Table 1.
True and estimated QTL effects for the simulated data with main and epistatic effects.
| Markersa | Position | Trueb | EBLASSOc | EBc |
|---|---|---|---|---|
| (i, j) | (cM, cM) | β(h2) |  |
|
| (11,11) | (50,50) | 4.47(0.0975) | 4.5801(0.1612) | 4.8593(0.2075) |
| (26,26) | (125,125) | 3.16(0.0524) | 3.0768(0.1576) | 3.3221(0.2035) |
| (42,42) | (205,205) | -2.24(0.0250) | -2.3169(0.1796) | -2.2769(0.2262) |
| (48,48) | (235,235) | -1.58(0.0128) | -1.3171(0.1720) | -1.3634(0.2205) |
| (72,72) | (355,355) | 2.24(0.0247) | - | 1.6537(0.4277) |
| (73,73) | (360,360) | 3.16(0.0506) | 5.1247(0.1555) | 3.8771(0.4219) |
| (123,123) | (610,610) | 1.10(0.0062) | - | 1.5168(0.2432) |
| (127,127) | (630,630) | -1.10(0.0063) | - | -1.1834(0.2460) |
| (161,161) | (800,800) | 0.77(0.0030) | - | - |
| (181,181) | (900,900) | 1.73(0.0152) | - | - |
| (182,182) | (905,905) | 3.81(0.0725) | 5.6744(0.2400) | 5.5127(0.2894) |
| (185,185) | (920,920) | 2.25(0.0263) | 1.7123(0.2327) | 1.7070(0.2858) |
| (221,221) | (1100,1100) | -1.30(0.0088) | -1.4276(0.1506) | -1.0867(0.1956)d |
| (243,243) | (1210,1210) | -1.00(0.0051) | -0.8603(0.1486) | - |
| (262,262) | (1305,1305) | -2.24(0.0245) | -2.2539(0.1826) | -1.6078(0.2417) |
| (268,268) | (1335,1335) | 1.58(0.0120) | 2.4264(0.2040) | 2.1736(0.2509) |
| (270,270) | (1345,1345) | 1.00(0.0049) | - | - |
| (274,274) | (1365,1365) | -1.73(0.0147) | -1.4114(0.1800) | -1.4935(0.2254) |
| (361,361) | (1800,1800) | 0.71(0.0026) | 0.7856(0.1457) | 0.6520(0.1859)d |
| (461,461) | (2300,2300) | 0.89(0.0040) | - | - |
| (5,6) | (20,25) | 2.24(0.0230) | 1.7839(0.1654) | 1.5752(0.2886) |
| (6,39) | (25,190) | 2.25(0.0128) | 1.9691(0.2168) | - |
| (42,220) | (205,1095) | 4.47(0.0511) | 4.3836(0.2198) | 4.6414(0.3394) |
| (75,431) | (370,2150) | 0.77(0.0014) | 1.1360(0.2124)d | - |
| (81,200) | (400,995) | -2.24(0.0128) | -2.4190(0.2460) | - |
| (82,193) | (405,960) | 1.58(0.0063) | 1.6345(0.2442) | - |
| (87,164) | (430,815) | 3.16(0.0235) | 2.9263(0.2254) | 1.7059(0.3319)d |
| (87,322) | (430,1605) | 3.81(0.0342) | 4.1019(0.2274) | 3.7040(0.3632) |
| (92,395) | (455,1970) | 1.73(0.0081) | 1.5714(0.2065)d | - |
| (104,328) | (515,1635) | 1.00(0.0024) | 0.8081(0.1979)d | - |
| (118,278) | (585,1385) | -2.24(0.0120) | -2.0796(0.2221) | -2.2590(0.3460) |
| (150,269) | (745,1340) | 1.10(0.0028) | 1.0740(0.2142) | - |
| (237,313) | (1180,1560) | 0.71(0.0014) | - | - |
| (246,470) | (1225,2345) | -1.10(0.0032) | -1.2381(0.2114)d | - |
| (323,464) | (1610,2315) | 0.89(0.0020) | - | - |
| (328,404) | (1635,2015) | -1.73(0.0079) | -2.3036(0.2123) | -1.9428(0.3330) |
| (342,420) | (1705,2095) | -1.30(0.0041) | -1.3886(0.2121)d | - |
| (344,407) | (1715,2030) | -1.00(0.0025) | - | - |
| (373,400) | (1860,1995) | -1.58(0.0070) | -1.4732(0.2028) | - |
| (431,439) | (2150,2190) | 3.16(0.0278) | 2.6700(0.2121) | 2.2454(0.3366)d |
| μ | 100 | 100.70 | 100.59 | |
 |
10 | 11.76 | 0.25 | |
| CPU time | 3.4 mins | 249 hrs | ||
aWhen i = j, the QTL is a main effect; otherwise, it is an epistatic effect.
bThe true value of a QTL effect is denoted by β and the proportion of variance contributed by the QTL is denoted by h2.
cThe estimated QTL effect is denoted by 
and the standard error is denoted by 
. The EBLASSO algorithm used hyperparameters a = b = 0.1 and the EB algorithm used hyperparameters τ = -1 and ω = 0.001.
dThe estimated QTL effect was obtained from a neighboring marker (≤ 20 cM away) rather than from the maker with the true effect.