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Table 3 Chromosome-wise SNPs significantly associated with the IgAt trait as identified by the GWAS

From: Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array

OARa SNP name SNP position (Mb)b Allele substitution effect trait units (SD units)c, d Nominal P-value Corrected Pc-value (Pg-value)e TGI (Mb)f
8 OAR8_53084022.1 49,525,147 0.325 ± 0.075 (0.417) 2.04E−05 0.02 49.40–49.65
8 s42819.1 72,402,305 0.190 ± 0.045 (0.243) 3.77E−05 0.037 72.27–72.52
10 s56461.1 17,012,728 0.221 ± 0.050 (0.283) 1.51E−05 0.013 16.88–17.13
10 OAR10_23921485.1 24,187,107 0.203 ± 0.048 (0.260) 2.63E−05 0.022 24.06–24.31
10 s61799.1 30,924,195 0.210 ± 0.051 (0.269) 5.41E−05 0.045 30.79–31.04
11 DU232778_232.1 32,492,623 0.203 ± 0.048 (0.26) 3.74E−05 0.036 32.36–32.61
12 s68938.1 61,866,746 0.233 ± 0.047 (0.299) 1.28E−06 0.001 (0.033) 61.74–61.99
14 OAR14_21336208.1 20,773,096 0.284 ± 0.070 (0.364) 6.75E−05 0.041 20.64–20.89
15 s75729.1 24,870,677 0.266 ± 0.059 (0.341) 8.33E−06 0.007 24.74–24.99
25 s21640.1 13,152,201 0.224 ± 0.056 (0.287) 9.09E−05 0.048 13.02–13.27
  1. a OAR ovine chromosome
  2. bPosition of the significant SNP identified by the GWAS analysis based on the Oar_v3.1 version of the Ovine Genome Assembly (http://www.ensembl.org/Ovis_aries/Info/Index)
  3. c, dMagnitude of the allele substitution effect, and standard error, in trait units (Yield Deviations of IgAt) and in phenotypic standard deviations (SD) units (in brackets)
  4. eCorrected P-values at the 5 % chromosome-wise level (and 5 % genome-wise level) obtained after applying a Bonferroni correction considering the number of independent markers analyzed for each chromosome and for the whole genome, respectively
  5. f TGI Target genomic interval defined for the GWAS significant associations as 250 Kb long intervals centered on the significant SNP. The genes within that interval were extracted as positional candidate genes. In this case, none of these genes was identified as functional candidate by the candidate gene survey performed
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