Table 2 Genes in regions predicted to be under putative selection in Russian cattle breeds.
Chr* | Region start (Mbp) | Region end (Mbp) | Most significant SNP q-value | Breed/Group | No. genes in the region | Method | Candidate gene (rank) | Function |
|---|---|---|---|---|---|---|---|---|
1 | 28.402 | 28.899 | 0.002273827 | Kazakh Whiteheaded | 2 | DCMS | FKBP2 (2) | Milk |
2 | 15.069 | 15.083 | 0.012500925 | Yakut | 1 | DCMS | CERKL (1) | Light stress |
2 | 73.106 | 73.393 | 0.017181621 | Yaroslavl | 1 | DCMS | GLI2 (1) | Weight, growth |
3 | 9.348 | 9.751 | 0.004315819 | Bestuzhev | 13 | DCMS | COPA (3) | Coat colour |
3 | 9.348 | 9.722 | 0.001173551 | Black Pied | 10 | DCMS | COPA (1) | Coat colour |
3 | 9.386 | 9.529 | 0.046081992 | Holstein | 2 | DCMS | COPA (1) | Coat colour |
3 | 52.040 | 52.213 | 0.001189865 | Hanwoo | 1 | DCMS | HFM1 (1) | Reproduction |
3 | 52.075 | 52.231 | 0.010464401 | Holstein | 1 | DCMS | HFM1 (1) | Reproduction |
3 | 52.148 | 52.225 | 0.009368275 | Black Pied | 1 | DCMS | HFM1 (1) | Reproduction |
3 | 52.153 | 52.187 | 0.018393593 | Buryat | 1 | DCMS | HFM1 (1) | Reproduction |
3 | 52.174 | 52.267 | 0.000324907 | Kalmyk | 1 | DCMS | HFM1 (1) | Reproduction |
4 | 14.188 | 15.448 | 0.040960871 | ASIA | 6 | hapFLK | RPL7 (1) | Acclimation |
4 | 107.007 | 107.085 | 0.043707068 | Kalmyk | 3 | DCMS | TRPV5 (1) | Milk fever |
5 | 13.271 | 27.026 | 5.53E-08 | EUR2 | 71 | hapFLK | KITLG (4) | Coat colour |
5 | 16.357 | 21.155 | 0.001789011 | Yaroslavl | 13 | DCMS | KITLG (9) | Coat colour |
5 | 17.154 | 20.486 | 0.000398061 | EUR1 | 8 | hapFLK | KITLG (1) | Coat colour |
5 | 18.335 | 19.335 | 4.47E-05 | Bestuzhev | 1 | DCMS | KITLG (1) | Coat colour |
5 | 18.335 | 18.966 | 0.001068985 | Kazakh Whiteheaded | 1 | DCMS | KITLG (1) | Coat colour |
5 | 29.684 | 30.174 | 0.011869128 | Kholmogory | 10 | DCMS | AQP5 (3) | Acclimation |
5 | 47.752 | 48.287 | 0.033364267 | ASIA | 1 | hapFLK | HMGA2 (1) | Growth |
5 | 48.017 | 48.308 | 4.53E-10 | Buryat | 1 | DCMS | HMGA2 (1) | Growth |
5 | 48.017 | 48.506 | 7.46E-11 | Kalmyk | 1 | DCMS | HMGA2 (1) | Growth |
5 | 48.045 | 48.263 | 0.001471807 | Hanwoo | 1 | DCMS | HMGA2 (1) | Growth |
5 | 48.094 | 48.514 | 4.68E-06 | Bestuzhev | 1 | DCMS | HMGA2 (1) | Growth |
5 | 48.155 | 48.280 | 0.018053667 | Japanese Black | 1 | DCMS | HMGA2 (1) | Growth |
5 | 48.185 | 48.270 | 0.001526729 | Kostroma | 1 | DCMS | HMGA2 (1) | Growth |
5 | 60.624 | 60.624 | 0.048486709 | Buryat | 1 | DCMS | HAL (1) | Milk |
5 | 75.685 | 75.731 | 0.037717028 | Yaroslavl | 1 | DCMS | CSF2RB (1) | Milk |
5 | 107.338 | 108.490 | 0.004370697 | Yakut | 18 | DCMS | KDM5A (2) | Milk |
6 | 37.076 | 39.850 | 0 | EUR1 | 18 | hapFLK | NCAPG (1), LCORL (2), LAP3 (6), ABCG2 (11) | Growth, Milk |
6 | 37.855 | 38.000 | 1.04E-06 | Kalmyk | 2 | DCMS | ABCG2 (1) | Milk |
6 | 37.902 | 37.948 | 0.027503049 | Fleckvieh | 1 | DCMS | ABCG2 (1) | Milk |
6 | 37.983 | 38.188 | 0.006537637 | Kostroma | 3 | DCMS | ABCG2 (1) | Milk |
6 | 38.579 | 38.656 | 0.001009406 | Kholmogory | 3 | DCMS | LAP3 (2) | Milk |
6 | 38.580 | 38.616 | 0.000578482 | Buryat | 3 | DCMS | LAP3 (1) | Milk |
6 | 38.731 | 38.924 | 7.26E-07 | Jersey | 3 | DCMS | NCAPG (1), LCORL (3) | Growth |
6 | 38.735 | 38.931 | 0.000382606 | Kazakh Whiteheaded | 3 | DCMS | NCAPG (1), LCORL (2) | Growth |
6 | 38.924 | 39.100 | 0.006598304 | Fleckvieh | 1 | DCMS | LCORL (1) | Growth |
6 | 38.924 | 39.023 | 0.03478244 | Yaroslavl | 1 | DCMS | LCORL (1) | Growth |
6 | 59.928 | 74.936 | 0 | EUR1 | 63 | hapFLK | KIT (4) | Coat colour |
6 | 68.059 | 72.063 | 5.67E-07 | Kazakh Whiteheaded | 26 | DCMS | KIT (4) | Coat colour |
6 | 69.440 | 72.476 | 1.13E-06 | Fleckvieh | 10 | DCMS | KIT (4) | Coat colour |
6 | 71.240 | 71.959 | 0.000166418 | Yaroslavl | 3 | DCMS | KIT (2) | Coat colour |
7 | 23.035 | 23.183 | 0.001289242 | Kholmogory | 1 | DCMS | RAD50 (1) | Antimicrobial protection |
7 | 23.078 | 23.107 | 0.046379711 | Bestuzhev | 1 | DCMS | RAD50 (1) | Antimicrobial protection |
7 | 23.078 | 23.261 | 3.43E-08 | Kalmyk | 3 | DCMS | IL5 (1), IRF1 (2), RAD50 (3) | Antimicrobial protection |
7 | 23.113 | 23.228 | 2.35E-05 | Hanwoo | 2 | DCMS | RAD50 (1), IL5 (2) | Antimicrobial protection |
7 | 23.136 | 23.498 | 3.66E-06 | Bestuzhev | 4 | DCMS | IRF1 (1), IL5 (3) | Antimicrobial protection |
7 | 23.136 | 23.216 | 0.00265416 | Yakut | 2 | DCMS | IL5 (1), RAD50 (2) | Antimicrobial protection |
7 | 23.144 | 23.144 | 0.037325408 | Yaroslavl | 1 | DCMS | RAD50 (1) | Antimicrobial protection |
7 | 23.591 | 23.695 | 0.005771811 | Holstein | 1 | DCMS | CSF2 (1) | Reproduction |
7 | 23.613 | 23.699 | 0.000131001 | Black Pied | 1 | DCMS | CSF2 (1) | Reproduction |
7 | 23.683 | 23.698 | 0.002131539 | Yaroslavl | 1 | DCMS | CSF2 (1) | Reproduction |
7 | 23.691 | 23.696 | 0.028601712 | Kazakh Whiteheaded | 1 | DCMS | CSF2 (1) | Reproduction |
7 | 54.361 | 54.735 | 0.000687902 | Yakut | 6 | DCMS | HDAC3 (5) | Brown adipose tissue |
7 | 93.194 | 93.360 | 2.19E-07 | Kalmyk | 1 | DCMS | ARRDC3 (1) | Adipose tissue |
7 | 93.206 | 93.307 | 3.83E-10 | Buryat | 1 | DCMS | ARRDC3 (1) | Adipose tissue |
7 | 93.208 | 93.276 | 0.01177964 | Fleckvieh | 1 | DCMS | ARRDC3 (1) | Adipose tissue |
7 | 93.211 | 93.307 | 2.37E-07 | Hanwoo | 1 | DCMS | ARRDC3 (1) | Adipose tissue |
7 | 93.214 | 93.276 | 0.010240366 | Kostroma | 1 | DCMS | ARRDC3 (1) | Adipose tissue |
7 | 93.215 | 93.224 | 0.031503554 | Jersey | 1 | DCMS | ARRDC3 (1) | Adipose tissue |
7 | 93.242 | 93.282 | 0.017682048 | Yakut | 1 | DCMS | ARRDC3 (1) | Adipose tissue |
8 | 0.264 | 0.503 | 0.04889224 | Kholmogory | 1 | DCMS | ANXA10 (1) | Reproduction |
8 | 79.681 | 79.759 | 0.027035565 | Yaroslavl | 1 | DCMS | NTRK2 (1) | Antimicrobial protection |
8 | 88.219 | 88.589 | 0.002222339 | Black Pied | 1 | DCMS | SYK (1) | Brown adipose tissue |
8 | 88.420 | 88.465 | 0.027629081 | Kholmogory | 1 | DCMS | SYK (1) | Brown adipose tissue |
12 | 44.257 | 44.839 | 0.001059257 | Bestuzhev | 1 | DCMS | KLHL1 (1) | Milk |
12 | 80.782 | 81.010 | 0.012757213 | Buryat | 1 | DCMS | PCCA (1) | Milk |
12 | 80.803 | 81.092 | 0.010062102 | Yaroslavl | 1 | DCMS | PCCA (1) | Milk |
12 | 80.962 | 81.085 | 0.037912516 | Japanese Black | 1 | DCMS | PCCA (1) | Milk |
13 | 57.572 | 57.636 | 0.021930321 | Kazakh Whiteheaded | 1 | DCMS | EDN3 (1) | Coat colour |
14 | 1.489 | 1.893 | 0.032866336 | Kazakh Whiteheaded | 28 | DCMS | TONSL (2), DGAT1 (20) | Milk |
14 | 1.651 | 1.869 | 0.001653056 | Buryat | 11 | DCMS | TONSL (1), DGAT1 (11) | Milk |
14 | 1.696 | 1.893 | 0.038247912 | Kholmogory | 13 | DCMS | DGAT1 (1) | Milk |
14 | 23.258 | 23.269 | 0.02863779 | Yaroslavl | 1 | DCMS | NPBWR1 (1) | Reproduction |
14 | 24.419 | 25.135 | 1.02E-08 | Black Pied | 8 | DCMS | TMEM68 (2), XKR4 (8), PLAG1 (5) | Feed intake, Growth, Weight |
14 | 24.421 | 24.501 | 0.00525187 | Kazakh Whiteheaded | 1 | DCMS | XKR4 (1) | Weight |
14 | 24.426 | 25.135 | 1.50E-06 | Kholmogory | 8 | DCMS | TMEM68 (2), PLAG1 (5), XKR4 (7) | Feed intake, Growth, Weight |
14 | 24.431 | 24.434 | 0.047221525 | Kalmyk | 1 | DCMS | XKR4 (1) | Weight |
14 | 24.512 | 24.556 | 0.032774966 | Hanwoo | 1 | DCMS | XKR4 (1) | Weight |
14 | 24.699 | 25.010 | 0.000703648 | Bestuzhev | 3 | DCMS | TMEM68 (2) | Feed intake |
14 | 24.714 | 24.909 | 1.24E-06 | Kalmyk | 3 | DCMS | TMEM68 (3) | Feed intake |
14 | 25.447 | 25.849 | 5.88E-06 | Kazakh Whiteheaded | 1 | DCMS | IMPAD1 (1) | Growth |
14 | 25.460 | 25.617 | 4.79E-10 | Holstein | 1 | DCMS | IMPAD1 (1) | Growth |
14 | 25.497 | 25.667 | 0.002016879 | Angus | 1 | DCMS | IMPAD1 (1) | Growth |
14 | 25.497 | 25.546 | 0.014138416 | Kostroma | 1 | DCMS | IMPAD1 (1) | Growth |
14 | 25.499 | 25.541 | 0.015989917 | Jersey | 1 | DCMS | IMPAD1 (1) | Growth |
14 | 25.507 | 25.530 | 0.000738867 | Buryat | 1 | DCMS | IMPAD1 (1) | Growth |
15 | 35.637 | 36.167 | 0.013241977 | Black Pied | 5 | DCMS | NUCB2 (1) | Feed intake, Body temperature, Growth |
16 | 36.496 | 36.581 | 0.045474804 | Bestuzhev | 1 | DCMS | RGS7 (1) | Domestication, Acclimation |
20 | 4.046 | 4.102 | 0.00256072 | Jersey | 1 | DCMS | SH3PXD2B (1) | Growth, meat |
20 | 4.050 | 4.084 | 0.000859753 | Bestuzhev | 1 | DCMS | SH3PXD2B (1) | Growth, meat |
20 | 4.067 | 4.144 | 0.003706131 | Black Pied | 1 | DCMS | SH3PXD2B (1) | Growth, meat |
20 | 4.067 | 4.084 | 0.019181385 | Holstein | 1 | DCMS | SH3PXD2B (1) | Growth, meat |
20 | 4.593 | 4.784 | 0.0029386 | Kholmogory | 4 | DCMS | CREBRF (1) | Growth |
20 | 4.597 | 4.730 | 0.0004249 | Bestuzhev | 3 | DCMS | CREBRF (1) | Growth |
20 | 4.597 | 4.791 | 0.0145958 | Jersey | 4 | DCMS | CREBRF (3) | Growth |
20 | 4.628 | 4.782 | 0.0002944 | Holstein | 3 | DCMS | CREBRF (1) | Growth |
20 | 4.660 | 4.783 | 2.94E-05 | Hanwoo | 3 | DCMS | CREBRF (1) | Growth |
20 | 4.673 | 4.759 | 0.0010948 | Buryat | 2 | DCMS | CREBRF (1) | Growth |
20 | 4.692 | 4.782 | 0.0125848 | Black Pied | 2 | DCMS | CREBRF (1) | Growth |
20 | 4.692 | 4.761 | 6.08E-05 | Kalmyk | 2 | DCMS | CREBRF (1) | Growth |
20 | 31.912 | 32.005 | 0.019009149 | Black Pied | 1 | DCMS | GHR (1) | Milk, Growth |
20 | 32.098 | 32.460 | 0.032750776 | Bestuzhev | 1 | DCMS | GHR (1) | Milk, Growth |
20 | 52.303 | 57.558 | 0.009549042 | ASIA | 8 | hapFLK | RETREG1 (1) | Acclimation |
20 | 56.431 | 56.876 | 0.043882656 | Yakut | 3 | DCMS | RETREG1 (2) | Acclimation |
20 | 56.683 | 56.890 | 0.000763043 | Hanwoo | 2 | DCMS | RETREG1 (2) | Acclimation |
24 | 60.758 | 62.644 | 0.000623541 | EUR2 | 15 | hapFLK | BCL2 (1) | Reproduction |
27 | 24.577 | 24.803 | 0.001749199 | Yakut | 1 | DCMS | TNKS (1) | Feed intake, Adipose tissue |
28 | 21.176 | 26.909 | 0.00551179 | EUR2 | 30 | hapFLK | SIRT1 (2) | Antimicrobial protection |
28 | 24.039 | 24.885 | 0.01399301 | Yaroslavl | 6 | DCMS | SIRT1 (2) | Antimicrobial protection |
28 | 35.332 | 35.883 | 0.008902995 | Yaroslavl | 2 | DCMS | SFTPD (2) | Antimicrobial protection |
