Genome-wide selection in poultry

Abstract

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.

Applied Animal Genomics: Results from the Field

“…Although GS has the potential to be expensive, breeders have begun to implement various strategies to minimize the costs of genotyping and retraining. Higher accuracies can be obtained by combining data from populations with and without genomic data using single-step G-BLUP, and costs associated with large-scale genotyping can be reduced by imputing high-density genotypes from low-or reduced-density SNP chips (112). This method was demonstrated in a population of brown egg layers in which, after two generations of high-density genotyping of all parents, sires were high-density genotyped in generations three through five, and dams were either high-or reduced-density genotyped for one to two generations.…”

Microarray resources for genetic and genomic studies in chicken: A review

“…GS is being applied extensively for genetic improvement of dairy cattle and two major high density arrays (>500K) are now available for cattle (Rincon et al ., ). For chicken, several studies have reported the use of proprietary medium density arrays for GS in commercial broiler and layer breeds (Avendaño et al ., ; Dekkers JCM, ; Preisinger, ; Wolc et al ., ). For instance, the EW group of poultry breeding companies (including Aviagen Ltd., Hy‐Line International and Lohmann LTZ) developed a proprietary 42K Illumina iSelecta BeadChip for application to GS (Avendaño et al ., ).…”

Development of a high density 600K SNP genotyping array for chicken

“…In spite of all these resources no HD genotyping array is yet available for this species that can facilitate high throughput investigation of many individuals for research and commercial breeding. A number of studies, however, have reported the use of low to medium (3 K to 60 K) density panels for various purposes [4-7] but these panels were proprietary and have not been made available for wider use. In contrast, for cattle, for example, two HD genotyping arrays (both >600 K) are now available [8,9].…”