Skip to main content

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

From: Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits 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

  1. aMarkers in bold indicate a common lead SNP in at least two traits
  2. bLinkage group
  3. cPosition in base pairs
  4. dMinor allele frequency
  5. eBased on O_niloticus_UMD_NMBU as reference genome for Oreochromis niloticus. The full list of lead SNPs is available in S2 Table
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us