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Table 3 Information for all significant SNP related to body size and carcass traits

From: Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks

Trait Nbsnp Chr Position (ps) AF Beta p-value Var (%) Candidate gene Distance
BMW 2 3 11,176,648 0.276 −2.55E-01 2.53E-05 4.1 TMEM17 7442 bp upstream
10 1,656,050 0.366 −2.35E-01 2.96E-05 4.1 LOC101804888 11,627 bp downstream
BMWP 3 1 867,910 0.45 2.56E-01 3.18E-06 8.1 LOC101803092 within
1 47,950,429 0.397 −2.39E-01 6.71E-06 6.9 ATP2B1 107,815 bp upstream
1 47,950,615 0.402 −2.31E-01 1.82E-05 6.4 ATP2B1 107,629 bp upstream
BrW 4 2 19,666,206 0.479 −2.39E-01 1.45E-05 9.8 PLXDC2 5029 bp downstream
2 24,791,499 0.362 −2.60E-01 7.69E-06 10.8 LOC101799835 within
6 31,223,243 0.369 2.22E-01 2.14E-05 7.9 WDR11 29,320 bp upstream
21 1,548,509 0.427 2.31E-01 2.59E-05 9 EYA2 28,420 bp downstream
BW42 5 1 85,234,035 0.455 −2.29E-01 1.12E-05 4.1 LOC101789880 within
1 140,105,435 0.305 −2.64E-01 1.20E-07 4.6 ATP11A within
1 140,105,568 0.47 2.16E-01 6.54E-06 3.6 ATP11A within
2 19,666,336 0.229 −2.29E-01 2.25E-05 2.9 PLXDC2 5159 bp downstream
28 3,372,077 0.024 −6.23E-01 3.16E-05 2.8 LOC101803004 1892 bp downstream
DP 2 1 7,468,875 0.358 2.22E-01 1.07E-05 4.9 GRM3 121,336 bp downstream
6 33,060,881 0.368 2.35E-01 3.09E-06 5.6 CTBP2 30,880 bp downstream
DW 8 1 63,206,125 0.395 −2.41E-01 1.75E-05 4.6 CACNA1C within
1 85,234,035 0.455 −2.28E-01 7.68E-06 4.3 LOC101789880 within
1 140,105,435 0.305 −2.55E-01 1.65E-07 4.6 ATP11A within
1 140,105,568 0.47 2.06E-01 9.97E-06 3.5 ATP11A within
1 141,660,288 0.44 2.05E-01 1.72E-05 3.4 LOC101802568 26,100 bp downstream
1 158,535,990 0.35 −2.14E-01 1.54E-05 3.5 KLF5 44,712 bp upstream
2 19,666,336 0.229 −2.40E-01 5.01E-06 3.4 PLXDC2 5159 bp downstream
28 3,372,077 0.024 −6.41E-01 1.46E-05 3.2 LOC101803004 1892 bp downstream
EW 6 1 63,206,125 0.395 −2.47E-01 1.51E-05 5 CACNA1C within
1 140,105,435 0.305 −2.65E-01 1.02E-07 5.1 ATP11A within
1 140,105,568 0.47 2.02E-01 2.52E-05 3.5 ATP11A within
1 158,535,990 0.35 −2.22E-01 1.15E-05 3.9 KLF5 44,712 bp upstream
2 19,666,336 0.229 −2.32E-01 1.65E-05 3.3 PLXDC2 5159 bp downstream
28 3,372,077 0.024 −6.37E-01 2.02E-05 3.3 LOC101803004 1892 bp downstream
EWP 4 2 35,813,875 0.372 −2.27E-01 2.74E-05 5.5 CHN2 within
3 89,970,339 0.313 −2.24E-01 2.59E-05 4.9 LGSN 57,852 bp downstream
13 17,512,359 0.391 −2.18E-01 1.02E-05 5.1 FOXP1 2160 bp downstream
18 5,703,171 0.433 2.29E-01 8.74E-06 5.8 PPP1R26 37,536 bp upstream
FBL 3 2 40,157,075 0.49 2.44E-01 1.50E-05 6.6 OXSM 15,327 bp downstream
2 52,398,515 0.419 2.40E-01 1.13E-05 6.2 TNS3 within
2 137,295,017 0.372 −2.18E-01 3.17E-05 5 TMEM74 1377 bp upstream
FW 2 1 148,339,868 0.018 7.08E-01 7.73E-06 3.2 ABCC4 within
4 59,568,289 0.02 6.09E-01 1.62E-05 2.6 LDB2 17,964 bp downstream
HEW 6 1 63,206,125 0.395 −2.46E-01 1.85E-05 5 CACNA1C within
1 140,105,435 0.305 −2.72E-01 5.27E-08 5.4 ATP11A within
1 140,105,568 0.47 2.06E-01 1.98E-05 3.6 ATP11A within
1 158,535,990 0.35 −2.24E-01 1.02E-05 3.9 KLF5 44,712 bp upstream
2 19,666,336 0.229 −2.35E-01 1.38E-05 3.4 PLXDC2 5159 bp downstream
28 3,372,077 0.024 −6.28E-01 2.95E-05 3.2 LOC101803004 1892 bp downstream
HEWP 2 1 196,705,092 0.357 2.18E-01 2.95E-05 5.1 LOC101797437 5799 bp downstream
13 17,512,359 0.391 −2.12E-01 2.27E-05 5 FOXP1 2160 bp downstream
HW 4 1 158,535,990 0.35 −2.53E-01 2.06E-06 8.6 KLF5 44,712 bp upstream
3 64,428,149 0.434 2.29E-01 8.58E-06 7.6 GJA1 14,583 bp downstream
5 22,865,850 0.351 2.30E-01 6.43E-06 7.1 AQR 11,077 bp upstream
7 11,397,351 0.312 −2.35E-01 2.62E-05 7 PCNT within
LW 5 1 119,976,059 0.407 −2.12E-01 1.31E-05 3.6 LOC101803212 13,772 bp downstream
1 34,185,127 0.242 −2.24E-01 2.47E-05 3.1 PPM1H within
4 427,963 0.473 2.19E-01 9.55E-06 4 LOC101798797 148,591 bp downstream
4 59,555,379 0.016 6.79E-01 3.37E-05 2.4 LDB2 4954 bp downstream
8 23,698,948 0.419 2.21E-01 2.95E-05 4 AGBL4 within
LMWP 1 20 2,198,171 0.385 −2.40E-01 2.73E-05 3 AUTS2 30,531 bp downstream
NL 1 1 130,709,943 0.354 −2.01E-01 2.79E-05 4.4 XG within
WW 2 1 140,105,435 0.305 −2.44E-01 6.49E-07 4.4 ATP11A within
2 149,672,484 0.015 8.53E-01 2.67E-05 3.8 FAM135B 33,375 bp downstream
  1. Neck length (NL), Fossil bone length (FBL), Breast width (BrW), Dressed weight (DW), Dressed percentage (DP), Eviscerated weight (EW), Eviscerated weight percentage (EWP), Half-eviscerated weight (HEW), Percentage of half-eviscerated yield (HEWP), 42-day body weight (BW42), Heart weight (HW), Liver weight (LW), Foot weight (FW), Wing weight (WW), Breast muscle weight (BMW), Breast muscle weight percentage (BMWP), Leg muscle weight (LMW), Leg muscle weight percentage (LMWP). Chr, chromosomeID; Nbsnp, number of significant SNP, retaining the most significant one if the distance between multiple SNP of the same trait is less than 0.15 Mb; AF, minor allele frequency; Beta, the estimate coefficient; Var (%), % of genetic variance explained by the top SNP