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Table 1 Number of top 100 SNP effects from the least squares analysis without stratification correction that overlapped with the top 100 effects from EMMAX-IBS (E), GLS (G), and PCA (P) methods for stratification correction

From: Effect of sample stratification on dairy GWAS results

Traits E G P EG EP GP EGP
MY 7 15 6 2 2 4 1
FY 4 2 0 1 0 0 0
PY 1 5 0 0 0 0 0
FPC 28 23 22 23 22 22 22
PPC 8 3 3 1 1 3 1
PL 6 10 1 3 0 1 0
SCS 6 7 0 0 0 0 0
DPR 7 8 2 3 2 2 2
SCE 8 3 2 0 2 0 0
DCE 3 3 0 1 0 0 0
SSB 8 6 6 2 6 2 2
DSB 6 11 2 0 0 0 0
NM 4 1 0 0 0 0 0
Total 96 97 44 36 35 34 28
STA 11 24 1 5 1 0 0
STR 5 12 0 1 0 0 0
BD 7 14 0 2 0 0 0
RW 12 31 2 6 1 1 1
DF 8 7 1 1 1 1 1
RA 19 22 6 10 4 6 4
FUA 6 13 1 1 1 0 0
RUH 9 13 4 2 2 0 0
UD 5 14 0 3 0 0 0
UC 13 10 3 2 3 0 0
FTP 17 16 5 6 4 2 2
RTP 12 13 3 2 3 0 0
TL 16 8 5 3 5 1 1
FA 6 15 4 4 1 2 1
RLS 2 2 6 2 1 1 1
RLR 5 18 3 4 0 1 0
FL 11 14 3 6 2 2 2
FS 10 21 4 0 2 0 0
Total 174 267 51 60 31 17 13
  1. E, EMMAX-IBS; G, GLS; P, PCA; 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; DCE, daughter calving ease; SSB, service-sire stillbirth; DSB, daughter stillbirth; NM, net merit; STA, stature; STR, strength; BD, body depth; DF, dairy form; RA, rump angle; RW, rump width; FUA, fore udder attachment; RUH, rear udder height; UD, udder depth; UC, udder cleft; FTP, front teat placement; RTP, rear teat placement; TL, teat length; FA, foot angle; RLS, rear legs (side view); RLR, rear legs (rear view); FL, feet/legs score; FS, final score.