New method increases genetic selection efficiency

Although developed for use in any species, new breeding parameter was tested in dairy cattle because of the volume and quality of available data.

Brazilian scientists at São Paulo State University (UNESP) collaborating with colleagues at the University of Maryland and the U.S. Department of Agriculture have developed a dairy cattle breeding method that adds a new parameter to genetic selection and conserves or even improves a population's genetic diversity.

The study, published in Journal of Dairy Science, was funded by the São Paulo Research Foundation - FAPESP and USDA.

Besides genetic value associated with milk, fat and protein yields, the new method also takes into consideration the variance in gametic diversity and what the researchers call "relative predicted transmitting ability," defined as an individual animal's capacity to transmit its genetic traits to the next generation based on this variance, according to an announcement from FAPESP.

"Not all progeny of highly productive animals inherit this quality. The new method selects animals that will produce extremely productive offspring," said Daniel Jordan de Abreu Santos, who conducted the study while he was a postdoctoral fellow at UNESP's School of Agricultural & Veterinary Sciences in Jaboticabal, Brazil.

Santos is currently doing more postdoctoral research at the University of Maryland.

"Gamete diversity variance is generated by the separation of homologous chromosomes and the rate of recombination between genes linked to them. It isn't accounted for by the traditional selection method," Santos said.

The new method estimates the probability of the transmission of traits to the next generation on the basis of the genetic data of a parent or the possible combinations in a given mating, FAPESP said.

Although it was developed for the selection of any species, in this study, the method was applied to Holstein and Jersey dairy cattle because of the volume and quality of available data.

In computer simulations, the method produced genetic gains of up to 16% in 10 generations of Holstein cattle, compared with a control group for which gamete diversity was not a factor.

Genomics

FAPESP said the study was possible because matings can now be simulated using large genomic databases with genetic details for the animals involved, including genes associated with certain traits of interest in breeding programs.

Based on these data, scientists can estimate the possible combinations of the parents' genetic material and predict the traits of their progeny. However, traits are not uniformly distributed among offspring, the announcement explained.

Animals with the desired traits may produce offspring with very high or low levels of these same traits. As a result, the predicted traits of progeny in terms of milk, meat or fat yield are only an average of the parents' traits. The new method enables scientists to estimate the substantial variation around this average, FAPESP said.

"It's now possible to predict which animals will produce highly productive offspring, above the expected average, before they mate. Gamete diversity is the factor that generates this estimate, determining the animal's capacity to transmit the traits of interest to its progeny," Santos added.

To apply the theory to an actual breeding program, Santos used data for more than 160,000 Jersey cattle and approximately 1.4 million Holstein cattle from a USDA Agricultural Research Service database.

Software developed by the researchers was used to calculate the variation in all possible chromosome combinations and enabled them to separate individual animals with more or less gamete diversity variance, according to FAPESP.

"These variations can be used to select animals for specific purposes," Santos said. "You can select animals to have more homogeneous progeny, which you might want to do in order to obtain traits such as birth weight, or more heterogeneous progeny and, hence, some offspring that are more productive than the expected average."

Beyond guaranteeing that successive generations are as productive as their parents, the new parameter promises to produce major genetic gains in progeny bred from the same source animals, Santos said.

The researchers also investigated the possible impact of the method on actual dairy herds. The match between variance based on genomic data and the actual variance observed in adult female progeny reached 90% in the case of 400 offspring per sire.

The new parameter also helps mitigate the reductive impact of selection on a population's genetic diversity. In the case of livestock such as dairy cattle, genetic variability tends to be low because of inbreeding.

"The new method offers a means of maintaining genetic variability. Individuals considered better by the traditional method will often be endogamous — offspring from the same gene pool — but when the new parameter is taken into account, they can no longer be classed among the best," Santos said.