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. 2018 Aug 28;8:12984. doi: 10.1038/s41598-018-31304-w

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

*For a full list of selected regions and genes see Supplementary Table S1.