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Changing just one nucleotide in the DNA sequence can code for a different amino acid in a protein molecule, which can lead to a different function or structure for the protein. Photo courtesy Hy-Line
on October 7, 2009

Genomic selection: The race is on

Primary breeders are utilizing gene chips and chicken genome sequence information to try and increase the rate of genetic progress.

The race is on for primary breeding companies to make rapid improvements in their poultry breeding programs through the use of genome-wide selection. They are utilizing the latest developments in gene chips and chicken genome sequence information that could allow them to bypass conventional selection techniques and speed up delivery of commercially important improvements in genetic stock.

Completion of the chicken genome sequencing project has opened up this possibility, but the technology is not proven and comes with a relatively high price tag. In fact, developing genome-wide selection as a practical tool for poultry breeding requires technology, statistics, pedigree information, financial resources, test populations and a lot of brain power.

Poultry genetics companies, therefore, have opted to collaborate and combine resources with government and academia to test and implement genome-wide selection in their pedigree broiler and layer flocks. Two consortiums have been formed which are allowing genetics companies to leverage their combined knowledge and financial resources to tackle the question of how best to implement genome-wide selection. One consortium involves Aviagen, Hy-Line and Lohman Tierzucht, and the other includes Cobb-Vantress and Hendrix Genetics.

Genome-wide selection in turkeys will have to wait for completion of the sequencing of the turkey genome. Statistical and laboratory techniques developed in chicken genomic programs will likely be applicable to turkeys, but these cannot be applied until the turkey genome has been sequenced.

Why genome-wide selection?

“In classical marker assisted selection, you look for genes and gene markers for specific economic traits,” said Albert Paszek, director of biotechnology, Cobb-Vantress. This process has aided genetics companies in their efforts to deliver genetic improvement. But some traits can be controlled by multiple genes and this can make the process of associating genes with that trait a long and difficult one,” Paszek explained.

With the sequence information of the chicken genome now available, theoretically, all of the genes could be identified in the genome and they could all be tied to specific traits that they influence, but this would take a tremendous amount of time and resources. Genomic selection could allow breeders to bypass the process of identifying all of these genes and still allow for an increase in genetic progress.

Collaborating with USDA and academia

Cobb-Vantress and Hendrix Genetics are collaborating on a $10 million genome-wide selection project with the USDA and several universities in the U.S., Canada and Europe. For this project, a gene chip has been developed with 60,000 single nucleotide polymorphism (SNP) markers on it (see “What are SNPs?” and “Gene chips or DNA microarrays”).

In genome-wide selection, phenotype and pedigree information for individual birds is collected as usual. In addition, each bird’s DNA is tested on the gene chip to provide information on its SNPs. Statistical models are then used to find any associations between the birds’ phenotype information and SNPs. Thousands of birds are tested in this manner, and the cumulative information is used to calculate a breeding value for each bird.

For this project, Cobb-Vantress and Hendrix randomly assigned members of their pedigree flocks of broilers and layers to either the genome-wide test groups or the control groups. The breeding stock is selected by conventional means in the control group and by genome-wide selection in the test group. The rate of genetic progress of the two groups will be measured for key economic factors over several generations.

Cobb-Vantress will employ genome-wide selection for four generations on its broiler pedigree flocks. In the published portion of the study, Paszek said that they are looking at the progress on growth rate, breast meat yield and leg health characteristics, which are high-heritability, moderate-heritability and low-heritability traits, respectively.

The generation interval is shorter for broilers than for layers. That’s because traditional selection techniques take measurements all the way through the reproductive cycle in layers explained Dr. Ir. Gerard Albers, director, Hendrix Genetics Research and Technology Center. Genomic selection, on the other hand, allows for breeders to be chosen once the laying cycle commences. This will allow Hendrix to go through three generations in the genome-wide selection group in the study, while the traditional selection group only goes through two generations.

In the published portion of the study, Hendrix will be measuring progress in egg shell quality, a high-heritability trait, and egg production, a moderate- to low-heritability trait. Cobb-Vantress and Hendrix will also be measuring progress in numerous other phenotypic traits as a result of genome-wide selection, but this data will not be published.

Aviagen, Hy-Line and Lohman collaboration

A collaborative effort between Aviagen, Hy-Line, Lohman Tierzucht and an advisory panel of geneticists from several major universities in the U.S. and the United Kingdom will explore the application of genome-wide selection in the pedigree populations for the companies’ broilers and layers. No public money is used in this collaboration, and the cost of the project has not been revealed. The initial findings of this project were presented at scientific meetings this summer, and procedures and findings, including traits and responses, will be published in the future.

Aviagen’s genomics initiative started in 2005 after the first draft of the chicken genome sequence was released, according to Santiago Avendano, senior geneticist, Aviagen Group. The establishment of the collaborative efforts between Aviagen and Hy-Line was announced last year.

Dr. Neil O’Sullivan, research director, Hy-Line International, said the consortium is using 42,000 SNPs that were developed based on earlier genome research started at Hy-Line in 1996 and Aviagen in 2005.
Aviagen will be looking at improving three types of traits using genome-wide selection, according to Avendano. The first type has economic importance at this time, things like breast meat yield, feed conversion and body weight under different growing conditions, either high-hygiene and low-hygiene environments.

The second group of traits is the support group, livability under different growing conditions, cardiovascular function and leg health characteristics. The last group of traits includes things that the breeders can’t measure in their own selection environments, such as response to disease challenge. Such traits can only be looked at through birds in the field with customers.

Genome-wide selection will be used for six generations on Hy-Line’s layer pedigree flocks and the traditional selection will be employed for three generations on the controls in the project.

High cost but big returns?

Genetic testing is expensive. Depending on the number of samples, negotiating skill with vendors and the number of markers used, testing an individual bird’s genome could cost between $150 and $250, according to the geneticists contacted for this story. This is just for the test; it doesn’t include the cost of collecting samples and extracting the DNA.

The cost of the testing of thousands of pedigree birds, however, will be spread over billions of market broilers and layers. And the potential payback for the poultry industry can be great due to an accelerated rate of genetic improvement.

Another point to consider is that chicken primary breeders are not just competing against each other; they are also competing against the breeders of other species.

The USDA is partnering with beef cattle breeders on a genome-wide selection study that is part of the same genome-wide selection project in which Hendrix and Cobb-Vantress are participants. Dairy cattle breeders in both the U.S. and Europe have undertaken major genome-wide selection initiatives. Hendrix has embarked on a genome-wide selection study in its swine division.

Maintaining or expanding the relatively enviable competitive position of chicken protein as a human food source will continue to rely on the ability of primary breeders to rapidly adopt and develop new selection strategies like genome-wide selection.

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Each small glass plate or “gene chip” contains 12 lanes and in each lane a DNA sample is tested for 60k SNPs in multiple repeats for the Hendrix and Cobb-Vantress collaborative project. Photo courtesy Hendrix
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