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Table 2 Genomic regions that potentially display pairwise epistatic interaction based on the high frequency of it being descendent pair 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 SNP 1 SNP 2 Average depth P-value* Individual rank based on importance score
BTAb Locationb BTAb Locationb SNP 1 SNP 2
US Milk Yield 23 32,682,177 5 95,459,836 1.18 0.0003 1 5
30 140,296,904 20 69,528,142 1.24 0.0009 14 30
19 14,409,010 11 10,271,653 1.24 0.0009 3 46
Fat Yield 19 41,615,615 19 14,409,010 1.42 0.0002 2 1
19 41,615,615 2 83,919,557 1.36 0.0006 2 7
11 56,825,445 5 62,248,841 1.29 0.0006 6 10
12 12,685,397 7 96,192,503 1.16 <0.001 31 15
Protein Yield 23 32,682,177 1 24,549,757 1.41 0.0005 1 19
9 7,645,969 1 24,549,757 1.05 0.0009 65 19
25 29,428,407 2 113,716,333 1.30 0.0009 2 4
Calving Interval 7 82,173,456 2 83,616,368 1.53 0.0002 1 3
25 17,166,118 9 44,951,803 1.18 0.0006 7 2
26 30,607,485 7 82,173,456 1.15 0.0006 12 1
7 82,173,456 7 41,207,144 1.43 0.0007 1 5
8 34,242,903 7 82,173,456 1.43 0.0009 32 1
AU Milk Yield 22 39,545,402 1 112,497,788 1.03 0.0002 25 14
21 62,115,138 11 38,445,947 1.04 0.0003 35 47
14 16,526,322 1 13,304,658 1.27 0.0004 68 17
20 35,012,179 20 29,322,034 1.46 0.0006 51 3
22 31,649,896 16 42,262,470 1.32 0.0008 4 41
Fat Yield 6 56,522,979 2 13,411,225 1.08 0.0002 10 18
9 59,036,606 8 51,460,409 1.73 0.0005 5 3
8 51,460,409 7 8,860921 1.26 0.0009 3 4
Protein Yield 14 38,155,245 7 107,837,688 1.27 0.00007 2 18
17 38,275,065 17 5,445,294 1.38 0.0005 17 20
14 38,155,245 8 51,695,384 1.40 0.0006 2 22
16 64,623,464 11 109,818 1.00 0.0008 42 11
Calving Interval 24 37,002,274 24 7,380,047 1.04 0.0003 16 44
5 33,334,061 3 9,686,101 1.38 0.0004 1 3
15 16,416,329 10 53,560,658 1.25 0.0004 14 6
17 9,753,430 3 80,517,326 1.40 0.0009 8 27
  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. *P-values were generated based on a permutation test (Doerge and Churchill [23]) for each analysis