Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle

Frischknecht, Mirjam; Meuwissen, Theodorus H.E.; Bapst, Beat; Seefried, Franz R.; Flury, Christine; Garrick, Dorian; Signer-Hasler, Heidi; Stricker, Christian; Bieber, Anna; Fries, Ruedi; Russ, Ingolf; Sölkner, Johann; Bagnato, Alessandro; Gredler-Grandl, Birgit (2018). Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle Journal of Dairy Science, 101(2), pp. 1292-1296. Elsevier 10.3168/jds.2017-12890

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The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies. We estimated genomic breeding values for 3 traits (somatic cell score, nonreturn rate in heifers, and stature) and found differences in accuracy levels between traits. However, among different SNP sets, accuracy was very similar. In our analyses, sequence data led to a marginal increase in accuracy for 1 trait and was lower than 50K for the other traits. We concluded that the inclusion of imputed whole-genome sequence data does not lead to increased accuracy of genomic prediction with the methods.

Item Type:	Journal Article (Original Article)
Division/Institute:	School of Agricultural, Forest and Food Sciences HAFL > Resource-efficient agricultural production systems School of Agricultural, Forest and Food Sciences HAFL > Agriculture
Name:	Frischknecht, Mirjam; Meuwissen, Theodorus H.E.; Bapst, Beat; Seefried, Franz R.; Flury, Christine; Garrick, Dorian; Signer-Hasler, Heidi0000-0001-5193-5306; Stricker, Christian; Bieber, Anna; Fries, Ruedi; Russ, Ingolf; Sölkner, Johann; Bagnato, Alessandro and Gredler-Grandl, Birgit
Subjects:	S Agriculture > SF Animal culture
ISSN:	00220302
Publisher:	Elsevier
Language:	English
Submitter:	David Zimmer
Date Deposited:	03 Sep 2019 08:55
Last Modified:	18 Dec 2020 13:28
Publisher DOI:	10.3168/jds.2017-12890
Uncontrolled Keywords:	genomic prediction, Brown Swiss, whole-genome sequence data
ARBOR DOI:	10.24451/arbor.8162
URI:	https://arbor.bfh.ch/id/eprint/8162