Healthier chickens with more meat and less fat

Brazilian researchers discover new genes for the selection of chickens that make better use of feed nutrients and produce leaner meat

By Peter Moon  |  Agência FAPESP – In genetic terms, the chickens sold by supermarkets are the result of successive cross-breedings over many generations with the aim of maximizing weight gain. This process has produced chickens with more muscle, especially in the breast and thighs, which consumers prefer. The downside is the deposition and accumulation of fat alongside muscle growth.

Research conducted at the University of São Paulo’s Luiz de Queiroz College of Agriculture (ESALQ-USP) in Piracicaba, Brazil, seeks to understand the genetic reasons for fat accumulation in chickens to improve commercial lineages so that they have more muscle and less fat.

“There are two main chicken lineages in the poultry industry, one for egg production and the other for meat production. In the past, chicken breeders focused on genetic improvement for weight gain, which led to chickens with more breast and leg meat. As an undesirable side effect, they were also fatter,” said Luiz Lehmann Coutinho, Full Professor in ESALQ-USP’s Animal Science Department.

Most of the fat is deposited in and under the skin and in the abdominal cavity (abdominal fat pad).

“Consumers are more concerned about health nowadays. They want healthier food,” Coutinho told Agência FAPESP. “In the case of poultry, healthier food means chickens with lean meat and less fat. Poultry farmers want chickens that eat less, grow more, and grow faster. The aim of our research is precisely to obtain an animal that consumes less feed and makes better use of the nutrients, growing in good health and producing more muscle.”

The potential market for a new, leaner chicken line is huge. Brazil is the world’s leading producer of chicken meat. It had 1.45 billion birds in production in July 2018, according to IBGE’s agricultural census. Some 16 million chickens are slaughtered daily (5.86 billion per year in 2016). Brazil is also the largest exporter of chicken meat. In 2016, it exported 4.4 million metric tons to 143 countries, earning USD 6.8 billion.

The investigation of the genes responsible for fat deposition in chickens is described in an article published in the journal BMC Genomics. Identifying genes associated with fat deposition is comparable to looking for needles – the genes of interest or candidate genes – in a haystack – the chicken genome.

The complete genome of the chicken (Gallus gallus domesticus) was published in 2004. The latest assembly contains approximately 1.3 billion base pairs on 72 chromosomes. The human genome contains 3 billion base pairs on 46 chromosomes.

The study described in the published article is supported by FAPESP and the National Council for Scientific and Technological Development CNPq. The first author of the article is Gabriel Costa Monteiro Moreira, whose PhD research was supported by a scholarship from FAPESP.

The study was part of the Thematic Project “Identification of loci of interest for poultry production”, for which Coutinho is principal investigator. The participating researchers also include scientists at the Pig and Poultry Unit of the Brazilian Agricultural Research Corporation (EMBRAPA), São Paulo State University’s School of Veterinary Medicine and Animal Science (FMVZ-UNESP), Iowa State University (USA), and Massey University (New Zealand).

According to Coutinho, the material collected for the study consisted of broiler blood samples from EMBRAPA’s poultry breeding program in Concórdia, Santa Catarina State. The founding line of this population has been under multiple trait selection since 1992, mainly for body weight, feed conversion, carcass and cut yield, viability, fertility, hatchability, and reduced abdominal fat.

Genes identified

The broiler population analyzed in the study was developed in 2008 and comprised 1,430 chickens (652 males and 778 females) generated in hatches from 20 males and 92 females.

“In 2005, we performed a preliminary analysis of the chicken genome using the microsatellite marker technique. We identified 120 markers, which we then used in an initial search for regions of the genome associated with the traits of interest to the poultry industry. Later, however, thanks to the accelerating development of genetic research and the purchase of new equipment for our laboratory with support from FAPESP, we were able to deploy a more advanced genotyping method,” said, Coutinho, who heads ESALQ-USP’s Centralized Multiuser Laboratory for Functional Genomics Applied to Agriculture and Agroenergy.

Genotyping is the process of determining the genetic make-up (genotype) of an individual by examining their DNA sequence. SNP genotyping measures one of the most common forms of genetic variation between members of a species in terms of single nucleotide polymorphisms (SNPs, pronounced “snips”). The researchers at ESALQ-USP identified 355,000 SNPs in the 1.3 billion base pairs for the 1,430 chickens they genotyped.

Integrating knowledge in quantitative genetics, statistics and bioinformatics, they undertook a sophisticated search for regions of the chicken genome that control traits of economic interest. “We succeeded in identifying the genome region that contains the genes that influence fat deposition,” Coutinho said.

Their painstaking laboratory and bioinformatics analysis reduced the study universe to 419 genes, among which they initially selected 13 candidates. Finally, after an even more refined search, they arrived at four genes associated with fat deposition. Two of these genes were already known to science. The other two were discovered by Coutinho’s team at ESALQ-USP.

This is the point reached in the research so far. “We now have to perform in vitro tests on each of these genes, using chicken cells, to find out whether the genes are functional and whether they do in fact alter the cellular mechanism involved in fat deposition. If so, we’ll use the information to identify chickens that have the genes in question. They’ll then be selected as broiler breeders for genetic improvement to obtain a new line of leaner chickens,” Coutinho said.

When a new line of chickens that are leaner but have plenty of meat has been obtained, it will be offered to poultry farmers. According to Coutinho, this goal can be achieved within the next five years.

The article “A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens” (https://doi.org/10.1186/s12864-018-4779-6) by Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Priscila Anchieta Trevisoli, Maurício E. Cantão, Mônica Corrêa Ledur, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Ana Silvia Alves Meira Tavares Moura, Dorian Garrick and Luiz Lehmann Coutinho can be read at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4779-6.