TABLE 2.
Positional candidate genes in regions with the highest FST values between DSN and Holstein. Genes in bold are located directly inside the windows with the highest FST values. All other genes are located ± 250 kb from the start and end positions of the windows with the highest FST values. Consecutive windows displaying the same genes are shown together, this is the case for windows in BTA 1, 7, 8, and 10, whereof length is 20 kb.
| Location | SNP count | Length (kb) | Genes ± 250 kb |
|---|---|---|---|
| 1 : 29,280,001–29,300,000 | 279 | 20 | 1,4-alpha-glucan branching enzyme 1 ( GBE1 ), ENSBTAG00000008359 |
| 2 : 78,690,001–78,700,000 | 91 | 10 | Glycophorin C (GYPC) |
| 2 : 84,980,001–84,990,000 | 88 | 10 | HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 ( HECW2 ), coiled-coil domain containing 150 (CCDC150) |
| 3 : 41,600,001–41,610,000 | 97 | 10 | Olfactomedin 3 (OLFM3), ENSBTAG00000051863 |
| 7 : 41,060,001–41,080,000 | 346 | 20 | Germinal center associated signaling and motility like (GCSAML), olfactory receptor family 2 subfamily C member 3 (OR2C3), and 3B (OR2C3B), subfamily G member 2 (OR2G2), 3 (OR2G3), and 27 (OR2G27), subfamily W member 3 (OR2W3), and 3D (OR2W3D), subfamily AO member 1 (OR2AO1), subfamily T member 54 (OR2T54), family 5 subfamily AE member 3 (OR5AE3), and 4 (OR5AE4), family 6 subfamily F member 1 (OR6F1), subfamily AA member 1 (OR6AA1), subfamily AN member 1 (OR6AN1), family 9 subfamily E member 2 (OR9E2), family 11 subfamily L member 1 (OR11L1), family 14 subfamily P member 2 (OR14P2), tripartite motif containing 58 (TRIM58), ENSBTAG00000030735 |
| 8 : 110,900,001–110,920,000 | 265 | 20 | Doublecortin domain containing 2C ( DCDC2C ), gelsolin (GSN), stomatin (STOM), allantoicase (ALLC), collectin subfamily member 11 (COLEC11), ribosomal protein S7 (RPS7), ribonuclease H1 (RNASEH1), acireductone dioxygenase 1 (ADI1), trafficking protein particle complex subunit 12 (TRAPPC12), EARP complex and GARP complex interacting protein 1 (EIPR1), ENSBTAG00000049154 |
| 10 : 38,480,001–38,500,000 | 206 | 20 | Ubiquitin protein ligase E3 component n-recognin 1 (UBR1), transmembrane protein 62 (TMEM62), cyclin D1 binding protein 1 (CCNDBP1), erythrocyte membrane protein band 4.2 (EPB42), ENSBTAG00000046363 |
| 10 : 55,600,001–55,610,000 | 177 | 10 | Unc-13 homolog C (UNC13C) |
| 20 : 27,500,001–27,510,000 | 77 | 10 | ISL LIM homeobox 1 (ISL1) |
| 20 : 28,610,001–28,620,000 | 119 | 10 | Poly (ADP-ribose) polymerase family member 8 (PARP8), embigin (EMB) |
| 20 : 37,390,001–37,400,000 | 101 | 10 | Ciliosis and planar polarity effector 1 (CPLANE1), NIPBL cohesin loading factor (NIPBL), ENSBTAG00000050782, solute carrier family 1 member 3 (SLC1A3) |
| 22 : 52,820,001–52,830,000 | 105 | 10 | Coiled-coil domain containing 12 (CCDC12), parathyroid hormone 1 receptor (PTH1R), myosin light chain 3 (MYL3), serine protease 42 (PRSS42P), ENSBTAG00000037821, ENSBTAG00000052304, ENSBTAG00000049544, ENSBTAG00000050911, serine protease 45 (PRSS45), ENSBTAG00000038616, ENSBTAG00000005019, transmembrane inner ear (TMIE), ALS2 C-terminal like (ALS2CL), leucine rich repeat containing 2 (LRRC2), teratocarcinoma-derived growth factor 1 (TDGF1), receptor transporter protein 3 (RTP3), lactotransferrin (LTF), C-C motif chemokine receptor like 2 (CCRL2), receptor 5 (CCR5), and 2 (CCR2) |