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Table 1 The 40 most extreme genes by Phenotypic Impact Factor in High FE versus Low FE birds. These 40 genes have been reordered manually into functional groupings. The absolute DE expressed as a fold change has also been reported

From: Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

Gene symbol

Gene name

Fold Change HFE/LFE

Gene function

MB

Myoglobin

4.10 Down

Iron storage, highly expressed in red, slow fibres

MYH15

Myosin heavy chain 15, slow

4.46 Down

Slow twitch fibre isoform

TPM3

Tropomyosin 3, slow

2.67 Down

Slow twitch fibre isoform

MYOZ2

Myozenin 2, slow

2.54 Down

Slow twitch fibre isoform

TNNI1

Troponin I type I, slow

3.36 Down

Slow twitch fibre isoform

PLN

Phospholamban

2.78 Down

Highly expressed in slow twitch fibres, substrate for cAMP-dependent protein kinase.

COL3A1

Collagen 3A1

2.09 Down

ECM

COL12A1

Collagen 12A1

2.66 Down

ECM

FN1

Fibronectin 1

2.01 Down

ECM

BMP5

Bone morphogenetic protein 5

4.23 Down

Negative regulation of IGF1 signaling

RSFR

Leukocyte ribonuclease A2

2.56 Down

Angiogenesis

LY86

Lymphocyte antigen 86

2.42 Down

Inflammation, apoptosis

MGAT5B

beta-1,6-N-acetylglucosaminyltransferase

3.51 Down

Synthesis of cell surface n-glycans, ECM

NES

Nestin

2.64 Down

Expressed in nerve cells, implies motor unit

APOA1

Apolipoprotein A1

2.27 Down

Promotes cholesterol efflux from tissues. Highly expressed in liver.

MGP

Matrix Gla protein

1.84 Down

ECM

IGJ

Immunoglobulin J polypeptide

2.21 Down

Little known

SEPP1

Selenoprotein P

2.19 Down

Extracellular glycoprotein and antioxidant

CA3

Carbonic anhydrase III

1.93 Down

Response to oxidative stress, expressed at high levels in skeletal muscle

CTSS

Cathepsin S

2.24 Down

Lysosomal cysteine proteinase

H2AFY

Histone family member Y

2.47 Up

Associated with lipogenic genes

HIG2A (ENSGALG00000003348)

Hypoxia-inducible domain family

2.15 Up

Little known

TESK1

Testis specific kinase

1.95 Up

Cell matrix communication

C11ORF89 *

Uannotated ORF

2.44 Up

Unannotated

CKMT1

Creatine kinase mitochondrial 1

1.63 Up

Creatine metabolism, muscle energy supply

CNTFR

Ciliary Neurotrophic factor

2.20 Up

Skeletal muscle development

ENKD1

Enkurin domain containing

2.19 Up

Cytoplasmic microtubule protein

CA4

Carbonic anhydrase 4

3.95 Up

Respiration, acid base balance, expressed on luminal surface of capillaries

INSIG1

Insulin induced gene 1

1.92 Up

Regulation of intracellular cholesterol concentration and steroid biosynthesis

TTPA

Tocopherol (alpha) binding protein

2.84 Up

Binds alpha-tocopherol a form of vitamin E, response to pH

LINGO1

Leucine rich repeat and Ig domain containing 1

1.72 Up

Nervous system development

DCUN1D5

Defective in cullin neddylation 1, domain containing 5

2.10 Up

Ubiquitin conjugating enzyme binding

SNCG1

Synuclein gamma

3.40 Up

Synapse protein

C16ORF45

Unannotated ORF

1.88 Up

Protein function unknown

LIPG

Endothelial lipase

2.20 Up

Lipoprotein metabolism and vascular biology

(ENSGALG00000028983)

BLASTS to HOXA9

2.33 Up

Transcription Factor

(ENSGALG00000027955)

BLASTS to MHC

2.31 Up

MHC immune function

BFSP1

Beaded filament structural protein 1

3.16 Up

Cytoskeletal structure

MYL2_1 (MYL2A)

MYL2A

3.39 Up

Thought to be more highly expressed in cardiac muscle i.e. slow fibres

MYBPH

Myosin binding protein H

1.53 Up

Fast isoform

  1. * We further explored the possible function of the gene encoding an unannotated Open Reading Frame (ORF) C11ORF89, given it was in the top 20 upregulated genes in the HFE birds. The entry in GeneCards (under the alias PRR33) predicts the ORF to translate into a large protein containing regions of low complexity and comparative analysis suggests that the protein was present in the ancestor of the chordates. It is located in the G. gallus genome adjacent to TNNT3 and TNNI2, and cellular compartment analysis (http://compartments.jensenlab.org/) suggests there is moderate evidence it is a cytoskeletal protein