Table 1 Genomic region and associated genes of the top 5 significant iHS for each of the seven bovine breeds
From: Detection of selection signatures in dairy and beef cattle using high-density genomic information
Breeds | Genomic region (kb) | Mean |iHS| value | P value | Gene |
|---|---|---|---|---|
Angus | Chr3:98500-99000 | 7.373 | 1.6 × 10−13 | SPATA6, SLC5A9, LOC100295301, SLINT1, LOC100337055, LCO787081 |
Chr3:99500-100000 | 6.953 | 3.6 × 10−12 | CMPK1, STIL, TAL1, PDZK1IP1, LOC100847677, LOC784358, CYP4A11, LOC784417, LOC787638, CYP4A22, LOC787656, CYP4B1 | |
Chr16:46000-46500 | 6.726 | 1.7 × 10−11 | LCO513399, ERRFI1, PARK7, TNFRSF9, UTS2, LOC100848366, PER3, VAMP3, CAMTA1 | |
Chr3:100000-100500 | 6.262 | 3.8 × 10−10 | KIAA0494, ATPAF1-AS1, ATPAF1, MOB3C, MKNK1, KNCN, DMBX1, LOC513210, FAAH, NSUN4, UQCRH, LOC100847274, LRRC41, RAD54L, POMGNT1, C3H1orf190, TSPAN1 | |
Chr3:94000-94500 | 5.843 | 5.1 × 10−9 | ECHDC2, ZYG11A, ZYG11B, SELRC1, FAM159A, GPX7, ZCCHC11, LOC100138140 | |
Belgian Blue | Chr3:73000-73500 | 8.496 | 0 | NEGR1, LOC512165 |
Chr3:67500-68000 | 6.073 | 1.26 × 10−9 | AK5, PIGK, ST6GALNAC5 | |
Chr16:61000-61500 | 5.833 | 5.44 × 10−9 | RASAL2,C16H1orf49 | |
Chr21:29000-29500 | 5.681 | 1.34 × 10−8 | TJP1, TARSL2, TM2D3, LOC100335373 | |
Chr88:96000-96500 | 5.401 | 6.61 × 10−8 | ANTXR2 | |
Charolais | Chr14:500-1000 | 8.913 | 0 | LOC781635, LOC100140130, LOC100848009, LOC784799 |
Chr14:33000-33500 | 7.945 | 2 × 10−12 | SGK3, C14H80rf45, LOC784087, LOC100847363, TCF24, PPP1R42, COPS5, CSPP1, APFGEF1 | |
Chr9:13500-14000 | 7.000 | 2.56 × 10−12 | CD109, LOC100294729, LOC100336449 | |
Chr22:50000-50500 | 6.401 | 1.54 × 10−10 | DOCK3, MAPKAPK3, CISH, HEMK1, C22H3orf18, CACNA2D2 | |
Chr14:31000-31500 | 6.301 | 2.95 × 10−9 | CYP7B1 | |
Hereford | Chr6:70500-71000 | 6.142 | 8.15 × 10−10 | SCFD2, FIP1L1, LNX1 |
Chr6:69500-70000 | 5.893 | 3.79 × 10−9 | LRRC66, SGCB, LOC100335977, SPATA18, LOC100847183, USP46 | |
Chr6:70000-70500 | 5.794 | 6.88 × 10−9 | USP46, MIR2445, LOC100847282, RASL11B, SCFD2 | |
Chr6:69000-69500 | 5.760 | 8.43 × 10−9 | OCIAD1, OCIAD2, CWH43, DCUN1D4 | |
Chr24:31500-32000 | 5.607 | 2.06 × 10−8 | ZNF521 | |
Holstein- Friesian | Chr13:47000-47500 | 7.088 | 1.36 × 10−12 | DIP2C, ZMYND11, PRNP, PRND, RASSF2 |
Chr13:48000-48500 | 6.670 | 2.55 × 10−11 | GPCPD1, LOC513580, LOC100140729, C13H20orf196, CHGB, TRMT6, MCM8 | |
Chr12:73500-74000 | 6.194 | 5.88 × 10−10 | LOC100337129, LOC100299180, ABCC4, LOC530437 | |
Chr13:46500-47000 | 5.991 | 2.08 × 10−9 | ADARB2, LOC100297660, WDR37, IDI1, GTPBP4, LARP4B, DIP2C | |
Chr8:108000-109000 | 5.951 | 2.67 × 10−9 | ASTN2 | |
Limousin | Chr2:5000-5500 | 9.019 | 0 | LOC507930, PROC, MAP3K2, ERCC3, CYP27C1, LOC784980, LOC524236, BIN1, MIR2350 |
Chr2:6000-6500 | 10.551 | 0 | HIBCH, C2H2orf88, LOC100335775, MSTN, OLC100335809, PMS1 | |
Chr12:73000-73500 | 6.782 | 1.18 × 10−11 | LOC100849031, LOC528412 | |
Chr2:9000-9500 | 6.685 | 2.31 × 10−11 | CALCRL | |
Chr14:500-1000 | 6.648 | 2.98 × 10−11 | LOC781635, LOC100140130, LOC100848009, LOC784799 | |
Simmental | Chr14:500-1000 | 7.124 | 1.05 × 10−12 | LOC781635, LOC100140130, LOC100848009, LOC784799 |
Chr5:64000-64500 | 6.847 | 7.55 × 10−12 | LOC100300928, UHRF1BP1L | |
Chr17:75000-75500 | 6.835 | 8.18 × 10−12 | DGCR8, TRMT2A, RANBP1, LOC526847, LOC100848428, RTN4R, LOC100336451, LOC100138815, LOC100301173, HSFY2, LOC786340, LOC100336511 | |
Chr17:75000-475500 | 6.796 | 1.07 × 10−11 | ESYT1, ZC3H10, LOC100848780, PA2G4, ERBB3, RPS26, IKZF4, SUOX, RAB5B, CDK2, PMEL, DGKA, WIBG, LOC785991, MMP19, MGC142702, DNAJC14, ORMDL2, SARNP, GDF11, CD63, RDH5, BLOC1S1, ITGA7, METTL7B, LOC520938, OR10P1, OR6C4, LOC530539, LOC781363, LOC515967 | |
Chr7:46500-46000 | 5.914 | 3.34 × 10−9 | FSTL4 |