics Program Manager
  • Select Sires,Inc.
  • Email Jeff Ziegler