Table 2.
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 |
aAU refers to Australia and US refers to United States
bBTA refers to chromosome and the region and location are in Mb build UMD 3.1 (http://bovinegenome.org/cgi-bin/gbrowse/bovine_UMD31/)
*P-values were generated based on a permutation test (Doerge and Churchill [23]) for each analysis