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Table 1 Regions of the genome associated with a run of homozygosity of at least 4 Mb for milk and fertility traits across countries

From: Investigation of regions impacting inbreeding depression and their association with the additive genetic effect for United States and Australia Jersey dairy cattle

Countrya Trait BTA (Region)b Locationc Frequency P-value*
Single marker regression Gradient boosted machine
US Milk Yield 7 (96.2–96.7) 96,541,131 0.07 0.0005 0.07
13 (19.3–19.9) 19,388,240 0.10 0.0001 0.02
23 (32.7–33.3) 32,682,177 0.18 0.0001 0.0019
25 (24.8–27.5) 25,450,477 0.05 0.00009 0.03
25 (29.1–29.9) 29,113,430 0.06 0.0009 -
Fat Yield 8 (82.5–83.4) 83,048,502 0.08 0.0003 0.19
8 (106.6–107.1) 106,817,894 0.11 0.0002 0.07
19 (12.7–15.5) 14,409,010 0.07 0.0002 0.005
20 (34.7–36.3) 36,240,997 0.24 0.0003 0.04
23 (32.7–33.3) 32,682,177 0.18 0.0003 0.04
Protein Yield 7 (96.1–96.7) 96,192,503 0.07 0.0002 0.04
13 (19.3 – 19.5) 19,388,240 0.10 0.0004 0.16
23 (31.9–33.3) 32,682,177 0.18 0.00008 0.004
25 (24.8–30.7) 29,113,430 0.06 0.00002 0.02
Calving Interval 7 (82.1–83.0) 82,173,456 0.09 0.0004 0.003
AU Milk Yield 17 (72.1–73.5) 73,055,503 0.04 0.00004 0.03
20 (28.4–29.5) 29,322,034 0.33 0.0001 0.04
Fat Yield 2 (90.4–91.1) 91,117,564 0.16 0.0004 0.08
3 (113.8–114.2) 113,930,518 0.06 0.0007 0.20
7 (6.6–16.7) 8,860,921 0.17 0.00007 0.02
17 (72.1–75.0) 73,257,794 0.04 0.00002 0.006
18 (50.8–53.0) 52,024,379 0.15 0.00001 0.005
Protein Yield 3 (113.4–114.6) 113,845,303 0.06 0.000006 0.02
7 (8.8–12.8) 8,860,921 0.17 0.0003 0.05
17 (68.9–75.0) 73,055,503 0.04 0.0000008 0.005
18 (49.0–52.2) 49,446,631 0.13 0.0005 0.47
  1. aAU refers to Australia and US refers to United States
  2. bBTA refers to chromosome and the region and location are in Mb build UMD 3.1 (http://bovinegenome.org/cgi-bin/gbrowse/bovine_UMD31/)
  3. cReferrs to the location with regions with the highest significance based on Single Marker Regression Analysis
  4. *P-values were generated based on a permutation test (Doerge and Churchill [23]) for each analysis