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. 2014 Feb 25;55(2):267–271. doi: 10.1007/s13353-014-0199-8

Table 1.

Identified SNPs and position in the TLR4 gene of Salmonella low and persistent shedder pigs

Single marker association (P-value) GenBank accession number for the SNP Location in Sus Scrofa genome (bp) Amino acid
N Location Primers SNP designation Qualitative Quantitative Site Amino acid
1 5′Upstream

5′gaaccatgcagtagaacagg

3′ctggaagtctgtagtcaagg

 15′U:A-1082G# 0.033 0.064 No SSC1:289,774,983 – –
2 15′U:T-1019C# 0.033 0.064 No SSC1:289,775,046 – –
3 15′U:C-984T# 0.033 0.064 No SSC1:289,775,081 – –
4

5′cacaagaaggaagagatagc

3′ caccaagggaagctctagg

 15′U:C-522T# 0.133 0.244 No SSC1:289,775,543
5 15′U:G-400A 0.363 0.550 rs80830544 SSC1:289,775,665
6 15′U:G-75C# 0.025 0.056 No SSC1:289,775,979 – –
7 Intron 2

5′acagaagattggatggaagga

3′ gagataagaaagctgagacc

 22I:A232C 0.004 0.029 rs80881287 SSC1:289,780,226 – –
8 22I:C298T** 0.002 0.013 rs80787918 SSC1:289,780,292 – –
9 Intron 2

5′cctcacttgatatgtttgcc

3′gttcctccaggacagatttg

 22I:C2567T# 0.001 0.025 No SSC1:289,782,761 – –
10 Exon 3 3C318A 0.003 0.037 rs80923358 SSC1:289,782,834 – –
11 3G417A 0.003 0.037 rs80951861 SSC1:289,782,933 – –
12 3T611A* 0.007 0.054 rs80811682 SSC1:289,783,127 204 L/H
13 Exon 3

5′attcaaggtctggctggttc

3′ tgaagacatcaggaagcaag

 3G826A* 0.285 0.514 Shinkai et al. (2006) SSC1:289,783,342 276 V/I
14 3G960A 0.064 0.105 rs80981701 SSC1:289,783,476 – –
15 3G962A* 0.034 0.046 rs80955017 SSC1:289,783,478 321 R/H
16 3C1027A* 0.176 0.231 rs80894552 SSC1:289,783,543 343 Q/K
Exon 3

5′acatccacgttgtcttccg

3′cagttcattcctcacccag

 – – –
17 Exon 3

5′cttcctcctggtatctgtgg

3′ggcagtcctgtgtatctcg

 3G2397A 0.025 0.056 rs80834103 SSC1:289,784,913 – –
18 3′Downstream

5′actcccaacgtgtcccttg

3′ccaagaagtgccactttcaac

 43′D:C208T** 0.002 0.011 rs80907449 SSC1:289,785,250 – –

1to first codon of exon 1; 2position in intron 2; 3position in coding region; 4position in 3′UTR downstream of last codon; *non-synonymous SNPs; **haplotype components; # novel SNPs