Table 1. Descriptive statistics for phenotypic body traits recorded in a breeding Nile tilapia population.
Traits
|
Mean
|
CV (%)
|
SD
|
Min
|
Max
|
AT (days)
|
113
|
15.32
|
17
|
76
|
160
|
Age (days)
|
370
|
5.41
|
20
|
330
|
427
|
BWT
|
32.97
|
78.95
|
26.03
|
6.00
|
266.00
|
ADG
|
3.54
|
26.27
|
0.93
|
0.69
|
6.29
|
BWH
|
943.98
|
26.01
|
245.54
|
198.00
|
1654.00
|
WW
|
642.84
|
25.76
|
165.60
|
146.00
|
1139.00
|
HW
|
245.62
|
24.11
|
59.23
|
69.00
|
469.00
|
HON
|
556.19
|
26.86
|
149.39
|
108.00
|
993.00
|
BLH
|
27.59
|
9.28
|
2.56
|
17.00
|
37.00
|
FW
|
300.93
|
27.47
|
82.67
|
85.00
|
528.00
|
FY
|
31.76
|
6.86
|
2.18
|
20.00
|
42.04
|
AT: age at tagging; BWT: body weight at tagging (g); ADG: average daily gain (g); BWH: harvest weight (g); WW: waste weight (g); HW: head weight (g); HON: Hon weight (g); BLH: Harvest length (cm); FW: fillet weight (g); FY: fillet yield (%).
Table 2. Genetic parameters and comparison of association results between single- and multi-trait GWAS for Nile tilapia.
Trait
|
σ_a^2 |
h^2 |
SE
|
Single-trait
|
|
Multi-trait
|
Significant
SNP
|
-log (p-value)1
|
Mean χ^2
|
|
Significant
SNP1
|
-log (p-value)1
|
Mean χ^2
|
N GWAS equivalent
|
ADG
|
0.406
|
0.422
|
0.046
|
1
|
7.524
|
1.674
|
|
1359
|
14.581
|
1.815
|
1582
|
BWH
|
27334.76
|
0.423
|
0.045
|
1
|
7.632
|
1.693
|
|
1209
|
14.392
|
1.781
|
1474
|
WW
|
10937.59
|
0.386
|
0.046
|
1
|
7.454
|
1.718
|
|
1347
|
14.600
|
1.907
|
1654
|
HW
|
1658.12
|
0.450
|
0.045
|
0
|
5.706
|
1.727
|
|
1595
|
14.389
|
1.898
|
1617
|
HON
|
10516.63
|
0.435
|
0.045
|
1
|
7.452
|
1.514
|
|
1138
|
13.005
|
1.694
|
1766
|
BLH
|
2.855
|
0.414
|
0.045
|
0
|
5.631
|
1.749
|
|
827
|
17.147
|
2.081
|
1890
|
FW
|
2951.46
|
0.343
|
0.045
|
1
|
7.592
|
1.541
|
|
833
|
17.750
|
1.649
|
1605
|
FY
|
0.0001
|
0.210
|
0.039
|
1
|
8.503
|
1.273
|
|
1920
|
11.622
|
1.335
|
1569
|
1For the most significant SNP; ADG: average daily gain (g); BWH: harvest weight (g); WW: waste weight (g); HW: head weight (g); HON: Hon weight (g); BLH: Harvest length (cm); FW: fillet weight (g); FY: fillet yield (%).
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.
Marker1
|
LG2
|
Position3
|
Alleles
|
MAF4
|
p-value
|
Closest genes5
|
Average daily gain
|
12:24557870
|
12
|
24557870
|
[A/G]
|
0.069
|
2.627E-15
|
HSD17B4, SEMA6A
|
12:24557984
|
12
|
24557984
|
[T/C]
|
0.069
|
2.627E-15
|
HSD17B4, SEMA6A
|
22:11998439
|
22
|
11998439
|
[G/A]
|
0.059
|
2.800E-12
|
DPY19L4, GDF6
|
1:39153024
|
1
|
39153024
|
[G/A]
|
0.052
|
2.821E-11
|
CCDC102A, HDGFL3
|
1:39193509
|
1
|
39193509
|
[A/G]
|
0.052
|
2.821E-11
|
uncharacterized
|
Body weight at harvest
|
12:24557870
|
12
|
24557870
|
[A/G]
|
0.069
|
4.055E-15
|
HSD17B4, SEMA6A
|
12:24557984
|
12
|
24557984
|
[T/C]
|
0.069
|
4.055E-15
|
HSD17B4, SEMA6A
|
1:39153024
|
1
|
39153024
|
[G/A]
|
0.052
|
2.444E-10
|
CCDC102A, HDGFL3
|
1:39193509
|
1
|
39193509
|
[A/G]
|
0.052
|
2.444E-10
|
uncharacterized
|
1:39558113
|
1
|
39558113
|
[G/A]
|
0.052
|
2.444E-10
|
ZNF536, CCNE1
|
Waste weight
|
12:24557870
|
12
|
24557870
|
[A/G]
|
0.069
|
2.512E-15
|
HSD17B4, SEMA6A
|
12:24557984
|
12
|
24557984
|
[T/C]
|
0.069
|
2.512E-15
|
HSD17B4, SEMA6A
|
22:11998439
|
22
|
11998439
|
[G/A]
|
0.059
|
2.130E-12
|
DPY19L4, GDF6, KDM1B
|
16:20105934
|
16
|
20105934
|
[G/A]
|
0.053
|
5.481E-11
|
MYO16, IRS2
|
16:20116545
|
16
|
20116545
|
[T/C]
|
0.053
|
5.481E-11
|
MYO16, IRS2, COL4A1
|
Head weight
|
12:24557870
|
12
|
24557870
|
[A/G]
|
0.069
|
4.084E-15
|
HSD17B4, SEMA6A
|
12:24557984
|
12
|
24557984
|
[T/C]
|
0.069
|
4.084E-15
|
HSD17B4, SEMA6A
|
3:50439330
|
3
|
50439330
|
[C/T]
|
0.109
|
3.113E-13
|
uncharacterized
|
3:50439365
|
3
|
50439365
|
[T/C]
|
0.109
|
3.113E-13
|
uncharacterized
|
4:17899270
|
4
|
17899270
|
[G/T]
|
0.051
|
2.454E-10
|
uncharacterized
|
Hon weight
|
12:24557870
|
12
|
24557870
|
[A/G]
|
0.069
|
9.893E-14
|
HSD17B4, SEMA6A
|
12:24557984
|
12
|
24557984
|
[T/C]
|
0.069
|
9.893E-14
|
HSD17B4, SEMA6A
|
3:47137003
|
3
|
47137003
|
[A/C]
|
0.110
|
1.170E-10
|
TLR2
|
1:39153024
|
1
|
39153024
|
[G/A]
|
0.052
|
1.278E-10
|
CCDC102A, HDGFL3
|
1:39193509
|
1
|
39193509
|
[A/G]
|
0.052
|
1.278E-10
|
uncharacterized
|
Body length at harvest
|
22:11998439
|
22
|
11998439
|
[G/A]
|
0.059
|
7.129E-18
|
DPY19L4, GDF6, KDM1B
|
12:27146675
|
12
|
27146675
|
[C/T]
|
0.079
|
1.956E-13
|
GPX8, MCIDAS, ISCA1
|
1:39153024
|
1
|
39153024
|
[G/A]
|
0.052
|
3.146E-12
|
CCDC102A, HDGFL3
|
1:39193509
|
1
|
39193509
|
[A/G]
|
0.052
|
3.146E-12
|
CCDC102A, HDGFL3
|
1:39558113
|
1
|
39558113
|
[G/A]
|
0.052
|
3.146E-12
|
CCNE1, ZNF536
|
Fillet weight
|
13:30002073
|
13
|
30002073
|
[A/G]
|
0.174
|
1.778E-18
|
uncharacterized
|
4:34954382
|
4
|
34954382
|
[T/C]
|
0.107
|
1.193E-14
|
SAMD14, PSMD3
|
4:34954397
|
4
|
34954397
|
[A/G]
|
0.107
|
1.193E-14
|
SAMD14, PSMD3
|
4:34958811
|
4
|
34958811
|
[A/G]
|
0.107
|
1.193E-14
|
SAMD14, PSMD3
|
4:34958990
|
4
|
34958990
|
[G/A]
|
0.107
|
1.193E-14
|
SAMD14, PSMD3
|
Fillet yield
|
12:26984411
|
12
|
26984411
|
[G/A]
|
0.066
|
2.388E-12
|
uncharacterized
|
6:33824877
|
6
|
33824877
|
[T/G]
|
0.055
|
4.496E-10
|
XYLT1, RPS15A, COQ7
|
14:30148797
|
14
|
30148797
|
[G/T]
|
0.056
|
3.015E-09
|
uncharacterized
|
13:17730096
|
13
|
17730096
|
[C/A]
|
0.113
|
2.012E-08
|
MARCH8
|
13:17730605
|
13
|
17730605
|
[C/A]
|
0.113
|
2.012E-08
|
MARCH8
|
1Markers in bold indicate a common lead SNP in at least two traits. 2Linkage group. 3Position in base pairs. 4Minor allele frequency. 5Based on O_niloticus_UMD_NMBU as reference genome for Oreochromis niloticus. The full list of lead SNPs is available in S2 Table.
Table 4. Genes intercepted by a lead SNP associated with body traits based on multi-trait GWAS in Nile tilapia.
Gene1
|
LG2
|
Position3
|
N SNP4
|
p-values5
|
Genomic
location
|
Traits
|
Min
|
Max
|
CCDC102A
|
1
|
39153024
|
1
|
3.146E-12
|
3.474E-10
|
Intronic
|
ADG, BWH, WW, HW, HON, BLH
|
ADAMTS9
|
5
|
29062243
|
1
|
3.446E-11
|
-
|
Exonic
|
FW
|
SRGAP1
|
7
|
60999336 - 61005198
|
3
|
4.614E-09
|
4.614E-09
|
Intronic
|
HW
|
SLC4A2
|
9
|
14670077 - 14674835
|
2
|
5.225E-08
|
5.225E-08
|
Intronic
|
WW
|
MALRD1
|
9
|
16267509 - 16328834
|
2
|
1.678E-10
|
5.325E-08
|
Intronic
|
ADG, BWH, HON
|
PTPRN2
|
9
|
16433765 - 16435917
|
2
|
4.091E-09
|
4.758E-09
|
Intronic
|
ADG, HW
|
DMXL1
|
12
|
24525556
|
1
|
2.379E-11
|
-
|
Intronic
|
FW
|
MARCH8
|
13
|
17730096 -17730605
|
1
|
2.012E-08
|
2.012E-08
|
Intronic
|
FY
|
MSH6
|
13
|
21626153 -21626426
|
1
|
3.796E-08
|
3.796E-08
|
Exonic/Intronic
|
ADG
|
FUT8
|
15
|
14457958
|
1
|
4.861E-08
|
-
|
Intronic
|
ADG
|
TMEM121
|
15
|
14662118
|
1
|
9.425E-10
|
9.844E-09
|
Intronic
|
ADG, BWH, WW
|
MYO6
|
15
|
23976527
|
1
|
5.175E-08
|
-
|
Intronic
|
HON
|
HEG1
|
16
|
12574352
|
1
|
3.836E-08
|
-
|
Intronic
|
FY
|
DOCK9
|
16
|
17284162
|
1
|
1.673E-08
|
-
|
Intronic
|
HW
|
MYO16
|
16
|
20105934 - 20116545
|
2
|
3.340E-11
|
1.988E-09
|
Intronic/Exonic
|
ADG, BWH, WW, HON, BLH
|
NUP107
|
17
|
19609147 - 19612729
|
2
|
3.815E-08
|
4.102E-08
|
Intronic/Exonic
|
BWH, HON
|
KTN1
|
19
|
11094375
|
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: Hon weight (g); BLH: Body length at harvest (cm); FW: fillet weight (g); FY: fillet yield (%).
1Genes intercepted for at least one lead SNP based on O_niloticus_UMD_NMBU as reference genome for Oreochromis niloticus. 2Linkage group. 3In base pairs. 4Number of lead SNPs. 5Minimum (Min) and maximum (Max) p-value for coincident lead SNP for at least two traits.