Table 2.
Chromosome-wise significant results (Pc-value <0.01) from the combined linkage disequilibrium and linkage analysis (LDLA)
| 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 | – |
a OAR ovine chromosome
bAnalyzed traits: LFEC log-transformed faecal egg count, IgA t Box-Cox-transformed optical density ratio (ODR) values of immunoglobulin A activity
cPosition of the chromosome (in centiMorgans) at which the maximum likelihood ratio test (LRT) is reached in the LDLA
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)
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
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
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