Genomics

The selection of breeding animals has historically been based on the test of bulls by observing the performance of their daughters. This was a lengthy process and required the used of a large number of cows.

More recently, genomics has allowed for reduced time in the selection process by the study of the genome of bulls and cows that can predict their performance and disease risk. Genomic analysis can be completed at an early age, which means that the generation interval is shortened substantially, and genetic progress is therefore faster. Knowing the DNA of the parents, heifers that inherited the best traits from their parents can be introduced in the herd. Genomics in cattle reproduction, then, works in two ways:

  • It allows farmers to know the DNA of the parents at a younger age
  • It allows farmers to select the offspring at an earlier age

Several studies have shown that genomic selection has1:

  • Doubled the rate of genetic progress for traits of economic importance in Holstein bulls since the implementation of genomic evaluation in 20101
  • Increased selection accuracy
  • Reduced costs
  • Identified lethal recessive traits

Breeding companies are currently looking into increasing the merit of next-generation animals through integrating the latest genomic selection tools with the most advanced reproductive technologies. Producers have accepted genomic evaluations as accurate indications of bull and heifer evaluations, and over half of heifers mate with young bulls with genomic evaluations. Also, artificial insemination organizations now only purchase young bulls based on genomic evaluations1.

High reliability is now obtained for many traits, enabling selection of female replacements on the basis of genotype results.

A recent study in U.S. Holstein dairy cattle compared the effects of selective breeding programs before genomic selection was introduced and after its implementation, focusing on the rate at which the improvement in traits was changing. As predicted, there was a marked reduction in generation interval2. The introduction of genomic selection in dairy cattle in 2008 produced a 37% reduction in generation interval in six years, and about a 50% increase in the rate at which genetic improvements were contributing to improvements in milk, fat, and protein yield.

Improving Fertility Through Genomics

There is a genetic antagonism between fertility and milk yield, and that negative genetic correlation has resulted in a steady decline in fertility in Holsteins until 2005. To cease the decline in reproductive performance in the Holstein cattle population, Daughter Pregnancy Rate (DPR) was added to the genetic merit in 2004, and since then, breeding values for DPR have slightly increased but are still lower than the ones observed in the 1960s.

Reproductive traits have low heritability, thus genetic progress has traditionally been slow. Recent advances in genomic tools for prediction of breeding values and inclusion of genomic merit for DPR (GDPR) and heifer conception rate (GHCR) in selection programs, have allowed to significantly increase the genetic progress for these low-heritability traits3.

genomics

Lastly, recent advancements in genomics research can further improve reproductive performance, integrating reproductive technologies, such as semen sexing, multiple ovulation and embryo transfer, ovum pick-up followed by in vitro fertilization, embryo genotyping, and cloning of the best breeders.

For example, genome-wide association studies have been successfully applied to fertility related traits. In addition, genomic approaches have been applied to some traits such as early embryo development and conceptus–maternal interactions, which are important for a successful gestation. Recently, studies based on gene expression and epigenetics were used to analyze heifer fertility traits4.

References

  1. Wiggans GR, Cole JB, Hubbard SM, Sonstegard TS. Genomic selection in dairy cattle: The USDA experience. 2017. Annual Rev Anim Bioscience, 5:309-327.
  2. Garcia-Ruiz, Adriana & B. Cole, John & M. VanRaden, Paul & Wiggans, G.R. & Ruiz, Felipe & P. Van Tassell, Curtis. 2016. Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection. Proceedings of the National Academy of Sciences. 113.
  3. Veronese A Marques O, Peñagaricano F, Bisinotto RS, Pohler KG, Bilby TR, Chebel RC. Genomic merit for reproductive traits. II: Physiological responses of Holstein heifers. J Dairy Sci. 2019 Jul;102(7):6639-6648
  4. Fleming A, Abdalla EA, Maltecca C, Baes CF. 2018. Reproductive and genomic technologies to optimize breeding strategies for genetic progress in dairy cattle. Arch. Anim. Breed., 61, 43–57.