Interest of Genotyping-by-Sequencing technologies as an alternative to low density SNP chips for genomic selection in layer chicken

To reduce the cost of genomic selection, low density SNP chip can be used in combination with imputation for genotyping the selection candidates instead of using high density (HD) SNP chip. Concurrently, next-generation sequencing (NGS) techniques has been increasingly used in livestock species but remain expensive to be routinely used in selection. An alternative and costefficient solution is the Genotyping by Genome Reducing and Sequencing (GGRS) techniques to sequence only a fraction of the genome by using restriction enzymes. This approach was simulated from sequences of 1027 individuals in a pure layer line, using four enzymes (EcoRI, TaqI, AvaII and PstI). Imputation accuracy on HD genotypes was assessed as the mean correlation between true and imputed genotypes. Egg weight, egg shell color, egg shell strength and albumen height were evaluated with single-step GBLUP methodology. The impact of imputation errors on the genomic estimated breeding values (GEBV) was also investigated.AvaII or PstI led to the detection of more than 10K SNPs in common with the HD SNP chip resulting in imputation accuracy higher than 0.97. The impact of imputation errors on the ranking of the selection candidates was reduced with Spearman correlation (between GEBV calculated on true and imputed genotypes) higher than 0.97 for AvaII and PstI. Finally, the GGRS approach can be an interesting alternative to low density SNP chip for genomic selection. However, with real data, heterogeneity between individuals with missing data has to be taken into account

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