Skip to main content

Table 2 Chromosome-wise significant results (Pc-value <0.01) from the combined linkage disequilibrium and linkage analysis (LDLA)

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

OARa Traitb Pos of max LRTc (cM) Significant LDLA interval (cM)d Pc-value
(Pg-value)e
TGI (Mb)f Positional candidate genes involved in immune responseg
1 LFEC 136.9 136.9–143 <0.05 136.9–143 CXADR, NRIP1
  IgAt 242.4 <0.05 242.1–242.5
2 LFEC 78.3 <0.05 78.17–78.36
  IgAt 188.3 188.01–188.44 <0.05 188.01–188.44
3 IgAt 159.8 <0.05 159.67–160.06
   177.7 <0.05 177.52–177.89
4 LFEC 57.9 54–58 <0.05 54–58 DOCK4, IFRD1, LRRN3
  IgAt 8.9 <0.0019 (<0.05) 8.66–9.49
5 LFEC 5.2 <0.0019 (<0.05) 5.02–5.43 FCHO1, JAK3, MAP1S, UNC13A
   89.9 <0.0019 (<0.05) 89.68–90.14
6 LFEC 36 <0.05 35.84–36.28
   72.5 72.3–77.2 <0.0019 (<0.05) 72.3–77.2
   89.9 85–90.2 <0.05 85–90.2 ALB, AMBN, AMTN, ANKRD17, AREG, BTC, EREG, IGJ, IL8, PF4, PPBP, RASSF6
7 LFEC 22.8 12.65–25.5 <0.0019 (<0.05) 12.65–25.5 ACIN1, AJUBA, BBS4, CCNB1IP1, CD276, CDH24, CEBPE, CHD8, CIDEB, CMTM5, DAD1, EFS, EMC4, FEM1B, IL25, IRF9, ITGA11, LRP10, LTB4R, MAP2K1, NEO1, NFATC4, NOX5, NPTN, PIAS1, PSMB5, PSME1, PSME2, RIPK3, RNASE2, RNF31, SMAD3, SMAD6, TRAV16, TRAV21, TRAV24, TRAV27, TRAV36DV7, TRAV39, TRAV4, TRAV41, TRAV5, TRDC, TRDV2, TRDV3, UACA, ZNF219, ZWILCH
   36.8 36.8–37.3 <0.05 36.8–37.3
   53.3 <0.05 53.08–53.46 UNC13C
8 LFEC 2.3 0.3–12.8 <0.05 0.3–12.8 CD109, COL12A1, IBTK, IRAK1BP1, MYO6, PHIP, SNAP91, TPBG
   38.3 37.7–39.2 <0.05 37.7–39.2
   49.8 49.59–50.04 <0.05 49.59–50.04
   64.1 61.1–64.1 <0.05 61.1–64.1 BCLAF1, CITED2, IFNGR1, IL20RA, IL22RA2, MAP3K5, PERP, TNFAIP3
   71.4 71.2–73.8 <0.0019 (<0.05) 71.2–73.8 PPIL4, STXBP5
9 LFEC 5.8 <0.05 5.64–6.03 PRKAR1A
   16.9 <0.05 16.75–17.16
   24.5 <0.05 24.34–24.78
   41.7 <0.05 41.56–41.96
  IgAt 56.6 55.9–56.6 <0.05 55.9–56.6 TPD52
   67.8 63.4–67.8 <0.05 63.4–67.8 EBAG9
10 LFEC 71.6 <0.05 70.01–71.55
  IgAt 27.2 21.5–27.2 <0.05 21.5–27.2 CKAP2, FOXO1, FREM2, POSTN, SMAD9
   52.9 <0.05 52.68–53.06
   78.6 <0.05 78.39–78.8 SLC10A2
11 LFEC 4.2 4.1–4.27 <0.05 4.1–4.27
  IgAt 51.1 45.4–51.1 <0.05 45.4–51.1 ACE, ARHGDIA, B3GNTL1, CD7, CD79B, DDX42, ERN1, FSCN2, GCGR, ICAM2, ITGB3, MAP3K3, MRC2, MYADML2, PSMC5, PSMD12, SMARCD2, SMURF2
12 LFEC 3.6 <0.05 3.34–3.84 IKBKE, IL10, MAPKAPK2
12 IgAt 1.7 <0.05 1.52–1.98 LRRN2, MDM4, NFASC
   17.7 <0.05 17.56–17.96
   72.3 69.5–75.4 <0.05 69.5–75.4 CAMK1G, CD34, CD46, CFHR5, IRF6, LAMB3, TRAF5
13 IgAt 3.7 3.7–6.3 <0.05 3.7–6.3
15 IgAt 33.6 33.56–33.93 <0.0019 (<0.05) 33.56–33.93
   47 47–53.2 <0.05 47–53.2 ARHGEF17, ARRB1, DNAJB13, FCHSD2, FOLR1, IL18BP, INPPL1, PAAF1, PGAP2, RELT, RPS3, STIM1
   70.2 70.06–70.47 <0.0019 (<0.05) 70.06–70.47
16 IgAt 10.5 <0.05 10.29–10.74
   64.8 63.8–64.8 <0.0019 (<0.05) 63.8–64.8 SEMA5A
17 IgAt 18.4 14.6–30.1 <0.0019 (<0.05) 14.6–30.1 ELMOD2, IL15, PCDH10, PCDH18, PLK4, UCP1
   36 <0.05 35.8–36.22
   46 <0.05 45.85–46.27 STX2
   62.3 62–66.8 <0.0019 (<0.05) 62–66.8 CMKLR1, CORO1C, HPS4, PIWIL3, PLA2G1B, PXN, RAB35, SART3, SPPL3, TRIAP1, UNG, WSCD2
20 LFEC 4.8 <0.05 4.58–5.04 BMP5
21 LFEC 8.1 8.07–8.35 <0.05 8.07–8.35
   31.8 31.7–32.24 <0.05 31.7–32.24
   43.9 43.7–44.03 <0.05 43.7–44.03 ACTN3, CTSF, SPTBN2
21 IgAt 17.5 16.5–17.5 <0.0019 (<0.05) 16.5–17.5 GAB2
   46 45.97–46.25 <0.05 45.97–46.25 FGF19
22 IgAt 6.7 5.3–7.3 <0.05 5.3–7.3 MBL2, PCDH15
   19.5 <0.05 19.26–19.85 NKX2-3
23 IgAt 8.3 <0.05 8.15–8.47
   23.3 23.3–28.5 <0.05 23.3–28.5 DSC1, DSC2, DSC3, DSG1, DSG2, DSG3, DSG4,
   33.9 32.8–38 <0.05 32.8–38 ADCYAP1, COLEC12, EMILIN2, GATA6, LAMA3, MIB1, NPC1, ROCK1, THOC1, USP14
   45.8 41.7–48.5 <0.05 41.7–48.5 ATP5A1, CIDEA, PIAS2, PSMG2, RALBP1,SIGLEC15, SKOR2, SLC14A1, SMAD2
   54.9 54.56–55.06 <0.05 54.56–55.06 TCF4
24 LFEC 2.2 1.91–2.65 <0.05 1.91–2.65 CLDN6, CLDN9, HCFC1R1, TNFRSF12A
   17.9 <0.05 17.68–18.12 UMOD
25 LFEC 37 36.89–37.21 <0.0019 (<0.05) 36.89–37.21
  1. a OAR ovine chromosome
  2. bAnalyzed traits: LFEC log-transformed faecal egg count, IgA t Box-Cox-transformed optical density ratio (ODR) values of immunoglobulin A activity
  3. cPosition of the chromosome (in centiMorgans) at which the maximum likelihood ratio test (LRT) is reached in the LDLA
  4. dA significant LDLA interval (in centiMorgans) was defined by clustering consecutive significant 5 % chromosome-wise LDLA associations on a chromosome (allowing gaps no greater than 5 Mb)
  5. ePc-value: chromosome-wise P-value established through 1000 simulations. Pg-value: genome-wise P-value obtained from the Pc-values corrected for the total number of chromosomes analyzed
  6. f TGI (Mb) Target genomic interval. For each significant LDLA association, target genomic intervals were defined as the genomic region based on the sheep reference genome assembly Oar_v3.1 that corresponded to the defined significant LDLA intervals (for those regions with consecutive significant positions) and a 250-kb long interval centered on each of the significant isolated haplotypes detected by LDLA
  7. gPositional candidate genes extracted from the LDLA significant associations (within the significant LDLA interval if identified, or within a ±125 kb interval from the position of maximum LRT-value for the significant QTL based on isolated significant haplotypes) that were identified as potential functional candidate genes in the search for immune-related genes
\