Accuracy of genomic prediction is key for genetic progress in breeding programs and including genome functional annotation may help. Here we report on the added value of Combined Annotation Dependent Depletion (CADD) scores to weigh SNPs in GBLUP analyses. Multiple transformations of CADD scores were considered and empirically validated on a layer dataset including 5 traits and 18K animals with 27K SNP genotypes. This initial analysis revealed that the use of (squared) CADD scores yielded marginally higher accuracy for 3 traits. We anticipate that the added value of CADD scores will increase by using a higher number of SNPs and ultimately whole genome sequence SNPs.
Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)
Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges
EditorsR.F. Veerkamp and Y. de Haas
Published: 2022 Pages: 3364
eISBN: 978-90-8686-940-4
Book Type: Conference Proceedings
304. Predictive ability of genomic prediction in layers when including CADD scores as genome function information
M.C.A.M. Bink Related information
1Hendrix Genetics, P.O. Box 114, 5830 AC Boxmeer, the Netherlands.
*Corresponding author: marco. bink@hendrix-genetics. com
, M.P.L. Calus Related information*Corresponding author: marco.
2Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6700 AH Wageningen, the Netherlands.
, M.F.L. Derks Related information2Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6700 AH Wageningen, the Netherlands.
, J. Visscher Related information1Hendrix Genetics, P.O. Box 114, 5830 AC Boxmeer, the Netherlands.
, B.C. Perez Related information1Hendrix Genetics, P.O. Box 114, 5830 AC Boxmeer, the Netherlands.
Pages: 1278 - 1281
Published Online: February 09, 2023
Abstract: