The sequencing of the chicken genome and its subsequent release into the public domain in 2004 catapulted the poultry breeding industry into the genomics field. Major poultry breeding companies are actively investigating the use of genomic information to enhance breeding programs and improve selection efficiencies. However, the following are still significant gaps in basic information needed for application:
• The current chicken genome build has errors and is missing many of the gene-rich smaller chromosomes, thus compromising application.
• Current technologies use one type of genetic variation (single nucleotide polymorphisms). It is likely that other types of variation are relevant for improved production, and research is needed for identification and rapid detection (e.g., copy number variants, alternative RNA splicing, imprinting).
• The maximal value of publicly funded genomic research will occur if industry, academia, and funding agencies work together synergistically to ensure that resources and tools are placed rapidly into the public domain.
• Recent funding emphasis has been placed on genomic information and tools, whereas fundamental research on the biology of birds has been neglected. Birds are not a variation of mammals.
• A tremendous loss of poultry genetic diversity has occurred within research institutions in the United States and Canada over the past 4 decades, yet this genetic variability is fundamental for understanding gene function and the effect of variation on traits.
• Microbial genomics has the possibility of transforming the breeding industry as adjustments of the microflora could reduce environmental impact and improve sustainability.