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Table 3 Differentially expressed transcripts located to QTL-regions for bone traits

From: Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits

Genbank ID

Pos.1

Ensembl gene2

Annotation 3

QTL4

DE 5

M-values6

[GenBank:CN234847]

1:30.2

ENSGALG00000009494

Putative orthologue to human THAP domain containing 5 (THAP5)

ecirc1

M

0.36

-0.02

0.18

[GenBank:CN232736]

1:31.3

ENSGALG00000009547

Putative orthologue to human periphilin 1 (PPHLN1)

ecirc1

F P

-0.09

-0.29

-0.19

[GenBank:CN220162]

1:32.4

 

NA

ecirc1

P

-0.17

-0.19

-0.18

[GenBank:CN223165]

1:34.4 ±

ENSGALG00000009762

Gag polyprotein

ecirc1

M P

0.49

0.32

0.40

[GenBank:CN217879]

1:35.5

ENSGALG00000009829

Putative orthologue to Ribosomal protein L18 A (RPL18A)

ecirc1

P

-0.20

-0.34

-0.27

[GenBank:BU128191]

1:35.7

ENSGALG00000009867

Wnt inhibitory factor 1 (WIF1) *

ecirc1

F

0.17

0.68

0.43

[GenBank:BU118286]

1:35.7

ENSGALG00000009867

Wnt inhibitory factor 1 (WIF1) *

ecirc1

F

0.15

0.64

0.39

[GenBank:CN224091]

1:43.5

ENSGALG00000010992

Putative orthologue to Solute carrier family 6, member 15 (SLC6A15)

nc-bmd1

P

0.26

0.14

0.20

[GenBank:CN221299]

1:47.0

 

NA

nc-bmd1

M P

0.41

0.21

0.31

[GenBank:CN226131]

1:47.2

ENSGALG00000011325

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (NDUFA12)

nc-bmd1

M

0.30

-0.00

0.14

[GenBank:CN223612]

1:49.5

ENSGALG00000011651

Putative orthologue to ADP-ribosylation factor-like 1 (ARL1)

nc-bmd1

P

0.36

0.35

0.36

[GenBank:CN229035]

1:49.9

ENSGALG00000023235

NA

nc-bmd1

M P

-0.33

-0.27

-0.30

[GenBank:CN217578]

1:50.1

ENSGALG00000011798

Putative orthologue to heme-binding protein1 (HEBP1)

nc-bmd1

M

0.71

0.42

0.55

[GenBank:CN230393]

1:51.0

ENSGALG00000011856

NA

nc-bmd1

P

0.16

0.14

0.15

[GenBank:CN224774]

1:51.0

ENSGALG00000011859

Eye-globin [UniProt:Q5QRU6]

nc-bmd1

P

-0.20

-0.20

-0.20

[GenBank:CN219273]

1:51.8

ENSGALG00000012013

Putative orthologue to Solute carrier family 25, member 17 (SLC25A17)

nc-bmd1

F

0.08

0.31

0.20

[GenBank:CN223291]

1:52.6

 

NA

nc-bmd1

M P

0.48

0.26

0.37

[GenBank:CN221539]

1:52.6

 

NA

nc-bmd1

P

0.21

0.30

0.26

[GenBank:CN223252]

1:52.7

ENSGALG00000019317

Putative orthologue to Josephin domain-containing 1 (JOSD1)

nc-bmd1

M P

0.29

0.17

0.23

[GenBank:CN230599]

1:52.8

 

NA

nc-bmd1

M

-0.16

0.00

-0.08

[GenBank:CN235584]

1:52.8

ENSGALG00000012247

Putative homologue to DEAD/H BOX 17 (DDX17)

nc-bmd1

F

0.09

-0.30

-0.10

[GenBank:CN231378]

1:52.8

 

NA

nc-bmd1

P

0.15

0.13

0.14

[GenBank:CN220256]

1:52.9

ENSGALG00000012272

NA

nc-bmd1

P

0.38

0.36

0.37

[GenBank:CN221882]

1:53.3

ENSGALG00000012456

Putative orthologue to Ras-related C3 botulinum toxin substrate 2 (RAC2)

nc-bmd1

M

-0.52

-0.15

-0.34

[GenBank:CN234446]

1:55.1

 

NA

nc-bmd1

F P

-0.20

-0.32

-0.26

[GenBank:CN227045]

1:55.3

ENSGALG00000012569

Putative orthologue to F-box only protein 7 (FBXO7)

nc-bmd1

F

-0.00

-0.13

-0.07

[GenBank:CN226884]

1:55.3

ENSGALG00000012619

NA

nc-bmd1

F

-0.02

-0.12

-0.07

[GenBank:CN223798]

1:56.2

 

NA

nc-bmd1

M P

0.42

0.27

0.35

[GenBank:CN219664]

1:59.3

 

NA

nc-bmd1

M P

0.41

0.23

0.32

[GenBank:CN222216]

1:61.2

 

NA

nc-bmd1

M

0.18

-0.05

0.06

[GenBank:CN231349]

1:63.0

 

NA

nc-bmd1

P

0.11

0.13

0.12

[GenBank:CN222823]

1:63.7

 

NA

nc-bmd1

P

0.31

0.22

0.26

[GenBank:BU329405]

1:63.9

ENSGALG00000013039

BH3-interacting domain death agonist (BID)

nc-bmd1

M P

-0.14

-0.11

-0.12

[GenBank:CN219432]

2:57.4

 

NA

bmd1

M P

-0.25

-0.19

-0.22

[GenBank:CN233407]

2:63.3

 

NA

bmd1

M

0.24

0.02

0.13

[GenBank:CN231046]

2:65.5

ENSGALG00000012784

Putative orthologue to Thioredoxin domain-containing protein 5 (TXNDC5)

bmd1

M

0.29

0.09

0.19

[GenBank:BU318588]

2:66.2

ENSGALG00000012802

Putative orthologue to human Coagulation factor XIII A chain precursor (F13A1)

bmd1

P

-0.44

-0.46

-0.46

[GenBank:CN225543]

2:67.0

ENSGALG00000012809

Peroxisomal D3,D2-enoyl-CoA isomerase (PECI)

bmd1

ALL

-0.42

-0.42

-0.42

[GenBank:CN222249]

2:78.1

ENSGALG00000012965

Putative orthologue to family with sequence similarity 105, member A (FAM105A)

bmd1

P

-0.14

-0.17

-0.15

[GenBank:CN227494]

2:80.5

ENSGALG00000013041

Putative orthologue to T-complex protein 1 subunit epsilon (CCT5)

bmd1

M

-0.27

-0.06

-0.16

[GenBank:BU303036]

2:83.0

ENSGALG00000013094

Dopa decarboxylase (DDC)

bmd1

ALL

-0.26

-0.40

-0.33

[GenBank:CN232630]

2:85.8

 

NA

bmd1

M

-0.21

-0.01

-0.11

[GenBank:CN217215]

20:1.4

ENSGALG00000001903

Putative orthologue to microtubule-associated protein 1, light chain 3 alpha (MAP1LC3A)

tors

M

0.34

0.07

0.20

[GenBank:CN222258]

20:1.7

 

NA

tors

P

0.18

0.22

0.20

[GenBank:CN220691]

20:3.8

 

NA

tors

F P

-0.15

-0.19

-0.17

[GenBank:CN221589]

20:5.2

ENSGALG00000004143

Putative orthologue to tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta isoform (YWHAB)

tors

M P

-0.23

-0.06

-0.15

[GenBank:CN227581]

20:5.3

ENSGALG00000023846

NA

tors

F

0.01

0.16

0.09

[GenBank:CN236828]

20:5.3

ENSGALG00000004170

Adenosine deaminase (ADA)

tors

F P

-0.27

-0.69

-0.48

[GenBank:CN235806]

20:5.3

 

NA

tors

M

-0.26

-0.09

-0.18

[GenBank:CN219753]

20:5.5

 

NA

tors

ALL

0.21

0.28

0.25

[GenBank:CN232642]

20:8.4

ENSGALG00000005635

Transcription factor-like 5 (TCFL5)

tors

P

-0.12

-0.11

-0.11

[GenBank:CN227039]

20:8.4

ENSGALG00000005652

NA

tors

P

-0.12

-0.22

-0.17

[GenBank:CN220570]

20:9.0

ENSGALG00000005849

Putative orthologue to chromosome 20 open reading frame 149 (C20orf149)

tors

M

-0.38

0.01

-0.18

[GenBank:CN218403]

20:9.0

ENSGALG00000005887

 

tors

M P

0.52

0.26

0.39

[GenBank:CN223304]

20:9.5

ENSGALG00000006046

Putative orthologue to DnaJ homolog subfamily Cmember 5 (DNAJC5)

tors

M P

0.37

0.29

0.33

[GenBank:CN231170]

20:9.8

 

NA

tors

P

0.15

0.23

0.19

[GenBank:BU199756]

20:10.2

ENSGALG00000006657

Microtubule-associated protein RP/EB family member 1 (MAPRE1) *

tors

M P

-0.20

-0.13

-0.16

[GenBank:CN228069]

20:10.2

ENSGALG00000006657

Microtubule-associated protein RP/EB family member 1 (MAPRE1) *

tors

M P

-0.35

-0.18

-0.26

[GenBank:CN236120]

20:10.4

ENSGALG00000006817

Putative orthologue to catenin, beta like 1 (CTNNBL1)

tors

P

0.08

0.10

0.09

[GenBank:CN232968]

20:11.9

ENSGALG00000007768

Putative orthologue to Aurora kinase A (AURKA)

tors

P

0.34

0.43

0.39

  1. * WIF1 and MAPRE1 are represented by two clones on the microarray± [GenBank:CN223165] may represent a retroviral element and may be present also elsewhere in the genome
  2. 1 Chromosome and positions (in Megabases) of transcripts are based on build 2.1 of the chicken genome
  3. 2 Where applicable, Ensembl gene from which transcripts are derived
  4. 3 Gene annotation. If applicable, gene name or name of putative orthologue are presented. NA = Not applicable, due to lacking annotation.
  5. 4 Previously identified QTLs for traits of femoral bone. ecirc1 = sex independent QTL for endosteal circumference, nc-bmd1 = female specific QTL for noncortical bone mineral density (BMD), bmd1 = female specific QTL for various measurements of BMD, tors1 = female specific QTL affecting femoral elasticity in torsion test.
  6. 5 The comparison between WL and RJ in which transcript was found differentially expressed (FDR-adjusted p-value < 0.0015. M = males, F = females, P = population (all WL compared to all RJ), ALL = M, F and P.
  7. 6 M-values log2(fold change) for M, F and P-comparison, respectively. Negative M-values indicate lower expression in WL.
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BMC Genomics

ISSN: 1471-2164

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