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 2 Top five Gene Ontology (GO) terms with GFBLUP between breeds 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:0040018	0.360	0.826	0.200	0.103	962	Positive regulation of multicellular organism growth	Biological regulation
	GO:0042572	0.342	0.808	0.182	0.171	678	Retinol metabolic process	Metabolic process
	GO:0034605	0.336	0.805	0.176	0.178	1621	Cellular response to heat	Response to stimulus
	GO:0045944	0.331	0.805	0.171	0.190	11,185	Positive regulation of transcription from RNA polymerase II promoter	Cellular process
	GO:0032496	0.325	0.798	0.165	0.129	1702	Response to lipopolysaccharides	Response to stimulus
Fat	GO:0042572	0.246	0.680	0.176	0.262	678	Retinol metabolic process	Metabolic process
	GO:0000122	0.238	0.642	0.168	0.348	8755	Negative regulation of transcription from RNA polymerase II promoter	Cellular process
	GO:0032496	0.200	0.577	0.130	0.219	1702	Response to lipopolysaccharides	Response to stimulus
	GO:0007283	0.176	0.538	0.106	0.313	4950	Spermatogenesis	Reproduction
	GO:0034605	0.171	0.558	0.101	0.271	1621	Cellular response to heat	Response to stimulus
Protein	GO:0042742	0.232	0.767	0.134	0.010	1333	Defence response to bacteria	Response to stimulus
	GO:0042475	0.224	0.732	0.126	0.011	3244	Odontogenesis of dentin-containing teeth	Developmental process
	GO:0006665	0.197	0.721	0.099	0.011	805	Sphingolipid metabolic process	Metabolic process
	GO:0042572	0.178	0.699	0.080	0.010	678	Retinol metabolic process	Metabolic process
	GO:0006810	0.168	0.693	0.070	0.040	6999	Transport	Localization
Mastitis	GO:0043066	0.077	0.277	0.135	0.064	8831	Negative regulation of apoptotic process	Biological regulation
	GO:0032496	0.067	0.176	0.125	0.020	1702	Response to lipopolysaccharides	Response to stimulus
	GO:0032091	0.045	0.171	0.103	0.032	702	Negative regulation of protein binding	Biological regulation
	GO:0043280	0.018	0.178	0.076	0.003	583	Positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	Metabolic process
	GO:0071346	0.014	0.115	0.072	0.020	3494	Cellular response to interferon-gamma	Response to stimulus

^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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