Table 2

Haplotype blocks, marker and candidate gene information
Effect of Major Allele r MKG – RZR within genotypes
Chr. HTB size Kb (sig. markers/total) Most significant marker (bp) MAF Traits DIM ø first 60 DIM 305-days A1A1 A2A2 # Genes in HTB Candidate genes
5 381.05 (1/3) ARS-BFGL-NGS-116999 (99,656,229) 0.21 FC 41-60 ns −0.008 −0.26 *** −0.17 0
383.08 (2/8) Hapmap49734-BTA-74577 (101,015,511) 0.09 FC 31-60 ns −0.011 −0.26 *** 0.08 3
56.34 (1/3) Hapmap60021ss46526426 (101,979,582) 0.43 FC 51-60 ns +0.006 −0.27 *** −0.20*** 2
6 322.61 (1/7) Hapmap50464-BTA-77021 (84,174,079) 0.12 PC 11-20 −0.004 ns −0.25 *** −0.41 † 1
38.98 (1/2) Hapmap25708-BTC-043671 (88,263,656) 0.27 PC 11-50 −0.003 ns −0.25 *** −0.30 *** 1 CSN1S1
181.84 (1/3) ARS-BFGL-NGS-112872 (89,212,072) 0.32 PC 11-40 −0.003 ns −0.29 *** −0.20 *** 4
44.76 (1/2) ARS-BFGL-NGS-118182 (89,774,922) 0.44 PC 11-60 −0.003 ns −0.26 *** −0.22 ** 0
90.40 (1/5) BTB-00277427 (106,066,499) 0.13 NRh ns +0.59 −0.23 *** −0.19 1 KLHL8
14 393.07 (7/7) ARS-BFGL-NGS-4939 (443,937) 0.32 MY 11-60 +1.435 +66.195 −0.21 *** −0.39 *** 25 DGAT1
FY 11-60 −0.073 −1.905
PY 51-60 +0.024 +1.051
FC 11-60 −0.018 −0.028
PC 11-60 −0.005 −0.009
83.26 (2/2) ARS-BFGL-NGS-107379 (679,600) 0.37 MY 11-60 +1.397 +58.401 −0.20 *** −0.39 *** 3
FY 11-60 −0.053 −1.415
PY 31-60 +0.025 +1.040
FC 11-60 −0.015 −0.023
PC 11-60 −0.004 −0.007
21.46 (2/2) ARS-BFGL-NGS-18365 (741,867) 0.29 MY 41-60 −0.840 −32.466 0
FY 11-60 +0.043 +1.160
FC 11-60 +0.010 +0.016
PC 21-60 +0.003 +0.005
21.84 (2/2) Hapmap25384-BTC-001997 (835,054) 0.49 MY 21-60 +0.872 +33.402 3
FY 11-60 −0.030 −0.849
FC 11-60 −0.008 −0.013
PC 11-60 −0.003 −0.004
102.73 (3/3) BTA-35941-no-rs (894,252) 0.44 MY 31-60 +0.824 +30.112 −0.22 *** −0.30 *** 8
FY 11-60 −0.044 −1.254
FC 11-60 −0.010 −0.015
PC 11-60 −0.003 −0.005
UA-IFASA-6878 (1,044,041) 0.49 MY 21-60 −1.000 −41.885 −0.29 *** −0.20 *** 0
FY 11-60 +0.041 +1.053
PY 305d ns −0.666
FC 11-60 +0.011 +0.017
PC 11-60 +0.003 +0.006
91.70 (3/3) ARS-BFGL-NGS-103064 (1,193,336) 0.48 MY 31-60 −0.850 −29.853 3 CYP11B
FY 11-60 +0.027 +0.763
FC 11-60 +0.007 +0.011
PC 31-60 +0.002 +0.003
29.09 (2/2) Hapmap30086-BTC-002066 (1,490,178) 0.47 MY 31-60 −0.801 −29.959 −0.31 *** −0.24 *** 2
FY 11-60 +0.050 +1.338
FC 11-60 +0.010 +0.016
PC 21-60 +0.003 +0.004
60.69 (2/2) ARS-BFGL-NGS-74378 (1,889,210) 0.34 FC 11-60 −0.005 −0.008 1
115.11 (1/3) UA-IFASA-9288 (2,201,870) 0.30 FC 305d ns −0.007 1
95.92 (1/3) ARS-BFGL-NGS-56327 (2,580,414) 0.38 FC 41-60 −0.027 −0.811 1
FC 41-60 −0.005 −0.007
82.03 (1/3) UA-IFASA-5306 (2,711,615) 0.30 FC 305d ns −0.007 0
18 271.14 (1/3) ARS-BFGL-NGS-109285 (57,125,869) 0.13 PC 11-30 +0.004 ns −0.27 *** −0.26 † 17 SICLEC12
27 89.19 (1/4) ARS-BFGL-NGS-57448 (38,878,780) 0.35 FY 11-40 +0.030 ns −0.19 *** −0.29 *** 2 AGPAT6
FC 11-60 +0.006
28 21.15 (1/2) ARS-BFGL-NGS-103007 (6,863,680) 0.13 NRh ns −0.59 −0.24 *** −0.27 1 NID1

This table summarizes the information for the most significant marker in each haplotype block. We give the minor allele frequency, trait and the days in milk for which this marker showed significant effects. The days in milk cover one or more intervals used in the analyses and the effects of the major allele are given as an average over all intervals that this marker had significant effects. The correlations r in this table refer to the correlations between the traits milk yield and fertility index where we separated these correlation for homozygous animals carrying the major or minor allele. In the last two columns are the number of genes given that lay within the haplotype block and the possible candidate genes that might have an effect on the traits under investigation.

P-values *** < 0.0001 ** < 0.001 * < 0.01 † < 0.05 NA non-significant.

HTB: haplotype block; MY: milk yield; FY: fat yield; PY: protein yield; FC: fat content; PC: protein content; RZR: fertility index, summarizing all fertility traits; NRh: non-return rate for heifers; DIM: days in milk; ns: non-significant; A1 is the major allele.

Strucken et al.

Strucken et al. BMC Genetics 2012 13:108   doi:10.1186/1471-2156-13-108

Open Data