Table 2.
DNA regions of chromosomes 18, 21, 25 and X containing SNPs that were significantly associated with body conformation traits of dairy cows
| Chromosome | Trait | Position | SNP name | P‐Value | Nearest gene | Distance 1 | Reference | Alteration | MAF |
|---|---|---|---|---|---|---|---|---|---|
| 18 | AW | 65402237 | BovineHD1800019049 | 4.75E − 07 | LOC789374 | Within | C | T | 0.2143 |
| FS | 4463083 | Hapmap57004‐rs29011610 | 1.17E − 06 | MON1B | D: 5928 | G | A | 0.3129 | |
| FS | 65405023 | BovineHD1800019051 | 2.04E − 06 | LOC789374 | Within | A | G | 0.1179 | |
| MSS | 55956772 | ARS‐BFGL‐NGS‐60829 | 6.86E − 07 | NUCB1 | D: 1160 | C | T | 0.4172 | |
| RA | 55309510 | ARS‐BFGL‐NGS‐116541 | 2.37E − 06 | LIG1 | Within | C | A | 0.4487 | |
| RA | 55514759 | BovineHD1800016250 | 7.28E − 08 | SYNGR4 | Within | T | C | 0.2494 | |
| RA | 55621823 | ARS‐BFGL‐NGS‐31529 | 2.12E − 06 | LMTK3 | Within | T | G | 0.2426 | |
| 21 | FS | 57552028 | BovineHD2100016535 | 8.46E − 07 | SLC24A4 | U: 44433 | A | G | 0.2340 |
| AW | 57583470 | BovineHD2100016545 | 2.26E − 06 | SLC24A4 | U: 12991 | A | G | 0.4478 | |
| AW | 57584406 | BovineHD2100016546 | 2.33E − 06 | SLC24A4 | U: 12055 | A | C | 0.4477 | |
| AW | 57587712 | BovineHD2100016549 | 2.26E − 06 | SLC24A4 | U: 8749 | C | T | 0.4478 | |
| AW | 57620878 | BovineHD2100016561 | 9.13E − 07 | SLC24A4 | Within | G | A | 0.2823 | |
| AW | 57623572 | BovineHD2100016563 | 9.13E − 07 | SLC24A4 | Within | G | A | 0.2823 | |
| 25 | RA | 42364359 | ARS‐BFGL‐NGS‐101981 | 1.32E − 06 | ADAP1 | D: 1441 | T | C | 0.2823 |
| UD | 35623801 | ARS‐BFGL‐NGS‐28167 | 2.16E − 06 | CUX1 | D: 12155 | A | G | 0.4023 | |
| UD | 36266951 | BovineHD2500010029 | 1.27E − 07 | LOC100298352 | Within | T | C | 0.3560 | |
| RA | 31147780 | Hapmap24744‐BTC‐028427 | 1.82E − 08 | LOC100301342 | Within | T | C | 0.3898 | |
| FS | 40192570 | BovineHD4100017518 | 1.07E − 06 | SDK1 | Within | T | C | 0.03061 | |
| X | FS | 12103258 | BovineHD3000003945 | 8.38E − 07 | ACTRT1 | U: 55118 | G | A | 0.1497 |
| RA | 2037499 | BovineHD3000000680 | 2.28E − 06 | KLHL13 | Within | C | A | 0.03855 | |
| AG | 116273044 | BovineHD3000032546 | 6.55E − 07 | LOC537655 | Within | C | A | 0.3061 | |
| MS | 138304543 | BovineHD3000039710 | 5.31E − 07 | LOC782196 | U: 18403 | T | C | 0.2130 | |
| AG | 110222328 | BTA‐116883‐no‐rs | 1.56E − 06 | LOC786124 | D: 27320 | G | A | 0.2404 | |
| AG | 132705219 | BovineHD3000037672 | 5.10E − 08 | LOC786725 | U: 54284 | T | C | 0.4490 | |
| MSS | 132705219 | BovineHD3000037672 | 7.03E − 08 | LOC786725 | U: 54284 | T | C | 0.4490 | |
| RA | 141936249 | BTA‐21001‐no‐rs | 2.16E − 06 | MSL3 | U: 105193 | C | T | 0.1939 |
AW, Attachment width; FS, conformation final score; MSS, mammary system score; RA, rump angle; UD, udder depth; AG, angularity; MS, median suspensory; MAF means minor allele frequency.
1
The distance from the SNP locus to the gene (unit: bp); D and U indicate that the SNP site is located downstream and upstream of the gene, respectively; ‘Within’ indicates that the SNP locus is located within the gene.