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Genomics

Ruminating over information

Bovine DNA sequencing opens the way to understanding and improvement in breeds

MICHAEL MCNEAL/USDAGenetic fame: Dominette is 93% identical to her father (above)MICHAEL MCNEAL/USDA

Domesticated almost 10,000 years ago, bulls and cows are a food source in the form of milk and meat for more than 6 billion people in the world. Now, scientific knowledge of this animal has just taken a further step with the sequencing of its genetic material. The achievement, in which more than 300 researchers from 25 countries took part, was announced in April on the cover of Science journal. The project was coordinated by the United States with the participation of Brazilians from the Brazilian Agriculture and Livestock Research Company (Embrapa), from the Araçatuba and Assis campuses of the Paulista State University (Unesp) and from the University of São Paulo in Ribeirão Preto (USP-RP).

“We’ve compiled a veritable telephone directory, containing the name and address of all the genes; we just have to find out their profession”, is the analogy drawn by veterinarian José Fernando Garcia, from Unesp in Araçatuba. The Science article shows that cattle have around 22,000 genes in each cell, which is a number similar to that of other mammals. Comparison of these results with the results of other genomes (dogs, human beings, mice, rats, marsupials and duck-billed platypuses) allowed the geneticists to make a first assessment of the evolution of each of these groups. In the case of cows the most important genetic alterations happened in genes linked to reproduction, immunity, lactation and digestion. “Ruminants have a large number of microorganisms in their stomach”, explains Garcia. “It’s possible that genetic alterations allow them to maintain these microorganisms as intestinal flora and not as the causers of disease”, he explains, pointing out that these interpretations are still speculative. “We’ve created the inventory, now we’re going to start exploring it.”

The laboratory work as such was centralized in the United States and managed to sequence 92% of the DNA of Dominette, a Hereford cow. Then, a computer program was used to outline the genes that had been revealed. These data were subsequently analyzed by researchers from all over the world in a process called annotation. There were 13 groups which divided the genetic material according to its physiological function in order to check, gene by gene, if the automatic forecast was correct; but not for all the genes sequenced. “It was done by sampling; each group examined the genes that most interested them”, says geneticist Alexandre Rodrigues Caetano, from Embrapa, who coordinated the annotation of genes related to reproduction, embryonic development and the hormonal system. Even though only part of the genes have been annotated (between 10% and 20% in his estimate), the researcher is commemorating the fact that we now have an overall view of the genome, which allows us to know how genes relate to one another. The group from Araçatuba, coordinated by Garcia, was responsible for genes related to the skin and blood.

Diversity
According to the vet from Unesp, the bovine genome project, which began in 2003, took into consideration the successes and limitations of the Human Genome project that ended in 2002. “The researchers realized that it was not enough just to know the genome; it was necessary to explore the variability between individuals”, states Garcia. “There are more than 800 breeds of cow that are raised and kept by man and the work of improving them is based on the particular aspects to be developed”, he says. Because of this, in parallel with the sequencing of the genome, another international consortium worked on outlining the map of the genetic diversity that exists between bovine breeds. The results are in a second article published in the same edition of Science, which compares Dominette’s DNA with DNA strands from 19 other breeds of cow. Caetano, from Embrapa, coordinated including samples of the Gir and Nelore cattle, the main breeds in the Brazilian herd (the biggest in the world) in the work. Garcia took part in this phase of the work, directing the collection in Ethiopia of samples of the Sheko breed, which is resistant to the sleeping sickness transmitted by the tsetse fly.

MICHAEL MCNEAL/USDADominetteMICHAEL MCNEAL/USDA

The map of genetic variation corroborated what was already known about the domestication of cattle: between 8000 and 10,000 years ago the original domestication took place in two centers. From India came the zebu, cows with humps, like the main Brazilian breeds, and from the Middle East came the taurines, a group of which the Hereford breed forms part. The results show that the initial population of zebus was bigger than the one that gave rise to the taurines, which as a result already started out having a smaller genetic diversity.

Classic artificial selection, in which breeders, in their search to obtain tame animals that are highly productive and resistant to disease, choose only some animals as reproducers, undoubtedly contributed a lot to the evolution of cows, favoring the conservation of genes responsible for these characteristics. In these improvement strategies only a few animals contribute to the genetic pool of the herd and the result is in the DNA: the genetic diversity of herds becomes more and more reduced. This is not yet serious; if it were genetic defects would be an important cause of mortality in herds. But this is precisely why it is important to assess the genetic diversity of each breed: using this information to maintain variability.

Caetano emphasizes that the genome and the diversity map are important tools that are now available to researchers and breeders. “My function at Embrapa is to help researchers design and carry out experiments using the best technology for each project”, he says. In a single DNA chip it is now possible to examine the genetic markers in each animal in one go. This is a tool that makes it very much faster, simpler and cheaper to carry out genetic assessment and select cows that have the best resistance to disease or parasites, that produce offspring that give more milk or that have more tender meat. This is an immense saving in time for breeders. “Instead of crossing with a bull and waiting until its daughters starting breeding and beginning to produce milk to assess their productivity we’ll be able to select bulls before they even reach their reproductive age”, says the geneticist.

It will be necessary to wait in order to apply this knowledge, given that most of the genes have not yet been revealed. The next few years should bring a rapid advance in our knowledge of genetic markers that are economically interesting. This not only speeds up selection, but allows for breeds to be improved in a more controlled way. “So far we can only select animals by looking at them from the outside”, says Garcia, “Now we’re managing to look at them inside, too”. Brazil has 200 million head of cattle, the biggest commercial herd in the world. It is the country that exports most but not the one that makes the biggest profit. According to the researcher, this is because Brazilian breeds do not have some of the qualities that Argentinean cattle have, for example.

The researcher from Unesp also forecasts that when it becomes possible to use these tools to obtain something like genetic certification Brazilian animals may become attractive enough to establish breeds in other countries. “These cattle resist heat, disease and poor quality food, characteristics that may be very valuable in other tropical countries”, he imagines.

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