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Table 1 qPCR primers

From: Application of genomic tools to study and potentially improve the upper thermal tolerance of farmed Atlantic salmon (Salmo salar)

Gene Name (GenBank Accession Number)

Nucleotide sequence (5’-3’)

Amplification Efficiency (%)

r2

Amplicon Size (bp)

Source

angiopoietin-related protein 4 (angl4) (NM_001139941.1)

F: CAACCCTGACTCTGTGCCTG

85.1

0.992

126

This study

R: TCACATTCACGTCGTCCCAC

   

annexin A5b (anxa5b) (NM_001141036.1)

F: CAGTGTGAGAGCCAGTGGAA

89.5

0.998

132

Xu et al. [54]

R: TGTCTCTGGCTGTTGCTACG

   

C-C motif chemokine 20 (ccl20) (XM_014159437.2)

F: AGGCTACACCTTCCAGGACA

98.3

0.996

119

This study

R: GCAGTACCCTCTTGGTCCAG

   

E74-like factor 3 (elf3) (XM_014131843.2)

F: CCAGAGCCTGGTGGAACTAA

98.4

0.994

90

This study

R: GGGAAGTCTGGGAACTCCTC

   

eosinophil peroxidase-like (epx) (XM_014147274.2)

F: CACCCATCAAGTGCAACAAC

99.1

0.996

100

This study

R: TCCTGGTCCGAATACTCCTG

   

HtrA serine peptidase 1b (htra1b) (XM_014158365.2)

F: ATGATGACTCTCACACCAATGC

97.8

0.996

104

Caballero-Solares et al. [80]

R: GTTTTTGGGATGACCTCGATT

   

serine protease HTRA2, mitochondrial-like (htra2) (XM_014180216.2)

F: CTTCCTGAACCAAGCCTCTG

94.7

0.991

128

This study

R: GATCCCTCAGCTTCAACTCG

   

inhibitory synaptic factor 2a (insyn2a) (XM_014154695.2)

F: TGCCAACCCTTCTACCAAGC

110.3

0.981

116

This study

R: CTAGACCTTCCACCTGCGTC

   

potassium inwardly rectifying channel subfamily J member 11, like (kcnj11l) (BT059682.1)

F: GTATGCAGCACAGCCAGAGA

107.3

0.989

115

This study

R: TCCCAGACCTTCCACCTCAA

   

lipoprotein lipase (lpl) (XM_014148677.2)

F: GGTGTCAGCGCTGTATGAGA

101.3

0.981

90

This study

R: GCGGCTACAGGATACTGGTT

   

platelet-derived growth factor subunit A-like (pdgfa) (XM_045708160.1)

F: TCATCTGGCCTCCCTGTGTA

89.9

0.991

114

This study

R: CCACCTTAGCCACCTTGACA

   

serine peptidase inhibitor, clade H, member 1a-1 (serpinh1a-1; alias hsp47a-1) (OQ814177)

F: GGGCGAGAAGATGAGAGATG

110.0

0.968

199

Ignatz et al. [77]

R: GCACGAATGTTGGCACATAG

   

serine peptidase inhibitor, clade H, member 1a-2 (serpinh1a-2; alias hsp47a-2) (OQ814179)

F: CCAATGTCTTCCATGCCTCT

93.8a

-

94

Ignatz et al. [77]

R: TTGGGGTTCTTCAGCTTGTC

   

serine peptidase inhibitor, clade H, member 1b-1 (serpinh1b-1; alias hsp47b-1) (OQ814181)

F: CCAAAGTCAGCATGGAGGTT

101.3

0.994

151

Ignatz et al. [77]

R: ATTGAAGAGGCGTGGAACAC

   

serine peptidase inhibitor, clade H, member 1b-2 (serpinh1b-2; alias hsp47b-2) (OQ814182)

F: CTCATCATGCCCTACCACCT

103.3

0.995

188

Ignatz et al. [77]

R: TCCACAGCTTCAGTCACACC

   

vitellogenin (vtgAsa1) (XM_014168660)

F: TGAAGGACTTTGGTCTGGCTTACACA

103.4

0.999

50

Andersen et al. [59]

R: CTGCTGGCACTCTACACACTTC

   

elongation factor 1 alpha (ef1a) (NM_001141909)b

F: GTGGAGACTGGAACCCTGAA

99.6

0.998

155

Jones et al. [60]

R: CTTGACGGACACGTTCTTGA

   

polyadenylate-binding protein 1 (pabpc1) (EG908498)b

F: TGACCGTCTCGGGTTTTTAG

94.0

0.999

108

Xu et al. [54]

R: CCAAGGTGGATGAAGCTGTT

   

60 S ribosomal protein 32 (rpl32) (BT043656)c

F: AGGCGGTTTAAGGGTCAGAT

96.8

0.998

119

Xue et al. [61]

R: TCGAGCTCCTTGATGTTGTG

    
  1. a Expression was too low to calculate an amplification efficiency in the current study. This value comes from Ignatz et al. [77] where an efficiency was calculated from other Atlantic salmon liver cDNA
  2. b Normalizer gene chosen for this study
  3. c Normalizer gene tested, but ultimately not chosen for this study
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BMC Genomics

ISSN: 1471-2164

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