Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle

BMC Genomics

Table 3 Traits that are enriched or depleted for TAVs in both dairy and beef cattle for annotation classes

Trait	Cattle breed	Intergenic	Upstream	Downstream	Intragenic	Intron	CDS	Synonymous	Missense	UTR (5’ & 3’)	Non-coding conserved	TFBS	micro RNA target
Fat	Dairy	ns	+	+	+	-	+	+	+	ns	ns	ns	ns
Fat Percent	Dairy	-	+	+	+	ns	+	+	+	ns	ns	ns	+
Milk	Dairy	-	+	+	+	+	+	+	+	ns	ns	ns	+
Protein	Dairy	-	+	+	+	+	+	ns	+	ns	-	ns	ns
Protein Percent	Dairy	-	+	+	+	+	+	+	+	+	ns	ns	ns
Angularity	Dairy	-	+	+	+	+	ns	ns	+	ns	ns	ns	ns
BCS	Dairy	ns	+	+	ns	ns	+	ns	+	ns	ns	ns	ns
Mammary System	Dairy	ns	+	+	-	-	+	ns	ns	ns	ns	ns	+
Fertility	Dairy	+	+	ns	-	-	ns	ns	ns	ns	ns	ns	ns
Survival Direct	Dairy	ns	+	+	-	-	ns	ns	ns	+	ns	ns	ns
SCC	Dairy	ns	ns	ns	ns	ns	ns	ns	ns	ns	ns	ns	ns
LLPF	Beef	-	+	+	+	+	+	+	ns	+	ns	ns	+
CIMF	Beef	-	+	ns	+	+	ns	ns	ns	ns	ns	ns	ns
CRIB	Beef	ns	+	ns	ns	ns	ns	ns	ns	ns	ns	ns	ns
SEMA	Beef	ns	ns	ns	-	-	ns	ns	ns	ns	ns	ns	ns
SC12	Beef	+	+	+	-	-	ns	ns	ns	ns	+	ns	ns
PNS24	Beef	+	+	+	-	-	ns	ns	ns	ns	ns	ns	-
AGECL_BB	Beef	ns	ns	-	ns	ns	ns	ns	ns	ns	ns	ns	ns
AGECL_TC	Beef	ns	ns	-	ns	ns	ns	ns	ns	ns	ns	ns	ns
PPAI_BB	Beef	ns	-	ns	ns	ns	ns	ns	ns	ns	ns	ns	ns
PPAI_TC	Beef	-	ns	ns	+	+	ns	ns	ns	ns	ns	ns	ns

Traits were deemed to be significant by permutation testing. The null distribution for the permutation testing was constructed by testing the same number of SNP in each class, but randomly chosen, for the number of significant SNP at P<0.0001, and random selection of SNP was performed 1000 times for each class. A class was enriched if the actual number of SNP significant in that class was greater than the number significant in the 950^th highest random set, and depleted if the number of significant SNP was less than the number significant than the 50^th lowest random set. Traits that are enriched for TAVs in a functional class are indicated with +, those that were depleted are marked with -, and traits where no significance occurred is indicated with ns.

ISSN: 1471-2164