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Table 1 Significant chromosome-wise QTL detected by linkage analysis (LA)

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

Traita OARb Across-family analysis Within-family analysis
Pos of max LRT (cM)c Pc-valued CI (cM)e
TGI (Mb)f
Positional candidate genes involved in immune responseg Segregating family identifier (Pos of max LRT)h CI (cM)i Size effect trait units (SD units)j
LFEC 6 88.1 <0.05 80.8–91.4 AFP, ALB, AMBN, AMTN, AREG, BTC, CXCL1, CXCL10, CXCL11, CXCL9, EREG, GC, IGJ, IL8, MUC7, PF4, PPBP, RASSF6, SCARB2, TMPRSS11D Fam. 1 (94.9) 70.0–96.8 0.468 ± 0.015 (0.30)
      Fam. 7 (90.6) 80.4–94.8 −0.499 ± 0.012 (0.32)
      Fam. 11 (86.7) 76.4–96.4 −0.777 ± 0.029 (0.50)
  8 2 <0.05 1–3.4 CD109, COL12A1, MYO6 Fam. 4 (31.2) 25.4–35.8 1.218 ± 0.024 (0.78)
       Fam. 11 (1.8) 0–2.9 0.738 ± 0.024 (0.47)
IgAt 22 3.4 <0.05 0.3–5.8 PCDH15 Fam. 8 (6.4) 0.3–9.9 0.527 ± 0.046 (0.68)
  1. aAnalyzed traits: LFEC log-transformed faecal egg count, IgA t Box-Cox-transformed optical density ratio (ODR) values of immunoglobulin A activity
  2. b OAR ovine chromosome
  3. c, hPosition of the chromosome (in centiMorgans) at which the maximum likelihood ratio test of the LA is reached in the analysis involving the 14 half-sib families included in this work (across-family analysis) or the individual analysis of the segregating families (those showing a Pc-value <0.05 in the within-family analysis), respectively
  4. d P c -value Chromosome-wise significance P-value established through 1000 permutation analysis
  5. e,i CI Confidence interval (in cM) estimated from the position of the max LRT for the across-family analysis and the within-family analyses, respectively, following the 1-LOD-drop-off method [38]
  6. f TGI Target genomic interval (Mb) defined as the corresponding genomic region, according to the sheep reference genome assembly Oar_v3.1, to the CI estimated for the LA significant QTL
  7. gPositional candidate genes included in the CI of the corresponding QTL that were highlighted by the immune response candidate gene survey performed in the present work as potential functional candidates
  8. jEstimated size effect of the QTL identified in the within-family analysis expressed in trait units (Yield Deviations of IgAt) and in phenotypic SD of the trait (in brackets)
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