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Table 2 Consensus between the top 20 AIPL effects and the top 20 significant effects of the four methods of SNP testing, LS, EMMAX-IBS, GLS, and PCA

From: Effect of sample stratification on dairy GWAS results

Traits Range of top 20  AIPL effects LS1 EMMAX -IBS1 GLS1 PCA1 Gene region
MY 9.1540 – 10.3909 - 1-16 2-1, 1–2, - BTA14: A5D786-CYHR1-
4-4, 7–5, VPS28-DGAT1,
3,6~8 2 A5D786-GML 2
FY 0.3717 – 3.1325 - 1-1 1-1 1-1 BTA14: DGAT1
PY 0.2409 – 0.6798 5-1 5-5 3-4,6 - BTA18: LOC100139758
53.95 Mb
BTA14: DGAT1
       BTA14: A5D786,VPS28
FPC 0.0022 – 0.0191 1-1, 11-9 1-1 1-1 1-1 BTA14: DGAT1
       BTA5: 93.2 Mb
PPC 9.00E-04 – 0.0047 - 1-1 1-1 1-1 BTA6: HERC3-PIGY
PL 0.0240 – 0.1608 2-16,2 1-2 - 1-1 BTA18: SIGLEC12
53.95 Mb and LOC787057
SCS 0.0026 – 0.0139 1-10 - 1-16 - BTA6: GC-NPFFR2
DPR 0.0175 – 0.0517 3-6 - - - BTA18: SIGLEC12, LOC787057
SCE 0.0231 – 0.0139 1-1,4 1-4 - 3-4 BTA18:SIGLEC12,
53.95 Mb and LOC787057
SSB 0.0096 – 0.0554 - - - 3-17 BTA18: SIGLEC12
DCE 0.0173 – 0.1061 1-1,2 - - - BTA18: SIGLEC12,
53.95 Mb and LOC787057
NM 2.2525 – 16.2685 2-1,4 - - - BTA18: SIGLEC12,
53.95 Mb and LOC787057
STA 0.0160 – 0.0453 3-19, - 3-14, - BTAX: MIR584-8~KAL1,
12-12   7,12-9,10 BTA11: LOC529399
     BTA11: LOC521556
     BTAX: 145.06 Mb
BD 0.0087 – 0.0458 - 3-1 - 5-2 BTA18: SIGLEC12
RW 0.0144 – 0.0394 1-4 5-1 - - BTAX: 145.24 Mb,
BTA18: SIGLEC12
DF 0.0140 – 0.0544 - 1-1 - - BTAX: MIR584-8~KAL1
FUA 0.0146 – 0.0465 2-16 - - - BTAX: MIR584-8~KAL1
RUH 0.0146 – 0.0767 1-6 - - - BTAX: MIR584-8~KAL1
FTP 0.0126 – 0.0482 - 17-7 - 17-2 BTA7: SNCAIP-ZNF474
FS 0.0100 – 0.0673 1-7 - - - BTAX: MIR584-8~KAL1
  1. MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; PL, productive life; SCS, somatic cell score; DPR, daughter pregnancy rate; SCE, service-sire calving ease; SSB, service-sire stillbirth; DCE, daughter calving ease; NM, net merit; STA, stature; BD, body depth; DF, dairy form; RW, rump width; FUA, fore udder attachment; RUH, rear udder height; FTP, front teat placement; FS, final score.
  2. 1 The number on the left is the AIPL effect rank and the number on the right is the significance rank of this method for the same marker effect.
  3. 2 Underlined ranking is not an exact match to an AIPL effect and the exact location is the underlined location in the same row under ‘Gene region’.