Table S1Phenotypic correlation coefficients between the recorded traits in the DLY and Duroc populations
DLY / CW / FBF / LBF / FBF / Duroc / BF100 / BF115 / BW160CW / 0.5927 / 0.5741 / 0.6199 / BF100 / 0.9998 / -0.1335
FBF / 0.4289 / 0.7749 / 0.9532 / BF115 / - / -0.1335
LBF / 0.4402 / 0.5594 / 0.9297 / BW160 / - / -
FBF / 0.4888 / 0.9237 / 0.8343
Notes: The symbols are defined in Table 1; all correlation coefficients are highly significant;the upper and lower triangles are the phenotypic correlation coefficients among the traits in males and in females, respectively.
Table S2The SNPs associated with recorded traits at P value ≤0.001 after genomic control
Trait / Population / SNP / SSC / Position, bp / P-Value / NSNPFBF / DLY / ALGA00089081 / 1 / 272080412 / 0.000216 / 4
FBF / DLY / MARC0029976 / 5 / 87357943 / 0.000720 / 1
FBF / DLY / H3GA0016438 / 5 / 63254325 / 0.000964 / 1
FBF / DLY / ALGA0114520 / 6 / 80246537 / 0.000785 / 1
FBF / DLY / M1GA00099331 / 7 / 34634619 / 0.000156 / 1
FBF / DLY / H3GA0021426 / 7 / 51583116 / 0.000692 / 3
FBF / DLY / ALGA0049814 / 8 / 139688641 / 0.000718 / 1
FBF / DLY / ALGA0055011 / 9 / 133614745 / 0.000880 / 1
FBF / DLY / M1GA0024018 / 9 / 72436024 / 0.000891 / 1
FBF / DLY / MARC0023610 / 10 / 36078578 / 0.000330 / 3
FBF / DLY / H3GA0029615 / 10 / 27028271 / 0.000949 / 1
FBF / DLY / H3GA0034394 / 12 / 43068568 / 0.000956 / 1
FBF / DLY / MARC00778301 / 13 / 66315906 / 0.000285 / 3
FBF / DLY / ASGA00666331 / 14 / 135699903 / 0.000325 / 2
FBF / DLY / ASGA00705021 / 15 / 131324583 / 0.000345 / 1
FBF / DLY / ALGA0086703 / 15 / 121528621 / 0.000828 / 1
FBF / DLY / H3GA0046969 / 16 / 73280603 / 0.000674 / 1
FBF / DLY / ASGA00777071 / 17 / 60017456 / 0.000213 / 1
FBF / DLY / H3GA00518941 / X / 111903249 / 0.000264 / 6
FBF / DLY / M1GA0002073 / 1 / 307442129 / 0.000149 / 7
FBF / DLY / DRGA0017627 / 1 / 2737789 / 0.000803 / 1
FBF / DLY / MARC0090364 / 3 / 78860474 / 0.000793 / 1
FBF / DLY / DIAS0001401 / 7 / 54527667 / 0.000284 / 3
FBF / DLY / H3GA0021435 / 7 / 51837521 / 0.000749 / 1
FBF / DLY / H3GA0024868 / 8 / 50479231 / 0.000382 / 1
FBF / DLY / ALGA0051635 / 9 / 15895538 / 0.000958 / 1
FBF / DLY / MARC0003307 / 10 / 38029552 / 0.000338 / 1
FBF / DLY / ASGA0099044 / 12 / 51581265 / 0.000629 / 1
FBF / DLY / MARC0096215 / 13 / 66268000 / 0.000372 / 2
FBF / DLY / ASGA0066633 / 14 / 135699903 / 0.000984 / 1
FBF / DLY / ASGA0070502 / 15 / 131324583 / 0.000107 / 2
FBF / DLY / DRGA0015754 / 16 / 7300334 / 0.000228 / 1
FBF / DLY / ASGA0077707 / 17 / 60017456 / 0.000358 / 3
FBF / DLY / H3GA0051894 / X / 111903249 / 0.000455 / 4
CW / DLY / ALGA0005851 / 1 / 138686941 / 0.000326 / 1
CW / DLY / ALGA0104903 / 2 / 156381110 / 0.000105 / 2
CW / DLY / ALGA0014120 / 2 / 86682429 / 0.000620 / 2
CW / DLY / H3GA0008910 / 3 / 15668269 / 0.000338 / 1
CW / DLY / ASGA0096867 / 3 / 2013852 / 0.000628 / 1
CW / DLY / ALGA0118917 / 6 / 140163451 / 0.000701 / 1
CW / DLY / ALGA0038146 / 7 / 4988931 / 0.000415 / 1
CW / DLY / ALGA0040388 / 7 / 37354942 / 0.000754 / 1
CW / DLY / H3GA0027354 / 9 / 54436875 / 0.000113 / 1
CW / DLY / MARC0113922 / 11 / 15065868 / 0.000106 / 1
CW / DLY / ALGA0103221 / 12 / 58890089 / 0.000147 / 2
CW / DLY / ASGA0059437 / 13 / 189534450 / 0.000619 / 1
CW / DLY / MARC0042258 / 14 / 140893834 / 0.000218 / 3
CW / DLY / ASGA0105517 / 14 / 151966127 / 0.000463 / 2
CW / DLY / CASI0007925 / 17 / 23438841 / 0.000847 / 2
CW / DLY / ALGA0110904 / X / 3623792 / 0.000805 / 1
LBF / DLY / ALGA0012867 / 2 / 32434203 / 0.000534 / 1
LBF / DLY / H3GA0006963 / 2 / 85053479 / 0.000927 / 1
LBF / DLY / INRA0016801 / 4 / 123080603 / 0.000495 / 1
LBF / DLY / MARC00299761 / 5 / 87357943 / 0.000915 / 1
LBF / DLY / ALGA0044931 / 7 / 119267329 / 0.000794 / 1
LBF / DLY / MARC0057714 / 9 / 132216287 / 0.000729 / 1
LBF / DLY / ASGA0046365 / 10 / 11654673 / 0.000332 / 1
LBF / DLY / ALGA0058320 / 10 / 36651543 / 0.000417 / 3
LBF / DLY / M1GA0015241 / 11 / 74740642 / 0.000447 / 1
LBF / DLY / MARC0090046 / 11 / 25423001 / 0.000559 / 3
LBF / DLY / H3GA00343941 / 12 / 43068568 / 0.000697 / 1
LBF / DLY / MARC0093666 / 13 / 79410199 / 0.000351 / 2
LBF / DLY / ALGA0093183 / 17 / 11400230 / 0.000573 / 1
LBF / DLY / H3GA0047628 / 17 / 2928586 / 0.000790 / 1
BW160 / Duroc / MARC0039494 / 6 / 4426420 / 0.000377 / 4
BW160 / Duroc / ALGA0042499 / 7 / 73072087 / 0.000331 / 7
BW160 / Duroc / ALGA0102181 / 8 / 32326986 / 0.000251 / 5
BW160 / Duroc / MARC0059309 / 8 / 79601958 / 0.000271 / 1
BW160 / Duroc / ALGA0049267 / 8 / 121712755 / 0.000627 / 1
BW160 / Duroc / MARC0073866 / 8 / 95129988 / 0.000648 / 2
BW160 / Duroc / ALGA0074054 / 13 / 215287502 / 0.000704 / 2
BW160 / Duroc / ALGA0078229 / 14 / 66172017 / 0.000670 / 2
BW160 / Duroc / ASGA0095765 / 17 / 8317267 / 0.000877 / 1
BF100 / Duroc / MARC0075909 / 1 / 176700629 / 0.000489 / 18
BF100 / Duroc / H3GA0007711 / 2 / 137241803 / 0.000267 / 6
BF100 / Duroc / INRA0024788 / 7 / 34978383 / 0.000301 / 11
BF100 / Duroc / ASGA0060563 / 14 / 4635326 / 0.000256 / 1
BF100 / Duroc / ALGA0099927 / X / 110912743 / 0.000146 / 9
BF100 / Duroc / ASGA0097714 / X / 9513017 / 0.000237 / 1
BF100 / Duroc / H3GA0052166 / X / 143488665 / 0.000520 / 2
BF115 / Duroc / MARC00759091 / 1 / 176700629 / 0.000464 / 16
BF115 / Duroc / H3GA00077111 / 2 / 137241803 / 0.000248 / 6
BF115 / Duroc / MARC00031841 / 5 / 92705274 / 0.000505 / 1
BF115 / Duroc / INRA00247881 / 7 / 34978383 / 0.000302 / 11
BF115 / Duroc / ASGA00605631 / 14 / 4635326 / 0.000240 / 1
BF115 / Duroc / ALGA00999271 / X / 110912743 / 0.000122 / 12
BF / META / ALGA0008905 / 1 / 272049666 / 0.000320 / 6
BF / META / DRGA0017490 / 2 / 129836792 / 0.000975 / 1
BF / META / ALGA0114520 / 6 / 80246537 / 0.000864 / 1
BF / META / H3GA0021426 / 7 / 51583116 / 0.000628 / 2
BF / META / MARC0069646 / 7 / 34103417 / 0.000653 / 2
BF / META / H3GA0024981 / 8 / 78209229 / 0.000897 / 1
BF / META / ASGA0040055 / 8 / 139053049 / 0.000963 / 1
BF / META / M1GA0024018 / 9 / 72436024 / 0.000494 / 1
BF / META / MARC0003307 / 10 / 38029552 / 0.000568 / 1
BF / META / ASGA0091759 / 13 / 68830081 / 0.000423 / 4
BF / META / ASGA0070502 / 15 / 131324583 / 0.000581 / 3
BF / META / ASGA0077707 / 17 / 60017456 / 0.000343 / 1
BF / META / ASGA0081564 / X / 138684852 / 0.000842 / 1
BW / META / ASGA0008026 / 1 / 304444668 / 0.000805 / 1
BW / META / ASGA0085878 / 2 / 156589069 / 0.000123 / 10
BW / META / ALGA0112844 / 3 / 19373384 / 0.000903 / 1
BW / META / H3GA0014351 / 4 / 127784764 / 0.000169 / 2
BW / META / ASGA0024405 / 5 / 10686539 / 0.000878 / 1
BW / META / ASGA0101351 / 6 / 140372952 / 0.000837 / 1
BW / META / ALGA0104633 / 8 / 32144020 / 0.000591 / 1
BW / META / MARC0113922 / 11 / 15065868 / 0.000709 / 1
BW / META / ALGA0103221 / 12 / 58890089 / 0.000456 / 1
BW / META / MARC0063986 / 12 / 2477621 / 0.000676 / 1
BW / META / ASGA0065815 / 14 / 114443273 / 0.000140 / 22
Multi_trait / DLY / ALGA0008905 / 1 / 272049666 / 0.000198 / 1
Multi_trait / DLY / CASI0009733 / 1 / 113658130 / 0.000238 / 1
Multi_trait / DLY / ALGA0104903 / 2 / 156381110 / 0.000752 / 1
Multi_trait / DLY / ALGA0105286 / 6 / 74623829 / 0.000852 / 3
Multi_trait / DLY / ASGA0032310 / 7 / 33057283 / 0.000569 / 2
Multi_trait / DLY / H3GA0024981 / 8 / 78209229 / 0.000799 / 1
Multi_trait / DLY / H3GA0027354 / 9 / 54436875 / 0.000382 / 2
Multi_trait / DLY / ALGA0056284 / 10 / 2870481 / 0.000145 / 1
Multi_trait / DLY / M1GA0014096 / 10 / 48960017 / 0.000516 / 2
Multi_trait / DLY / H3GA0056142 / 11 / 74825658 / 0.000128 / 2
Multi_trait / DLY / ASGA0049733 / 11 / 10299410 / 0.000812 / 1
Multi_trait / DLY / MARC0093666 / 13 / 79410199 / 0.000632 / 1
Multi_trait / DLY / CASI0007925 / 17 / 23438841 / 0.000271 / 1
Multi_trait / DLY / ALGA0099948 / X / 112884986 / 0.000791 / 2
Multi_trait / Duroc / ALGA0006336 / 1 / 162671533 / 0.000138 / 6
Multi_trait / Duroc / ASGA0090367 / 1 / 285800052 / 0.000234 / 3
Multi_trait / Duroc / DRGA0000296 / 1 / 27469814 / 0.000768 / 3
Multi_trait / Duroc / ALGA0010569 / 1 / 302114766 / 0.000817 / 1
Multi_trait / Duroc / ALGA0109617 / 5 / 103826114 / 0.000793 / 1
Multi_trait / Duroc / ASGA0039066 / 8 / 80503659 / 0.000207 / 4
Multi_trait / Duroc / ASGA0101895 / 8 / 32355125 / 0.000323 / 10
Multi_trait / Duroc / ALGA0056240 / 10 / 2204509 / 0.000492 / 2
Multi_trait / Duroc / ASGA0099340 / 12 / 60089678 / 0.000790 / 1
Multi_trait / Duroc / ALGA0073889 / 13 / 211884452 / 0.000239 / 5
Multi_trait / Duroc / ASGA0103240 / 13 / 4023767 / 0.000483 / 1
Multi_trait / Duroc / H3GA0054884 / 16 / 68067101 / 0.000760 / 1
Multi_trait / Duroc / ALGA0105315 / X / 3059014 / 0.000981 / 1
Multi_trait / Duroc / ASGA0081500 / X / 129909517 / 0.000159 / 1
Multi_trait / Duroc / ASGA0097714 / X / 9513017 / 0.000185 / 1
Multi_trait / Duroc / ALGA0099927 / X / 110912743 / 0.000276 / 2
Multi_trait / Duroc / H3GA0052163 / X / 143191017 / 0.000975 / 5
Table S3The unmapped SNPs associated with recorded traits at P value ≤0.001 after genomic control
Trait / Population / SNP / P-valueBF / META / ALGA0113446 / 0.0005104
BF / META / M1GA0010841 / 0.0005234
BF100 / Duroc / INRA0024786 / 0.0003013
BF100 / Duroc / MARC0056859 / 0.0003013
BF100 / Duroc / ASGA0098791 / 0.0004759
BF100 / Duroc / H3GA0008030 / 0.0006237
BF100 / Duroc / ASGA0086185 / 0.0008536
BF100 / Duroc / MARC0060948 / 0.0008549
BF115 / Duroc / INRA00247861 / 0.0003017
BF115 / Duroc / MARC00568591 / 0.0003017
BF115 / Duroc / ASGA00987911 / 0.0005623
BF115 / Duroc / H3GA00080301 / 0.0006117
BF115 / Duroc / MARC00609481 / 0.0008040
BF115 / Duroc / ASGA00861851 / 0.0009265
BW / META / DIAS0001614 / 0.0000079
BW / META / MARC0026068 / 0.0000471
BW / META / ALGA0112586 / 0.0001164
BW / META / ASGA0102768 / 0.0001693
BW / META / ASGA0101024 / 0.0001759
BW / META / ASGA0099432 / 0.0001874
BW / META / ASGA0096881 / 0.0003016
BW / META / H3GA0056575 / 0.0006148
BW / META / DIAS0001074 / 0.0007309
BW160 / Duroc / MARC0062432 / 0.0000400
BW160 / Duroc / ASGA0093016 / 0.0004742
BW160 / Duroc / MARC0028961 / 0.0004825
CBF / DLY / ASGA0093858 / 0.0005174
CBF / DLY / ALGA0119267 / 0.0006943
CBF / DLY / ALGA0120676 / 0.0008105
CBF / DLY / ASGA0100167 / 0.0008580
CBF / DLY / MARC0027512 / 0.0008699
CBF / DLY / ALGA0123282 / 0.0008760
CBF / DLY / M1GA0010841 / 0.0009739
CW / DLY / MARC0026068 / 0.0000234
CW / DLY / DIAS0001614 / 0.0000827
CW / DLY / ALGA0112586 / 0.0003322
CW / DLY / DRGA0007499 / 0.0008144
CW / DLY / ASGA0103523 / 0.0009871
FBF / DLY / MARC0060112 / 0.0003034
FBF / DLY / ASGA00938581 / 0.0005100
FBF / DLY / M1GA00108411 / 0.0005299
FBF / DLY / ALGA0113446 / 0.0005588
FBF / DLY / ASGA0088953 / 0.0006305
FBF / DLY / MARC0074901 / 0.0007608
LBF / DLY / ALGA0060737 / 0.0003036
LBF / DLY / ALGA0060733 / 0.0004846
LBF / DLY / ALGA0116693 / 0.0004846
LBF / DLY / ASGA0049720 / 0.0005967
LBF / DLY / MARC00601121 / 0.0009197
Multi_trait / Duroc / ASGA0061305 / 0.0002140
Multi_trait / Duroc / ALGA0075240 / 0.0002338
Multi_trait / Duroc / ASGA0098791 / 0.0002737
Multi_trait / DLY / ASGA0090469 / 0.0003198
Multi_trait / DLY / MARC0063422 / 0.0004135
Multi_trait / Duroc / ALGA0108018 / 0.0004251
Multi_trait / DLY / DIAS0001614 / 0.0004834
Multi_trait / DLY / ALGA0112991 / 0.0004923
Multi_trait / Duroc / MARC0062432 / 0.0005332
Multi_trait / DLY / MARC0026068 / 0.0005491
Multi_trait / Duroc / ALGA0045598 / 0.0006203
Multi_trait / Duroc / ASGA0060105 / 0.0006644
Multi_trait / Duroc / ALGA0119892 / 0.0007603
Multi_trait / Duroc / ASGA0100790 / 0.0007614