TABLE 1.
Results from the full linear model of the epistatic network underlying murine reproductive fatpad weight in the LG,SM AI line
| Chr 1 | C.I. 1 begin (Mb) | C.I. 1 end (Mb) | Peak 1 (Mb) | Chr 2 | C.I. 2 begin (Mb) | C.I. 2 end (Mb) | Peak 2 (Mb) | slQTL LPR | Peak SNP 1 | Peak SNP 2 | Epistatic LPR | Effect(s) | Threshold type | Threshold | Reported Adipose QTL in CI(s) | QTL reference(s) | Candidates (C.I. 1) | Candidates (C.I. 2) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 16.40 | 21.28 | 20.15 | NA | NA | NA | NA | 4.26 | rs6334092 | NA | NA | A,D | Pointwise | 3.32 | Adip1; Obq2 | Cheverud et al. 2001; Fawcett et al. 2008; Taylor and Phillips 1996 | Pkhd1 | NA |
| 1 | 65.79 | 74.08 | 70.77 | NA | NA | NA | NA | 4.76 | rs6323094 | NA | NA | A | Pointwise | 6.60 | Obq7 | Taylor et al. 2001 | Vwc2l; Fn1 | NA |
| 1 | 118.37 | 138.01 | 134.82 | NA | NA | NA | NA | 9.17 | gnf01.132.831 | NA | NA | A | Pointwise | 3.32 | Obsty1; Gwth1; Obq17 | Cheverudet al. 2004; Yi et al. 2006; Ishimori et al. 2004 | Pik3c2b | NA |
| 3 | 20.54 | 27.82 | 22.51 | NA | NA | NA | NA | 5.56 | rs13477017 | NA | NA | A | Pointwise | 3.32 | None | None | Nlgn1; Ghsr | NA |
| 4 | 9.71 | 11.92 | 10.83 | NA | NA | NA | NA | 4.78 | rs13477558 | NA | NA | D | Pointwise | 3.32 | Unnamed RI QTL | Cheverudet al. 2004 | Plekhf2 | NA |
| 4 | 78.28 | 90.30 | 79.46 | NA | NA | NA | NA | 11.87 | CEL-4-78089985 | NA | NA | A | Pointwise | 3.32 | Adip11; Adip24; Adip11a | Fawcett et al. 2008; Fawcett et al. 2010; Stylianou et al. 2006 | Tyrp1 | NA |
| 6 | 114.73 | 121.97 | 117.73 | NA | NA | NA | NA | 5.01 | mCV23042866 | NA | NA | D | Pointwise | 3.32 | Adip2; Igf1sl1 | Cheverud et al. 2001; Rosen et al. 2005 | Adipor2; Ankrd26; Pparg | NA |
| 6 | 133.92 | 142.67 | 134.20 | NA | NA | NA | NA | 8.89 | rs13479053 | NA | NA | A | Pointwise | 3.32 | Adip2 | Cheverud et al. 2001 | Lrp6; Grin2b; Cdkn1b | NA |
| 7 | 30.18 | 44.44 | 37.21 | NA | NA | NA | NA | 4.08 | rs6217275 | NA | NA | D | Pointwise | 3.32 | Adip3; Adip3A; Adip3Ab | Cheverud et al. 2001; Fawcett et al. 2008; Fawcett et al. 2010 | Tshz3; Plekhf1 | NA |
| 7 | 59.83 | 77.73 | 63.51 | NA | NA | NA | NA | 6.85 | rs3717293 | NA | NA | A,D | Pointwise | 3.32 | Tabw; Adip3Ad; Adip25; Obq1 | Kim et al. 2001; Fawcett et al. 2010; Taylor and Phillips 1996 | Nipa1; Nipa2; Gabrg3; Gabra5; Gabrb3 | NA |
| 7 | 132.03 | 143.20 | 135.24 | NA | NA | NA | NA | 6.38 | CEL-7-116160192 | NA | NA | A | New slQTL chr7 | 6.36 | Bsbob2 | Yi et al. 2004 | Trim72 | NA |
| 8 | 64.98 | 90.95 | 84.79 | NA | NA | NA | NA | 4.76 | rs13479860 | NA | NA | A | Pointwise | 3.32 | Adip4 | Cheverud et al. 2001; Fawcett et al. 2008 | Il15 | NA |
| 9 | 61.70 | 67.72 | 65.39 | NA | NA | NA | NA | 6.98 | rs13480247 | NA | NA | A | New slQTL chr9 | 6.38 | None | None | Mtfmt | NA |
| 9 | 118.30 | 125.00 | 118.88 | NA | NA | NA | NA | 9.64 | rs6316481 | NA | NA | A | Pointwise | 3.32 | Adip5; Adip5a; Adip5b; Adip5c; Obq18 | Cheverud et al. 2001; Fawcett et al. 2008; Fawcett et al. 2010; Ishimori et al. 2004 | Acvr2b | NA |
| 12 | 60.62 | 67.43 | 64.06 | NA | NA | NA | NA | 5.24 | mCV24690992 | NA | NA | A | Pointwise | 3.32 | Adip6; Adip16; Fob2 | Fawcett et al. 2008; Stylianou et al. 2006; Horvat et al. 2000 | Lrfn5 | NA |
| 13 | 40.74 | 55.35 | 53.54 | NA | NA | NA | NA | 4.90 | rs3699522 | NA | NA | A | Pointwise | 3.32 | Adip7; Adip18; Adip18a; Pfat3 | Cheverud et al. 2001; Fawcett et al. 2008; Fawcett et al. 2010; Keightley et al. 1998 | Cplx2; Drd1a | NA |
| 18 | 24.19 | 56.21 | 48.82 | NA | NA | NA | NA | 4.83 | rs3684561 | NA | NA | A | Pointwise | 3.32 | Adip8; Adip8a; Adip8b; Kcal1; Mnif2 | Cheverud et al. 2001; Fawcett et al. 2010; Smith Richards et al. 2002 | Sema6a; Hsd17b4 | NA |
| 18 | 58.77 | 80.76 | 63.84 | NA | NA | NA | NA | 12.31 | rs13483398 | NA | NA | A | Pointwise | 3.32 | Adip8; Adip8c; Adip8d; Obsty4 | Cheverud et al. 2001; Fawcett et al. 2008; Fawcett et al. 2010; Cheverudet al. 2004 | Adrb2; Htr4 | NA |
| 1 | 42.41 | 52.71 | 51.38 | 9 | 68.10 | 95.10 | 77.25 | NA | rs13475863 | rs13480288 | 5.52 | DD | QTL × QTL epi | 3.44 | Adip1; Obq7; Adip5; Mob8 | Cheverud et al. 2001; Taylor et al. 2001; Mehrabian et al. 1998 | Gls | Gclc |
| 1 | 118.37 | 138.01 | 128.52 | 6 | 133.92 | 142.67 | 141.48 | NA | rs6228473 | rs8268650 | 4.95 | AD | QTL × QTL epi | 3.44 | Obsty1; Gwth1; Obq17; Adip2 | Cheverud et al. 2001; Cheverudet al. 2004; Yi et al. 2006; Ishimori et al. 2004 | Gpr39 | Pde3a |
| 1 | 118.37 | 138.01 | 128.84 | 12 | 73.42 | 89.12 | 75.11 | NA | rs13476100 | rs3687032 | 4.64 | DD | QTL × QTL epi | 3.44 | Obsty1; Gwth1; Obq17; Adip6 | Cheverud et al. 2001; Cheverudet al. 2004; Yi et al. 2006; Ishimori et al. 2004 | Gpr39 | Hif1a |
| 1 | 174.21 | 189.05 | 186.63 | 13 | 0.00 | 24.24 | 23.48 | NA | mCV24555989 | gnf13.020.621 | 10.27 | AA | QTL × chr1 epi | 5.25 | Obq9 | Taylor et al. 2001 | Hlx | Abt1 |
| 4 | 30.53 | 39.16 | 36.58 | 9 | 118.30 | 125.00 | 123.70 | NA | rs13477649 | rs8241505 | 6.03 | DD | QTL × QTL epi | 3.44 | Unnamed RI QTL; Dob2; Obq18 | Cheverudet al. 2004; Ishimori et al. 2004; West et al. 1994 | Cga | Slc6a20a; Slc6a20b |
| 4 | 125.68 | 139.92 | 130.91 | 7 | 132.03 | 143.20 | 139.70 | NA | rs3673061 | rs8236684 | 4.93 | AD | QTL × QTL epi | 3.44 | Adip12; Qbis1; Afpq2; Adip3 | Cheverud et al. 2001; Stylianou et al. 2006; Togawa et al. 2006; Brockmann et al. 2000 | Ptpru | Oat |
| 4 | 143.52 | 154.77 | 152.94 | 7 | 132.03 | 143.20 | 141.88 | NA | rs6378384 | rs3719258 | 4.69 | AD | QTL × QTL epi | 3.44 | Adip12; Adip3 | Cheverud et al. 2001; Stylianou et al. 2006 | Ajap1 | Adam12 |
| 6 | 33.46 | 46.84 | 37.64 | 9 | 118.30 | 125.00 | 123.70 | NA | rs13478717 | rs8241505 | 5.11 | DA | QTL × chr6 epi | 5.09 | Dob2; Obq18 | Ishimori et al. 2004;West et al. 1994 | Trim24 | Ccr9 |
| 6 | 53.92 | 71.82 | 54.18 | 7 | 102.32 | 108.47 | 105.10 | NA | rs13478762 | UT-7-90.803899 | 5.13 | AA | QTL × chr7 epi | 4.96 | Adip2; Obq13 | Cheverud et al. 2001; Taylor et al. 2001 | Crhr2; Ghrhr | Capn5 |
| 7 | 132.03 | 143.20 | 137.17 | 8 | 42.26 | 57.10 | 50.65 | NA | rs8236684 | rs13479769 | 5.08 | AA | QTL × chr8 epi | 4.73 | Bsbob2 | Yi et al. 2004 | Fgfr2 | Ing2 |
| 8 | 124.83 | 129.12 | 127.97 | 9 | 20.24 | 39.76 | 23.57 | NA | rs6300613 | rs13480112 | 5.57 | AD | QTL × chr9 epi | 4.99 | Obsty2 | Cheverudet al. 2004 | Disc1 | Npsr1 |
| 9 | 20.24 | 39.76 | 31.31 | 12 | 108.99 | 120.28 | 111.04 | NA | CEL-9-29909656 | CEL-12-104545022 | 5.36 | AA,DD | QTL × chr9 epi | 4.99 | Carfhg2 | Corva et al. 2001 | Kcnj5 | Dlk1; Meg3; Rtl1 |
| 9 | 104.05 | 118.18 | 109.62 | 1 | 191.98 | NA | 193.61 | NA | rs3723953 | rs13476308 | 7.78 | AA | QTL × chr1 epi | 5.99 | Adip5;Dob2 | Cheverud et al. 2001; West et al. 1994 | Fbxw cluster | Nek2 |
| 12 | 108.99 | 120.28 | 113.11 | 1 | 191.98 | NA | 195.79 | NA | rs13481651 | rs13476312 | 6.06 | DA | QTL × chr1 epi | 5.25 | Adip6; Bsbob4; Mob3 | Cheverud et al. 2001; Fawcett et al. 2008; Yi et al. 2004; Warden et al. 1995 | Traf3 | Hsd11b1 |
| 13 | 0.00 | 24.24 | 14.85 | 1 | 118.37 | 138.01 | 119.02 | NA | rs13481702 | rs3694226 | 5.96 | AA | QTL × chr1 epi | 5.25 | Adip7 | Cheverud et al. 2001 | Inhba | Inhbb |
| 13 | 0.00 | 24.24 | 17.38 | 9 | 68.10 | 95.10 | 82.84 | NA | rs3678616 | rs13480312 | 4.54 | AA | QTL × QTL epi | 3.44 | Adip7; Adip5 | Cheverud et al. 2001 | Inhba | Htr1b |
| 13 | 0.00 | 24.24 | 20.21 | 12 | 73.42 | 89.12 | 82.08 | NA | rs6314295 | rs3654718 | 4.78 | AA | QTL × QTL epi | 3.44 | Adip7; Adip6 | Cheverud et al. 2001 | Olfactory receptor cluster | Slc8a3 |
| 13 | 40.74 | 55.35 | 43.69 | 6 | 80.99 | 92.88 | 89.62 | NA | rs13481789 | rs13479099 | 4.90 | AA | QTL × QTL epi | 3.44 | Adip7; Adip18; Adip18a; Pfat3; Adip2 | Cheverud et al. 2001; Fawcett et al. 2008; Fawcett et al. 2010; Keightley et al. 1998 | Ranbp9 | Alms1 |
| 13 | 40.74 | 55.35 | 45.45 | 4 | 143.52 | 154.77 | 152.94 | NA | rs3688207 | rs6378384 | 4.48 | AD | QTL × QTL epi | 3.44 | Adip7; Adip18; Adip18a; Pfat3; Adip12 | Cheverud et al. 2001; Fawcett et al. 2008; Fawcett et al. 2010; Stylianou et al. 2006; Keightley et al. 1998 | Atxn1 | Kcnab2 |
| 18 | 24.19 | 56.21 | 37.51 | 12 | 60.62 | 67.43 | 64.06 | NA | gnf18.033.953 | mCV24690992 | 5.88 | AD | QTL × QTL epi | 3.44 | Adip8; Adip8a; Adip8b; Kcal1; Mnif2; Adip6 | Cheverud et al. 2001; Fawcett et al. 2010; Smith Richards et al. 2002 | Pcdhb cluster | Lrfn5 |
| 18 | 24.19 | 56.21 | 37.93 | 13 | 0.00 | 24.24 | 15.11 | NA | gnf18.033.953 | rs13481702 | 5.87 | DA | QTL × QTL epi | 3.44 | Adip8; Adip8a; Adip8b; Kcal1; Mnif2; Adip7 | Cheverud et al. 2001;Fawcett et al. 2010; Smith Richards et al. 2002 | Pcdhb cluster | Gli3 |
| 18 | 24.19 | 56.21 | 50.47 | 7 | 30.18 | 44.44 | 30.56 | NA | rs13483356 | rs13479174 | 5.76 | AD | QTL × QTL epi | 3.44 | Adip8; Adip8a; Adip8b; Kcal1; Mnif2; Adip3 | Cheverud et al. 2001; Fawcett et al. 2010; Smith Richards et al. 2002 | Hsd17b4 | Lrfn3 |
Chromosome, confidence intervals (Mb), peak locations (Mb), peak LPR scores, nearest SNP to the peak, effect-type threshold, and threshold value are all given for each term. The appropriate references for any a priori hypotheses are listed along with positional candidate loci for both slQTL and epiQTL. Terms in boldface type are nominally significant (P > 0.05) when additive and dominance effects for all interactions are included in the model.