Table 3.
Genomic regions and the closest candidate genes for the top five lead SNPs associated with body traits based on multi-trait GWAS in Nile tilapia
| Markera | LGb | Positionc | Alleles | MAFd | p-value | Closest genese |
|---|---|---|---|---|---|---|
| Average daily gain | ||||||
| 12:24557870 | 12 | 24,557,870 | [A/G] | 0.069 | 2.627E-15 | HSD17B4, SEMA6A |
| 12:24557984 | 12 | 24,557,984 | [T/C] | 0.069 | 2.627E-15 | HSD17B4, SEMA6A |
| 22:11998439 | 22 | 11,998,439 | [G/A] | 0.059 | 2.800E-12 | DPY19L4, GDF6 |
| 1:39153024 | 1 | 39,153,024 | [G/A] | 0.052 | 2.821E-11 | CCDC102A, HDGFL3 |
| 1:39193509 | 1 | 39,193,509 | [A/G] | 0.052 | 2.821E-11 | uncharacterized |
| Body weight at harvest | ||||||
| 12:24557870 | 12 | 24,557,870 | [A/G] | 0.069 | 4.055E-15 | HSD17B4, SEMA6A |
| 12:24557984 | 12 | 24,557,984 | [T/C] | 0.069 | 4.055E-15 | HSD17B4, SEMA6A |
| 1:39153024 | 1 | 39,153,024 | [G/A] | 0.052 | 2.444E-10 | CCDC102A, HDGFL3 |
| 1:39193509 | 1 | 39,193,509 | [A/G] | 0.052 | 2.444E-10 | uncharacterized |
| 1:39558113 | 1 | 39,558,113 | [G/A] | 0.052 | 2.444E-10 | ZNF536, CCNE1 |
| Waste weight | ||||||
| 12:24557870 | 12 | 24,557,870 | [A/G] | 0.069 | 2.512E-15 | HSD17B4, SEMA6A |
| 12:24557984 | 12 | 24,557,984 | [T/C] | 0.069 | 2.512E-15 | HSD17B4, SEMA6A |
| 22:11998439 | 22 | 11,998,439 | [G/A] | 0.059 | 2.130E-12 | DPY19L4, GDF6, KDM1B |
| 16:20105934 | 16 | 20,105,934 | [G/A] | 0.053 | 5.481E-11 | MYO16, IRS2 |
| 16:20116545 | 16 | 20,116,545 | [T/C] | 0.053 | 5.481E-11 | MYO16, IRS2, COL4A1 |
| Head weight | ||||||
| 12:24557870 | 12 | 24,557,870 | [A/G] | 0.069 | 4.084E-15 | HSD17B4, SEMA6A |
| 12:24557984 | 12 | 24,557,984 | [T/C] | 0.069 | 4.084E-15 | HSD17B4, SEMA6A |
| 3:50439330 | 3 | 50,439,330 | [C/T] | 0.109 | 3.113E-13 | uncharacterized |
| 3:50439365 | 3 | 50,439,365 | [T/C] | 0.109 | 3.113E-13 | uncharacterized |
| 4:17899270 | 4 | 17,899,270 | [G/T] | 0.051 | 2.454E-10 | uncharacterized |
| Gutted head-on weight | ||||||
| 12:24557870 | 12 | 24,557,870 | [A/G] | 0.069 | 9.893E-14 | HSD17B4, SEMA6A |
| 12:24557984 | 12 | 24,557,984 | [T/C] | 0.069 | 9.893E-14 | HSD17B4, SEMA6A |
| 3:47137003 | 3 | 47,137,003 | [A/C] | 0.110 | 1.170E-10 | TLR2 |
| 1:39153024 | 1 | 39,153,024 | [G/A] | 0.052 | 1.278E-10 | CCDC102A, HDGFL3 |
| 1:39193509 | 1 | 39,193,509 | [A/G] | 0.052 | 1.278E-10 | uncharacterized |
| Body length at harvest | ||||||
| 22:11998439 | 22 | 11,998,439 | [G/A] | 0.059 | 7.129E-18 | DPY19L4, GDF6, KDM1B |
| 12:27146675 | 12 | 27,146,675 | [C/T] | 0.079 | 1.956E-13 | GPX8, MCIDAS, ISCA1 |
| 1:39153024 | 1 | 39,153,024 | [G/A] | 0.052 | 3.146E-12 | CCDC102A, HDGFL3 |
| 1:39193509 | 1 | 39,193,509 | [A/G] | 0.052 | 3.146E-12 | CCDC102A, HDGFL3 |
| 1:39558113 | 1 | 39,558,113 | [G/A] | 0.052 | 3.146E-12 | CCNE1, ZNF536 |
| Fillet weight | ||||||
| 13:30002073 | 13 | 30,002,073 | [A/G] | 0.174 | 1.778E-18 | uncharacterized |
| 4:34954382 | 4 | 34,954,382 | [T/C] | 0.107 | 1.193E-14 | SAMD14, PSMD3 |
| 4:34954397 | 4 | 34,954,397 | [A/G] | 0.107 | 1.193E-14 | SAMD14, PSMD3 |
| 4:34958811 | 4 | 34,958,811 | [A/G] | 0.107 | 1.193E-14 | SAMD14, PSMD3 |
| 4:34958990 | 4 | 34,958,990 | [G/A] | 0.107 | 1.193E-14 | SAMD14, PSMD3 |
| Fillet yield | ||||||
| 12:26984411 | 12 | 26,984,411 | [G/A] | 0.066 | 2.388E-12 | uncharacterized |
| 6:33824877 | 6 | 33,824,877 | [T/G] | 0.055 | 4.496E-10 | XYLT1, RPS15A, COQ7 |
| 14:30148797 | 14 | 30,148,797 | [G/T] | 0.056 | 3.015E-09 | uncharacterized |
| 13:17730096 | 13 | 17,730,096 | [C/A] | 0.113 | 2.012E-08 | MARCH8 |
| 13:17730605 | 13 | 17,730,605 | [C/A] | 0.113 | 2.012E-08 | MARCH8 |
aMarkers in bold indicate a common lead SNP in at least two traits
bLinkage group
cPosition in base pairs
dMinor allele frequency
eBased on O_niloticus_UMD_NMBU as reference genome for Oreochromis niloticus. The full list of lead SNPs is available in S2 Table