Table 2.
Genome-wide and chromosome-wide significant SNP and potential candidate genes associated with six morphometric traits from four indigenous breeds in Benin
| SNP_rs | SNP | CHR | BP_ARS1.2 | Alleles | MAF | BETA | P-value | SNP in Gene | Gene Name | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A1 | A2 | PLINK | GCTA | PLINK | GCTA | |||||||
| Height at withers | ||||||||||||
| rs109126926a | ARS-BFGL-NGS-57889 | 1 | 110,160,486 | A | G | 0.26 | 2.24 | 2.16 | 1.12e-06 | 1.44e-05 | Yes | VEPH1 |
| rs43347748 | ARS-BFGL-NGS-31952 | 3 | 81,139,242 | C | T | 0.10 | 2.60 | 1.96 | 6.44e-06 | 1.40e-03 | – | – |
| rs41634361 | Hapmap50686-BTA-41836 | 17 | 68,037,062 | G | A | 0.10 | 2.58 | 2.40 | 1.71e-05 | 1.99e-04 | Yes | CCDC117 |
| rs110369628 | ARS-BFGL-NGS-91812 | 19 | 20,892,297 | T | C | 0.02 | 5.58 | 4.55 | 4.82e-05 | 2.00e-03 | Yes | SSH2 |
| rs109889052 | ARS-BFGL-NGS-81151 | 19 | 28,301,046 | A | G | 0.13 | 2.35 | 2.08 | 4.57e-05 | 7.94e-04 | Yes | PIK3R6 |
| rs109872376 | ARS-BFGL-NGS-46597 | 21 | 7,674,101 | C | G | 0.44 | 1.62 | 1.54 | 5.04e-05 | 2.09e-04 | – | – |
| Sacrum height | ||||||||||||
| rs111001850 | ARS-BFGL-NGS-7310 | 7 | 42,545,291 | A | G | 0.45 | 1.53 | 1.50 | 2.35e-05 | 1.12e-04 | No | LYPD8 |
| rs110441360 | ARS-BFGL-NGS-110086 | 20 | 11,381,378 | A | G | 0.48 | −1.51 | −1.51 | 3.86e-05 | 1.19e-04 | No | PIK3R1 |
| Heart girth | ||||||||||||
| rs110404606 | ARS-BFGL-NGS-77689 | 2 | 32,163,209 | C | T | 0.38 | 2.83 | 2.55 | 1.17e-05 | 9.65e-05 | – | – |
| rs41579167 | BTA-49621-no-rs | 2 | 125,244,296 | G | A | 0.44 | −2.93 | −2.75 | 1.55e-05 | 5.59e-05 | No |
PTAFR EYA3 |
| rs41624005 | Hapmap48676-BTA-18047 | 19 | 46,729,603 | A | G | 0.50 | 2.72 | 2.64 | 1.60e-05 | 4.29e-05 | – | – |
| rs41637645 | Hapmap39844-BTA-54797 | 22 | 48,208,654 | C | A | 0.16 | −3.48 | −3.36 | 4.10e-05 | 8.96e-05 | Yes | PBRM1 |
| Hip width | ||||||||||||
| rs109866742 | ARS-BFGL-NGS-119529 | 8 | 103,907,956 | T | C | 0.02 | −3.12 | −3.06 | 2.11e-05 | 5.89e-05 | – | – |
| rs41569598 | BTA-39611-no-rs | 16 | 56,426,595 | C | T | 0.43 | −0.97 | −0.97 | 2.99e-05 | 3.88e-05 | – | – |
| rs42843320 | BTB-01732320 | 16 | 60,525,984 | C | T | 0.22 | −1.12 | −1.15 | 2.08e-05 | 1.47e-05 | Yes | ABL2 |
| Body length | ||||||||||||
| rs110694334a | ARS-BFGL-NGS-109828 | 2 | 76,610,609 | C | T | 0.03 | −17.96 | −11.94 | 8.19e-07 | 4.90e-04 | yes | CNTNAP5 |
| rs109186122 | ARS-BFGL-NGS-118432 | 2 | 78,925,610 | C | T | 0.25 | −7.18 | −3.43 | 9.33e-06 | 2.48e-02 | yes | GYPC |
| rs42301516 | BTB-01145402 | 2 | 113,155,761 | G | A | 0.43 | −5.45 | −4.31 | 1.38e-05 | 1.37e-04 | – | – |
| rs135705191 | BovineHD0300010335 | 3 | 33,048,892 | G | A | 0.20 | −6.85 | −3.72 | 2.49e-05 | 1.90e-02 | yes | SLC16A4 |
| rs43616983 | BTB-00409355 | 10 | 12,969,418 | G | A | 0.20 | 6.70 | 6.20 | 3.41e-05 | 2.94e-05 | yes | MEGF11 |
| rs42436268 | BTB-01308172 | 17 | 33,487,976 | G | T | 0.32 | 5.45 | 4.06 | 4.93e-05 | 8.18e-04 | – | – |
| rs41608167 | BTA-96370-no-rs | 21 | 3,408,269 | T | C | 0.02 | −18.36 | −9.53 | 3.74e-05 | 2.29e-02 | – | – |
| rs41607390a | Hapmap33092-BTA-51753 | 21 | 18,775,375 | T | C | 0.11 | −10.39 | −7.07 | 2.03e-07 | 2.20e-04 | – | – |
| rs41646754 | Hapmap44720-BTA-62525 | 27 | 24,546,315 | G | C | 0.27 | −6.28 | −4.04 | 1.91e-05 | 3.27e-03 | – | – |
| Ear length | ||||||||||||
| rs109212458 | ARS-BFGL-NGS-85383 | 7 | 96,266,192 | T | C | 0.33 | 0.42 | 0.38 | 2.54e-05 | 1.63e-04 | – | – |
| rs110608572 | ARS-BFGL-NGS-103122 | 10 | 12,919,428 | A | G | 0.03 | 1.10 | 1.07 | 1.86e-05 | 4.40e-05 | Yes | MEGF11 |
| rs41567897 | BTA-100327-no-rs | 12 | 41,375,572 | C | G | 0.17 | −0.59 | −0.49 | 1.08e-05 | 3.56e-04 | – | – |
| rs109985119 | ARS-BFGL-NGS-44763 | 20 | 40,060,386 | T | C | 0.14 | 0.56 | 0.54 | 1.90e-05 | 4.23e-05 | Yes | ADAMTS12 |
aGenome-wide significant SNP; the remaining SNP are the chromosome-wide significant SNP