Table 1.

Summary data for 11 bovine innate immune genes investigated in 37 cattle breeds

Bovine gene	BTA assigna	Total hapsb	Sires phased (%)c	MAFs ≤ 0.10d	Avg r2 alle	Avg r2B.t.t.e	Valid. SNPsf	Hap SNPsg	Valid. indelsh	Valid. nsSNPsi	Region sizej (kb)	QTL or assoc.k
PGLYRP1	BTA18	8	95	2	0.08	0.14	7	7	NA	1	1.6	Q
TLR1	BTA6	7	97	2	0.23	0.47	4	4	NA	1	1.5	Q, A
TLR2	BTA17	17	93	11	0.35	0.60	31	30	1	13	3.0	A
TLR3	BTA27	33	85	15	0.45	0.72	50	50	ND	3	10.6	Q
TLR4	BTA8	13	91	19	0.14	0.37	22	21	NA	6	9.8	Q, A
TLR5	BTA16	13	100	13	0.40	0.59	29	29	3	3	5.1	No
TLR6	BTA6	15	94	4	0.27	0.29	15	15	NA	7	1.9	Q
TLR7	BTAX	7	100	8	0.27	0.23	10	10	NA	1	3.9	Q
TLR8	BTAX	3	100	0	0.93	0.92	9	9	NA	6	2.3	Q
TLR9	BTA22	9	98	2	0.35	0.40	11	11	NA	1	4.3	Q
TLR10	BTA6	19	91	22	0.31	0.45	28	28	NA	12	3.8	Q
Total/Avgl		144	95l	98	0.34l	0.47l	216	214	4	54	4.3l

^aBTA assignments based on National Center for Biotechnology Information Refseq (Btau4.0) and radiation hybrid mapping (12).

^bTotal haplotypes predicted from all validated markers and best-pair reconstructions (35) with probabilities ≥0.90.

^cPercent of sires (n = 101) exhibiting best pair phase probabilities ≥0.90. BTAX haplotypes were direct observations.

^dTotal polymorphisms with minor allele frequencies ≤0.10.

^eAverage intragenic r² values estimated for adjacent SNP and indel sites for all cattle or for B. t. taurus (B.t.t.).

^fNumbers of putative SNPs validated as polymorphic.

^gNumbers of validated SNPs placed on discrete haplotypes.

^hNumbers of putative indels validated as polymorphic. NA = not applicable; ND = not determined.

ⁱNumbers of putative nonsynonymous SNPs validated as polymorphic.

^jSize of the genic region rounded to the nearest 100 bp. Kb = kilobase.

^kBovine health-related QTL overlapping or proximal to investigated gene (Q), or intragenic variation associated (A) with disease susceptibility in case-control studies (25–31).

^lAverage across all investigated genes.