Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds

Fang, Lingzhao; Sahana, Goutam; Ma, Peipei; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

doi:10.1186/s12864-017-4004-z

Table 1 Top five Gene Ontology (GO) terms with GFBLUP in Holstein for the four traits

From: Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds

Trait	GO ID	r ^a _ _GFBLUP	bias^b	Δr ^c	\( {\left({H}_f^2\right)}^{\mathrm{d}} \)	Nsets^e	GO term	GO family
Milk	GO:0042572	0.655	0.863	0.020	0.169	586	Retinol metabolic process	Metabolic process
	GO:0034605	0.655	0.864	0.020	0.185	1517	Cellular response to heat	Response to stimulus
	GO:0040018	0.650	0.863	0.015	0.116	914	Positive regulation of multicellular organism growth	Biological regulation
	GO:0008285	0.650	0.865	0.015	0.209	4972	Negative regulation of cell proliferation	Biological regulation
	GO:0032496	0.648	0.864	0.013	0.144	1579	Response to lipopolysaccharides	Response to stimulus
Fat	GO:0042572	0.648	0.804	0.041	0.257	586	Retinol metabolic process	Metabolic process
	GO:0034605	0.645	0.804	0.038	0.291	1517	Cellular response to heat	Response to stimulus
	GO:0040018	0.644	0.801	0.037	0.200	914	Positive regulation of multicellular organism growth	Biological regulation
	GO:0007283	0.640	0.802	0.033	0.323	4273	Spermatogenesis	Reproduction
	GO:0000724	0.639	0.802	0.032	0.352	1308	Double-strand break repair via homologous recombination	Cellular process
Protein	GO:0042572	0.612	0.782	0.010	0.051	586	Retinol metabolic process	Metabolic process
	GO:0030154	0.610	0.783	0.008	0.016	9840	Cell differentiation	Developmental process
	GO:0090502	0.609	0.782	0.007	0.011	735	RNA phosphodiester bond hydrolysis, endonucleolytic	Cellular process
	GO:0042742	0.608	0.782	0.006	0.010	1231	Defence response to bacteria	Response to stimulus
	GO:0050821	0.607	0.781	0.005	0.021	3162	Protein stabilization	Biological regulation
Mastitis	GO:0042104	0.513	0.873	0.009	0.006	331	Positive regulation of activated T cell proliferation	Immune system process
	GO:0050729	0.513	0.872	0.009	0.007	626	Positive regulation of inflammatory response	Response to stimulus
	GO:0043066	0.512	0.871	0.008	0.047	8158	Negative regulation of apoptotic process	Biological regulation
	GO:0032465	0.511	0.872	0.007	0.014	151	Regulation of cytokinesis	Biological regulation
	GO:0006914	0.510	0.871	0.006	0.018	1753	Autophagy	Cellular process

^aPrediction accuracy with GFBLUP
^bThe regression coefficient of de-regression proofs (DRP) on predicted genomic breeding values (GEBV)
^cThe change of prediction accuracy with GFBLUP relative to GBLUP
^dProportion of the total genomic variance explained by GO terms
^eThe number of SNPs in GO terms

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ISSN: 1471-2164

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