Signatures of selection in sheep bred for resistance or susceptibility to gastrointestinal nematodes

BMC Genomics

Table 1 Genomic regions containing the top 0.1% of SNP, ranked using a moving (5 SNP) average (WIN5) of –log ₁₀ (combined Peddrift P-values)

Region	Chr	Position (Mb)	SNP50 BeadChip SNP	Top SNP	Peak SNP	Peak SNP rank	F_STPeak		PEDDRIFT WIN5 -log₁₀(p-value)			Genes	Candidate gene(s) in region (OARv3.1)
Region	Chr	Position (Mb)	SNP50 BeadChip SNP	Top SNP	Peak SNP	Peak SNP rank	Romney	Perendale	Romney	Perendale	Combined	Genes	Candidate gene(s) in region (OARv3.1)
1	1	66.74-67.43	14	4	s43910	5	0.1632	0.3901	0.6799	3.0134	2.5988	1
2	1	87.38-88.13	10	3	OAR1_93166689	7	0.3475	0.1424	2.1441	1.3027	2.5124	18	CD53, CHI3L2, CHIA, DENND2D
3	3	78.72-79.32	12	3	s08153	11	0.4868	0.2270	1.7146	1.6205	2.4161	3
4	3	98.12-98.51	9	4	OAR3_104545117_X	2	0.6897	0.1148	3.1276	0.7050	2.8569	0
5	4	44.99-45.39	10	4	OAR4_47833230	10	0.2439	0.3645	0.6647	3.0036	2.4283	2	RELN
6	4	83.23-83.69	12	4	OAR4_88693058_X	20	0.4264	0.0256	2.9894	0.3238	2.2755	0
7	5	95.21-95.69	11	3	OAR5_103935962	14	0.4816	0.0927	2.7849	0.6253	2.3464	2
8	7	81.54-82.04	9	2	OAR7_89131104	15	0.3167	0.1509	1.8827	1.6553	2.3387	10
9	8	41.02-41.48	11	1	OAR8_44326031_X	39	0.2327	0.4345	0.9548	2.1834	2.0028	1
10	9	11.31-11.69	8	3	OAR9_11436829	26	0.3990	0.1750	1.8185	1.2966	2.1687	0
11	9	66.27-67.09	13	2	OAR9_70612779	4	0.4586	0.1935	1.9607	1.6057	2.6214	0
12	16	16.67-16.88	7	2	s59518	23	0.6775	0.1604	2.1737	0.9608	2.2246	2
13	16	17.33-17.7	11	5	s61002	1	0.5391	0.0953	3.2562	0.7822	3.0273	0
14	16	66.35-66.7	9	1	s54054	35	0.6238	0.0791	2.4545	0.4334	2.0232	4	NSUN2
15	19	54.68-55.19	9	1	OAR19_58095077	44	0.2582	0.2780	0.9065	2.1367	1.9812	3	HRH1
16	25	39.57-40.32	19	2	OAR25_41988307	31	0.5301	0.1371	2.5086	0.9984	2.0855	1

The top 5% of SNP were used to define the boundaries of each region (see Materials & Methods). Position is taken from build 3.1 of the sheep genome. The number of SNP50 BeadChip SNP and the number of top SNP (0.1%) are given in each region. Peak SNP is defined as the SNP with the lowest WIN5 –log₁₀(combined Peddrift P-value) in the region, and the rank of that SNP is also shown. Maximum F_ST and –log₁₀ (Peddrift P-value) are shown for each breed. The number of genes in each region, along with candidates (defined as those with a previously reported role in immunity) was taken from Ensembl release 74.

ISSN: 1471-2164