NC_OLD1170: Advanced Technologies for the Genetic Improvement of Poultry (was NC-168)
Statement of Issues and Justification
Poultry meat and eggs are major protein sources in the American diet, with steady per capita consumption increases yearly to current levels of broiler meat and eggs at 87 pounds and 256 eggs, respectively in 2006 and turkey per capita consumption at 17 pounds. The U.S. consumption of chicken meat is higher than either beef or pork, which are estimated at 66 and 49 pounds, respectively for the same year (USDA Economic Research Service). The U.S. also continues to be a leading exporter of poultry (broiler) meat with 5.3 billion pounds exported in 2006. To meet domestic and international demands for chicken meat, the U.S. boiler chicken industry produced 35.8 billion pounds in 2006. Turkey production is estimated at 5.8 billion pounds for 2007, up 2.4 percent from 2006. The U.S. egg industry reached a production level of 6,500 million dozen for 2006.The unprecedented growth of the poultry industry (five-fold increase in past 40 years; three-fold increase in the U.S. in the past 25 years) is partly due to the applications of modern scientific principles in genetic selection, disease control, nutrition, and management programs. To support and sustain the poultry sector, continuous improvements in science and technology must be made, tested, and transferred to the poultry industry which must then apply these new technologies to improve the production efficiency and performance of their populations. This is particularly important today due to increased international competition from Brazil and China.
Primary breeders are responsible for the genetic improvements in poultry, and the improved genetic products are multiplied through the hatchery system. The hatcheries, in turn, supply these more efficient birds to producers and growers in nearby states. The result is greater efficiency at all levels, with gains in production efficiency being passed to the consumer, as lower commodity prices.
Very few commercial poultry breeding operations remain in the world, and operate on a narrow profit margin. As a result any technologies that are developed by one company are kept for proprietary use. At the same time, they are heavily dependent upon public information from academia and other institutions that provide experimental results associated with new technologies. The important interactions of NC-1008 researchers with poultry industry representatives allow communication through a public knowledgebase and help to avoid many of the potentially serious problems in the industry associated with production and disease. Our efforts in advanced genetic and genomic technologies will be most useful to the primary breeders where the technologies can be applied to their breeding stocks. Because of the concentrated structure of the poultry breeding industry, this segment of animal agriculture is one of the best suited for applications of new and profitable technologies.
Complementary to the highly structured industry is the information that is readily available about the biology of the chicken including its short generation interval, large family size, well-documented biochemical and morphological mutations and clearly identified embryonic stages. All contribute to making the chicken an ideal model for development and application of biotechnological discoveries from emerging fields of scientific investigations. The advances in molecular biology and genetics point the way to new technologies that can be coupled with established breeding programs to provide the tools needed by the US. Poultry industry to maintain its competitive edge in the future.
Animal agriculture, to date, has depended upon effecting genetic improvement by estimating genotypic value by measuring phenotypic traits. This practice has severe limitations, especially in traits that are sex-limited (egg production) or require expensive testing (measurement of carcass traits or disease resistance) or testing late in life (reproductive traits). Progress made in molecular genetics and genomics will allow evaluation of some traits at the gene level, opening the possibility of early classification of live birds and use of marker-assisted selection in breeding programs. In addition to the identification of genes, understanding their action within regulatory pathways and the interactions across systems even when gene transfer is utilized will be important in the application of new discoveries.
The first genetic maps for the chicken were developed early in the 20th century and have expanded into a whole genome sequence and genomewide inquiry of gene expression and trait-associations. The chicken has also been an important model organism in development and immunology providing many discoveries including: the discovery of B cells, the isolation of the first oncogenes, and the model for molecular patterning in vertebrates, with the discovery of the apical ectodermal ridge and the polarizing region for limb development. Modern chicken genomics was born with the development of the first genetic-linkage maps based on molecular markers in the 1990s which were developed for mapping QTL for economically important traits. The creation of comparative maps between the gene-poor maps of the chicken with the gene-rich map of human was at first seen as the only realistic way of predicting the gene content of QTL. Complete physical maps of the chicken genome are now available based on large BAC clone assemblies.. Expressed sequence information for the chicken has reached approximately 600,000 ESTs, along with the full-length sequencing of 17,000 cDNAs. These resources have been used to create cDNA and oligo microarrays for high throughput gene expression studies.
The first draft sequence of the chicken genome, made public in 2004 (WASHUC1), was assembled using a whole genome shotgun sequencing strategy. This 6.6-fold coverage of the genome was produced using the DNA from a single inbred female Jungle Fowl. In 2006, additional data from 250,000 targeted sequencing reads were integrated with more extensive genetic and physical maps to produce a second assembly WASHU2. The new version has resolved many errors, in particular the assembly of the sex chromosome Z, which has increased from 34 to 75 Mb with the assembly now containing 1,030 Mb or 98% of the total genome. The microchromosomes are still to be resolved.
A significant contribution of the genome sequence has been the ability to predict gene sequences and compare them to mammalian genomes. Gene detection and comparisons for rapidly evolving genes such as those involved in the immune system remain unresolved. Information on gene function from model organisms and human to orthologs in the chicken has provided important clues to their role in birds. The availability of the chicken genome and a predicted genome-wide set of genes provides new opportunities for whole genome-based gene association and gene expression-based investigations. The chicken genome project has generated many new resources and experimental tools such as whole genome gene expression arrays, full-length cDNA clones, etc. for studies of gene function.
In the dbSNP, there are more than 2.9 million entries for chicken single nucleotide polymorphisms, most generated by a consortium led by the Beijing Genome Institute from a comparison of shotgun sequences from Silkie, broiler, and layer chicken lines with the Red Jungle Fowl as reference. Surprisingly, the segregation of large numbers of common SNP between and within broiler and layer populations provides information on a large number of potential genetic markers for QTL mapping in poultry. Recently, low-cost methods for typing 10,000 or more SNP have become available and with the ability to produce resource populations QTL detection will identify new trait-associations. QTL were first detected for susceptibility to Mareks disease and growth traits and since have expanded to include over 1,000 QTL for a wide range of traits which can be found in databases recording information on more than 200 traits, for almost 1,200 QTL loci, in addition to 400 gene associations. The chicken genome sequence has reinforced the importance of the chicken as a model avian species. Clearly, much has been achieved in our understanding of the chicken genome, but it has also highlighted how much is still to be learned about avian genomes as a whole.
Many of the Advanced Technologies that we are proposing in this new project derive from the remarkable progress that has been made in very recent years. The completion of the chicken genome sequence will clearly revolutionize the poultry industry and the future will be in the post-genome utilization of a systems biology approach to understand better the mechanisms of gene function to improve economics traits of poultry. Poultry researchers are now poised to apply these methods (genomics and transgenesis) to critical problems in the poultry industry, including viral and bacterial disease resistance, fertility, nutrient utilization, reproductive efficiency, and carcass yield.
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