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Genetic diversity and inbreeding: Before and after genomics

Filippo Miglior and Lynsay Beavers Published on 18 July 2014

Genomics has sped up genetic progress, but has it impacted inbreeding? Did genomics allow for a larger pool of bulls available for selection?

To answer these questions and to monitor inbreeding trends, Canadian Dairy Network (CDN) performed an analysis that included both pre-screened bulls and those that entered A.I. Pedigrees came from the International Bull Evaluation Service (Interbull), and bulls examined were born between 2002 and 2011.

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Two main analyses were performed, by birth year (2002, 2005, 2008 and 2011) and by geographical area (global or North America).

The information presented in Table 1 reveals bull numbers pre-genomics and post-genomics on a global scale and in North America. In addition, it shows the number of bulls pre-screened with genotyping and the number of those that went on to enter A.I.

Sire numbers

  • Number of young bulls: Before genomics, more than 5,000 young bulls were sampled worldwide annually, of which more than 1,600 were in North America.

    With genomics, more than 10,000 North American young bulls are being pre-screened with genotyping each year – a testament to the effort A.I. organizations are making to source new bloodlines. Of these 10,000 genotyped bulls, approximately 1,300 will go on to enter A.I. annually.

  • Number of sires of young bulls: Pre-genomics, sires of sons were predominately high-profile proven bulls. Post-genomics, the 1,300 bulls entering A.I. annually are the sons of 48 percent more sires (155 versus 105) than the bulls entering A.I. before genomics.

    This is a result of the shift toward young, unproven sires as sires of sons. In this regard, genomic technology is broadening the portfolio of bulls offered to farmers.

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  • Number of most popular sires representing 50 percent of young bulls: While the number of sires of sons has increased since genomics, the number of bulls siring 50 percent of the young bulls entering A.I. remains fairly constant.

    This shows that while A.I. is trying to cast a larger net to find new bloodlines, this isn’t translating into a greater number of bulls siring the majority of young bulls being offered to producers. In 2011, nine bulls sired 50 percent of the 1,300 young bulls that entered A.I. in North America, and 18 bulls sired 50 percent of the 3,000 that entered A.I. globally. These bulls can be seen in Table 2 .

  • Average number of sons per sire: Post-genomics, the average number of sons entering A.I. per sire has decreased significantly in North America from 15 to nine. With shorter generation intervals, the turnover of top bulls is faster than before, meaning sires of sons aren’t being used as long as they used to be.

Most popular sires

Overall, genomics has allowed A.I. organizations to sample fewer bulls, but those that are sampled are of greater genetic merit. The technology has diversified the portfolio of bulls available to producers, yet the number of bulls siring 50 percent of sons remains largely unchanged.

Inbreeding before and after genomics

The early ’90s saw intense selection for production, which resulted in increased levels of average inbreeding. Toward the latter half of the same decade, extension efforts by researchers and the A.I. sector improved awareness about the negative effects of inbreeding. In addition, A.I. mating programs were used to control inbreeding on a mating basis.

Selection goals broadened in the new millennium to include traits like somatic cell score and fertility. This expanded the sires of interest, broadening the genetic pool and subsequently decreasing average inbreeding rates.

Despite the fact that genomics has diversified bulls available for selection by producers, the arrival of the technology coincides with the highest average inbreeding levels among young bulls entering A.I. seen in the past 15 years ( Figure 1 ).

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Averaging inbreeding of bulls

Most noteworthy is the rate experienced from 2011 to 2012, which hovers at a 1 percent increase that year alone. Depending on how these young bulls are used in the breed, this increasing trend may also translate to average increases in the heifer population going forward.

On one hand, inbreeding is associated with an increased frequency of desirable genes in a population as a result of selection. On the other, it is related with lower-than-expected performance, especially for economically important traits.

At what extent does inbreeding hurt more than help the breed? This question still warrants more research. Of particular concern is the fact that with genomics, a shorter generation interval may not allow enough time for natural selection to counter-balance the negative effects of inbreeding.

Controlling inbreeding

On a breed level, CDN is exploring crediting outcross genomic young bulls in the LPI formula to promote the exposure and usage of bulls with superior genetics that are less related to the population.

While geneticists study ways to control inbreeding on a breed basis, producers should focus on controlling inbreeding in their own herds. For individual matings, CDN’s inbreeding calculator can be used to confirm inbreeding and genetic potential of possible mates.

In addition, A.I. mating programs can also be useful tools to monitor and maintain inbreeding at a level the producer has decided is acceptable to them.

In the U.S., the Council for Dairy Cattle Breeding (CDCB) accounts for inbreeding in a bull’s genetic predictions by taking into account what the expected future daughter inbreeding level will be and makes adjustments based on these figures for the official proof value.

For example, a bull that is expected to be highly unrelated to the population gets a slight increase in his PTAs, while a bull that is highly related is slightly reduced. This discounting is useful but apparently not enough to reduce the erosion in genetic diversity.

Another step CDCB is taking towards controlling inbreeding is the development of a genomic mating program. This software could help breeders identify potential mates with fewer alleles in common, as opposed to fewer ancestors in common, as is the practice with mating programs based on pedigrees.

While genomics provides an array of benefits, one of the technology’s current drawbacks is increased average level of inbreeding. Nevertheless, we wouldn’t trade today’s more productive and more inbred cow with her less productive and less inbred ancestors.

Maximizing genetic gain while controlling inbreeding levels will remain a high-priority goal of the dairy cattle breeding industry. PD

Lynsay Beavers is industry liaison services coordinator for Canadian Dairy Network.

Filippo Migliorr
  • Filippo Miglior

  • Chief, Research and Strategic Development
  • Canadian Dairy Network
  • Email Filippo Miglior

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