Identified genomic regions that might allow an increase in meat production

Brazilian researchers have discovered six genomic regions that are affected by selection for weight in Nelore cattle and could lead to improvement of the breed.

By Peter Moon  |  Agência FAPESP – Brazil has the world’s second-largest cattle inventory after India, with 218 million head, of which Nelore cattle account for 80%. Rapid growth is important to cattle farmers, who want animals to reach the ideal slaughter weight at the earliest possible age. 

A pioneering research project has identified genes potentially associated with functions such as growth and weight gain in the Nelore breed. These functions are key to beef production. The researchers pinpointed genomic regions that had changed owing to selection, referring to these as genomic signatures of selection. 

“We found six genomic regions containing genes associated with weight gain in the Nelore breed. Some of these hadn’t been reported in the scientific literature, even for other breeds of beef cattle,” said Diercles Cardoso, a postdoctoral fellow of São Paulo State University’s Agrarian & Veterinary Science School (FCAV-UNESP) at Jaboticabal, Brazil, with a scholarship from FAPESP.

“Four of these regions are classified as signatures of selection and are in chromosome 14, which was already known to contain genes for growth in the bovine genome,” Cardoso explained. “However, we identified two other signatures in chromosome 16. This was somewhat unexpected. It may be that genes in these two regions are associated specifically with growth traits in Nelore cattle and therefore offer immense potential for improvement of the breed in terms of weight gain.”

Cardoso is lead author of an article published in the journal Genetics Selection Evolution presenting the results of his PhD research, which was supervised by Professor Humberto Tonhati. In addition to these two researchers, the study also involved Lucia Galvão de Albuquerque, Full Professor at FCAV-UNESP, scientists at the University of Göttingen in Germany, and researchers affiliated with the Animal Science Institute of the São Paulo State Agribusiness Technology Agency (APTA).

The identification of the genes began with the collection of blood samples from animals belonging to three Nelore selection lines maintained under an experimental program run by APTA’s Beef Cattle Center at Sertãozinho, São Paulo State. The program was set up in 1980 to show producers the benefits of selection for growth traits and evaluate the economic benefits of selection for growth on the overall productivity of beef cattle herds. One of the three lines is a control and is not subjected to selection for weight gain. In the other two, known as Nelore Selection and Nelore Traditional, sires that perform best in weight gain tests are selected annually for reproduction.

Every year, between three and eight of the best bulls are used for reproduction in the lines selected for weight gain (Selection and Traditional). The animals now in the experimental herd are the result of eight generations of selection for weight gain. Those in the Selection line are much larger than those in the control line when animals of the same age are compared.

Cardoso used blood samples from 782 animals born between 2004 and 2012 – 92 from the control line, 192 from the Selection line, and 498 from the Traditional line. The samples were processed in the laboratory to extract DNA and genotyped with SNP chips (SNP stands for single nucleotide polymorphism).

Genotyping is the process of determining differences in the genetic makeup (genotype) of an individual by examining the individual's DNA sequence. SNPs (pronounced “snips”) are one of the most common types of markers of genetic variation. In the case of the bovine genome, Cardoso used a chip that can identify approximately 777,000 SNP markers in bovine DNA samples.

The analysis of DNA from all sampled animals using SNP chips entailed a comparison of the genotypes of animals in the control line with those of animals in the other two lines using three independent methods. The first identified 48 genomic regions that displayed signs of being linked to weight gain functions. The second and third methods identified only seven and 17 regions, respectively.

Cardoso compared the three sets of results and arrived at six regions that were identified by at least two of the methods. These were the six signatures of selection found to be associated with the animals’ weight.

Cardoso now plans to study the functions of the genes in these regions in search of evidence that they are indeed associated with growth in Nelore cattle.

Genomic database

The study was conducted under the aegis of the Thematic Project “Genomic tools for genetic improvement of economically important traits in Nelore cattle”, with Albuquerque as the principal investigator.

“Until the 1990s, few markers were known, and the cost of identifying them was prohibitive,” Albuquerque said. “The bovine genome was published in 2009, and a large number of markers have been identified throughout the genome since the mid-2000s.”

Brazil had no genomic databases for beef cattle until the 1990s, and little emphasis was placed on improving beef quality owing to its high cost and the difficulty of measuring the traits concerned. 

With the advent of genomics, it became easier to select for traits not routinely included in breeding programs, such as those that are hard to measure.

“A database for genotyped animals was created thanks to the Thematic Project, including data on traits associated with beef quality,” Albuquerque said.

“Enhanced quality of beef cattle means meat that’s more tender and has more marbling, which is intramuscular fat, the intermingling or dispersion of fat within the lean, making the meat tastier.

“Brazilian beef is very lean because most beef cattle are free-range, allowed to graze in open pasture rather than being fattened in feedlots, and also because until now the Nelore breed hasn’t been selected for meat quality. These traits need to be improved.”

Between 2011 and early 2017, the Thematic Project invested in studies designed to help improve meat quality and enhance Nelore food efficiency – the capacity to convert food into weight gain. 

“The idea is to obtain an animal that eats less, gains weight faster and produces high-quality meat. At the end of the project, we’d genotyped over 8,000 animals and measured a range of economically important traits such as food and reproductive efficiency, as well as meat quality,” Albuquerque said.

Taurine and indicine

The improvement of phenotypic traits in cattle by artificial selection has been practiced almost nonstop since Bos primigenius was domesticated in Eurasia 10,000 years ago, resulting in the dozens of breeds that exist today.

However, it was not until the twentieth century that veterinary or animal science labs in universities and research centers brought specialist knowledge to selective breeding. More recently, molecular biology tools have become a key element of the techniques used to improve the characteristics of cattle. 

The goal is to dissect the bovine genome to be able to manipulate cattle genes to obtain individuals that are more resistant to disease and better adapted to different climates, cows that produce more milk, and steers with more weight gain potential in less time and with less food consumption.

The bovine genome has been entirely sequenced and mapped, and the results were published in 2009. Bovine DNA comprises 30 pairs of chromosomes with 3 billion base pairs. For the sake of comparison, recall that the human genome also has 3 billion base pairs but only 23 pairs of chromosomes.

Once the bovine genome had been mapped, specialists in several countries began investigating molecular chains in search of genes or specific gene groups that might be associated with desired breeding characteristics such as weight gain. These genetic signatures are being located and identified. Indeed, several genes for weight gain in cattle are now known.

However, this is true only for the genome that has been sequenced and does not necessarily represent the total universe of genetic variability present in the range of different breeds. Although Nelore, Angus, Jersey, Charolais and other breeds all belong to the same species (B. primigenius), they were selected to obtain specific characteristics. In each case, their DNA contains specific genes that were selected in one breed and not in another.

Weight gain genes have thus far been identified in some breeds that are popular in other countries. Studies such as this one by Cardoso and colleagues have contributed to an increase in knowledge regarding Nelore cattle.

B. primigenius is divided into two subspecies, B. primigenius taurus (taurine) and B. primigenius indicus (indicine, zebu or humped). Animals of the former subspecies are better adapted to climates with harsh winters, as they gain weight in warm months, accumulating reserves to survive until winter is over and green pasture returns. Taurine breeds are therefore predominant in North American and European herds.

The indicine subspecies originated in India. Nelore zebu cattle were introduced to Brazil when it was a Portuguese colony. They have adapted very well to the climate.

The other side of the coin is that being a tropical breed and not needing to gain weight in order to survive the mild winters in the tropics, Nelore is naturally lean and gains less weight than taurine breeds. Hence the need to find specific genes responsible for weight gain in Nelore.

The article “Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle” (doi: https://doi.org/10.1186/s12711-018-0381- 2) by Diercles F. Cardoso, Lucia Galvão de Albuquerque, Christian Reimer, Saber Qanbari, Malena Erbe, André V. do Nascimento, Guilherme C. Venturini, Daiane C. Becker Scalez, Fernando Baldi, Gregório M. Ferreira de Camargo, Maria E. Zerlotti Mercadante, Joslaine N. do Santos Gonçalves Cyrillo, Henner Simianer and Humberto Tonhati can be read at gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0381-2.