Table 4.
Genes intercepted by a lead SNP associated with body traits based on multi-trait GWAS in Nile tilapia
| Genea | LGb | Positionc | N SNPd | p-valuese | Genomic location |
Traits | |
|---|---|---|---|---|---|---|---|
| Min | Max | ||||||
| CCDC102A | 1 | 39,153,024 | 1 | 3.146E-12 | 3.474E-10 | Intronic | ADG, BWH, WW, HW, HON, BLH |
| ADAMTS9 | 5 | 29,062,243 | 1 | 3.446E-11 | – | Exonic | FW |
| SRGAP1 | 7 | 60,999,336–61,005,198 | 3 | 4.614E-09 | 4.614E-09 | Intronic | HW |
| SLC4A2 | 9 | 14,670,077–14,674,835 | 2 | 5.225E-08 | 5.225E-08 | Intronic | WW |
| MALRD1 | 9 | 16,267,509–16,328,834 | 2 | 1.678E-10 | 5.325E-08 | Intronic | ADG, BWH, HON |
| PTPRN2 | 9 | 16,433,765–16,435,917 | 2 | 4.091E-09 | 4.758E-09 | Intronic | ADG, HW |
| DMXL1 | 12 | 24,525,556 | 1 | 2.379E-11 | – | Intronic | FW |
| MARCH8 | 13 | 17,730,096–17,730,605 | 1 | 2.012E-08 | 2.012E-08 | Intronic | FY |
| MSH6 | 13 | 21,626,153–21,626,426 | 1 | 3.796E-08 | 3.796E-08 | Exonic/Intronic | ADG |
| FUT8 | 15 | 14,457,958 | 1 | 4.861E-08 | – | Intronic | ADG |
| TMEM121 | 15 | 14,662,118 | 1 | 9.425E-10 | 9.844E-09 | Intronic | ADG, BWH, WW |
| MYO6 | 15 | 23,976,527 | 1 | 5.175E-08 | – | Intronic | HON |
| HEG1 | 16 | 12,574,352 | 1 | 3.836E-08 | – | Intronic | FY |
| DOCK9 | 16 | 17,284,162 | 1 | 1.673E-08 | – | Intronic | HW |
| MYO16 | 16 | 20,105,934–20,116,545 | 2 | 3.340E-11 | 1.988E-09 | Intronic/Exonic | ADG, BWH, WW, HON, BLH |
| NUP107 | 17 | 19,609,147–19,612,729 | 2 | 3.815E-08 | 4.102E-08 | Intronic/Exonic | BWH, HON |
| KTN1 | 19 | 11,094,375 | 1 | 7.954E-09 | – | Exonic | ADG |
ADG average daily gain (g), BWH body weight at harvest (g), WW waste weight (g), HW head weight (g), HON gutted head-on weight (g), BLH Body length at harvest (cm), FW fillet weight (g), FY fillet yield (%)
aGenes intercepted by at least one lead SNP based on O_niloticus_UMD_NMBU as reference genome for Oreochromis niloticus
bLinkage group
cIn base pairs
dNumber of lead SNPs
eMinimum (Min) and maximum (Max) p-value for coincident lead SNP for at least two traits