Table 2.
Genome-wide association study (GWAS) significant associated variants of dog herding, predation, temperament, and trainability behavior traits.
| Trait | Variant | Ref | Alt | Alt_Freq_cases | Alt_Freq_controls | p_value_a | p_value_b | Nearest gene symbol | Distance to gene (bp) |
|---|---|---|---|---|---|---|---|---|---|
| Herding | CFA6:40747205 | A | C | 0.1545 | 0 | 2.20E−09 | 2.75E−09 | LOC611691 | 0 |
| CFA6:41114381 | T | C | 0.1545 | 0 | 2.20E−09 | 2.75E−09 | OR28H03 | 13,451 | |
| CFA7:67137186 | T | G | 0.1759 | 0.0024 | 5.72E−10 | 2.07E−09 | THOC1 | 594 | |
| CFA7:67155662 | C | G | 0.1455 | 0.0023 | 6.50E−10 | 2.07E−09 | THOC1 | 19,070 | |
| CFA7:67163810 | A | T | 0.1132 | 0.0023 | 2.78E−09 | 1.03E−08 | THOC1 | 27,218 | |
| CFA9:40067785 | A | G | 0.0545 | 0 | 2.33E−09 | 4.03E−09 | ASIC2 | 0 | |
| CFA9:40068138 | T | C | 0.0545 | 0 | 2.33E−09 | 4.03E−09 | ASIC2 | 0 | |
| CFA10:8016660 | A | G | 0.8182 | 0.331 | 3.29E−09 | 1.33E−09 | MSRB3 | 0 | |
| CFA10:8116174 | T | G | 0.7455 | 0.2379 | 2.04E−09 | 3.66E−10 | LOC111097584 | 32,715 | |
| CFA10:8116175 | T | C | 0.7455 | 0.2402 | 1.73E−09 | 3.00E−10 | LOC111097584 | 32,716 | |
| CFA10:8116176 | C | G | 0.7455 | 0.239 | 1.38E−09 | 3.00E−10 | LOC111097584 | 32,717 | |
| CFA10:8581163 | C | T | 0.5091 | 0.1056 | 4.40E−10 | 9.63E−10 | LLPH | 50,728 | |
| CFA10:8583785 | T | A | 0.5 | 0.1056 | 1.26E−09 | 2.54E−09 | LLPH | 48,106 | |
| CFA10:8589159 | A | G | 0.4909 | 0.1033 | 2.05E−09 | 3.87E−09 | LLPH | 42,732 | |
| CFA10:8597348 | G | A | 0.4909 | 0.1033 | 1.52E−09 | 2.80E−09 | LLPH | 34,543 | |
| CFA10:8601766 | C | T | 0.5 | 0.1056 | 5.50E−10 | 1.10E−09 | LLPH | 30,125 | |
| CFA10:8604778 | C | T | 0.5091 | 0.1132 | 3.67E−10 | 1.49E−10 | LLPH | 27,113 | |
| CFA10:8614536 | CG | C | 0.5545 | 0.1479 | 2.00E−09 | 4.86E−10 | LLPH | 17,355 | |
| CFA10:8614872 | AAGCTC | A | 0.5545 | 0.1479 | 2.00E−09 | 4.86E−10 | LLPH | 17,091 | |
| CFA10:8615480 | G | A | 0.5545 | 0.1479 | 2.00E−09 | 4.86E−10 | LLPH | 16,411 | |
| CFA10:41504918 | C | CCCTTT | 0.1636 | 0.0236 | 2.98E−10 | 1.03E−09 | RFX8 | 0 | |
| CFA10:41505049 | T | A | 0.1545 | 0.0235 | 1.56E−10 | 5.89E−10 | RFX8 | 0 | |
| CFA10:41506217 | A | G | 0.1636 | 0.0258 | 2.70E−09 | 8.97E−09 | RFX8 | 0 | |
| CFA10:41506301 | C | T | 0.1636 | 0.0258 | 2.70E−09 | 8.97E−09 | RFX8 | 0 | |
| CFA10:41506568 | C | T | 0.1545 | 0.0235 | 2.31E−09 | 7.11E−09 | RFX8 | 0 | |
| CFA10:41506655 | T | C | 0.1636 | 0.0258 | 2.70E−09 | 8.97E−09 | RFX8 | 0 | |
| CFA10:41506849 | C | T | 0.1545 | 0.0235 | 2.31E−09 | 7.11E−09 | RFX8 | 0 | |
| CFA10:41507558 | G | A | 0.1636 | 0.0259 | 2.71E−09 | 8.99E−09 | RFX8 | 0 | |
| CFA20:16594598 | C | T | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 9,375 | |
| CFA20:16595519 | T | C | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 8,454 | |
| CFA20:16595717 | G | A | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 8,256 | |
| CFA20:16595938 | C | T | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 8,035 | |
| CFA20:16596248 | A | AAAG | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 7,725 | |
| CFA20:16596343 | A | G | 0.1296 | 0 | 2.48E−09 | 6.74E−09 | LOC111091431 | 7,630 | |
| CFA20:16596466 | C | T | 0.1273 | 0 | 1.65E−09 | 5.14E−09 | LOC111091431 | 7,507 | |
| CFA20:16596631 | A | G | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 7,342 | |
| CFA20:16597311 | C | T | 0.1455 | 0 | 1.30E−10 | 4.84E−10 | LOC111091431 | 6,662 | |
| CFA20:16598698 | C | G | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 5,275 | |
| CFA20:16603809 | A | C | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 164 | |
| CFA20:16604304 | T | G | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 0 | |
| CFA20:16607008 | A | T | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 0 | |
| CFA20:16607290 | T | C | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 0 | |
| CFA20:16610276 | C | T | 0.1364 | 0 | 8.74E−11 | 3.28E−10 | LOC111091431 | 0 | |
| CFA20:16610335 | G | A | 0.1364 | 0 | 8.48E−11 | 3.16E−10 | LOC111091431 | 0 | |
| Predation | CFA1:93319503 | C | T | 0.1528 | 0.8273 | 2.59E−09 | 1.64E−06 | JAK2 | 1,552 |
| CFA1:93319523 | C | CATG | 0.1528 | 0.8273 | 2.59E−09 | 1.64E−06 | JAK2 | 1,532 | |
| CFA1:93319862 | T | C | 0.1667 | 0.8364 | 1.28E−09 | 1.02E−06 | JAK2 | 1,193 | |
| CFA10:65924498 | T | C | 0.2639 | 0.9091 | 3.96E−10 | 6.02E−09 | MEIS1 | 25,784 | |
| CFA10:65924663 | G | A | 0.2639 | 0.9091 | 3.96E−10 | 6.02E−09 | MEIS1 | 25,949 | |
| CFA10:65924694 | C | G | 0.2639 | 0.9091 | 3.96E−10 | 6.02E−09 | MEIS1 | 25,980 | |
| CFA10:65924801 | G | A | 0.2639 | 0.9091 | 3.96E−10 | 6.02E−09 | MEIS1 | 26,087 | |
| CFA10:65925175 | C | G | 0.2639 | 0.9091 | 3.96E−10 | 6.02E−09 | MEIS1 | 26,461 | |
| CFA17:47109846 | C | T | 0.3056 | 0.8182 | 2.97E−09 | 4.16E−10 | LRRTM4 | 312,739 | |
| CFA17:47109848 | C | T | 0.3056 | 0.8182 | 2.97E−09 | 4.16E−10 | LRRTM4 | 312,741 | |
| CFA17:47109850 | T | A | 0.3056 | 0.8182 | 2.97E−09 | 4.16E−10 | LRRTM4 | 312,743 | |
| CFA17:47109882 | C | T | 0.3056 | 0.8182 | 2.97E−09 | 4.16E−10 | LRRTM4 | 312,775 | |
| Temperament | CFA15:23340008 | A | T | 0.7019 | 0.284 | 1.54E−08 | 1.92E−09 | ACSS3 | 0 |
| Trainability | CFA22:34873149 | A | G | 0.5941 | 0.1633 | 5.94E−08 | 7.92E−08 | LOC111091672 | 19,895 |
Bold indicates significantly associated variants that were identified in GWASs both without and with body size as a covariate.
p_value_a, GWASs without body size as a covariate; p_value_b, GWASs with body size as a covariate.