Genome-wide selection in poultry

Abstract

In poultry breeding programs owned by private companies, selection is done within closed populations based on comprehensive phenotypic data recording in both pure and cross line birds under standardised housing conditions. Due to sex-limited data recording, male selection for egg quality and production traits is based mainly on female sibling tests. Early selection of the most promising male within full sib families will improve the rate of genetic progress and can substantially reduce the generation interval. Several past studies, based mainly on microsatellites, have identified quantitative trait loci (QTL) for production and quality traits with only limited use in commercial programs. Genome-wide selection is still in its initial stages in which 10–40-K single nucleotide polymorphism (SNP) chips have been used so far. Due to sequencing of all major pure lines from DNA pools, a customised 600-K SNP chip has been developed for comprehensive genotyping of all commercial lines. Small-scale line-specific SNP chips will be developed afterwards in order to reduce costs for genotyping of male progeny during rearing periods. Only the most promising young males will be transferred to the breeding farm for performance testing and pedigree reproduction. Parental generation will still be genotyped with the comprehensive SNP chip and used for retraining and for imputing. The first results using 30-K SNP chips were obtained from a commercial line used for training, validation and selection, which have shown improved accuracy of prediction at a young age and so resulted in increased genetic gain. Genome-wide marker-assisted selection must prove its advantages over traditional methods including cost benefits.