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Table 1 Candidate genes mapped in a white clover F 1 population

From: An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago

T repens Locus

Annotation

Intron

Tr LG

Mt PM

Ref

Forward Primer (5'-3') Reverse Primer (5'-3')

TrPHR

MYB transcription factor

1

2-2

2

[36]

GTTGATGCTGTGGCTCAACTT CCCATAACTCTGAGGACCCCT

 

Phosphorus transport

     

TrCPS

Glutamine synthase

2

3-1

3

[37]

TGGATCAGGTTTGGACTTGAG GGAAGCTGTGAAGGGTCAGTA

 

In planta nitrogen cycling

     

TrMIP

Myo inositiol 1-P- synthase

9

3-1

3

[38]

GTTATCTGACCAAGGCTCCTCTG ACCACTGGTGTGCCCGGTGGAAC

 

Pinitol synthesis

     

TrLFY

LEAFY

1

3-2

3

[39]

TCTCGATGCTCTCTCTCAAGAAG TCGCTGCACCACCGGCTCCTCCG

 

Flowering

     

TrPLT1

PLETHORA

6

4-2

4

[40]

GTGAGCTTCATACCTTCCAGTCC AAGAACTTCGATATATCGCGGTG

 

Root growth

     

TrSHP - 2

SHATTERPROOF9

2

4-2

4

[41]

GAGGTACAAGAAAGCATGTTCAG CTTCAAGTATTCACGGTAACTGC

 

Dehiscence

     

TrSHP - 8

SHATTERPROOF9

9

4-2

4

[41]

AAAGCATGTTCAGATTCTTCTGG GCAGTTTGGCAGCTTCTTGCTGG

 

Dehiscence

     

TrPRP

ROOT PHOTOTROPISM2

3

5-2

5

[42]

AATCGACGATGATCTTTACCGCGCCG TTTGTTCTGTGACGCGTGCACACG

 

Root growth

     

TrDFR

Dihydroflavonol reductase (DFR)

1

6-1

2

[43]

CATTGGAAGAGTTAGAGATTTAG TCCAACTTCCATAAATGTTCAAC

 

Condensed Tannin

     

TrIAA

SOLITARY ROOT

4

6-1

2

[44]

TGAAAGGCTCTGATGCAATTGGG CTAGATTTTTCCATTGCTCTTGG

 

Root growth

     

TrSEP1

SEPELLATA1

2

7-1

7

[45]

GCAAACCTGCTAAAGAACTTGAG CTTCAAGTATTCACGGTAACTGC

 

Floral initiation

     

TrTT12

TRANSPARENT TESTA12

3

7-1

7

[46]

CAGATCCAAAGTTGGAGACATCGG AGCCCATAGGATATGGTGAAGTGC

 

Condensed Tannin

     

TrRMS5

RAMOSUS5

6

7-2

7

[47]

GGCGAAGAAGAAGATGATGG CATCTCTGCATTGAGGTAGCA

 

Branching

     

TrAlaAT

ACC SYNTHASE1

6

8-2

8

[48]

AACTGGTGCCTATAGTCATAGTC GCTATTGTATCACGTAAACCCTG

 

Flowering

     

TrVP1

Clover orthologue of AVP1

5

8-2

8

[49]

ACTGAATACTATACCAGCAATGC TGCAGGAGTCTGCAACATCTTGC

 

Drought tolerance

     

TrPPD

PEAPOD

2

1-1 1-2

no hit

[50]

GATATCGTGAAAAGCGAAAGGAC AGCTTCACTGGAAGGTTCAAATA

 

Leaf meristem activity

     

TrANR

Anthocyanidin reductase (ANR)

1

4-2

no hit

[51]

GAGTGCATGTTTGGTTTGCCA TGCAAAGTTCACAGGTGTAGC

 

Condensed tannin

     

TrSTP

STAMINA PISTILLOIDIA

n/i

4-1

AC235671

[52]

TGGAAGGTTTTCACCCATCTATG TATCCTGCTGTTCATCCATGGAG

 

Flowering

     
  1. Eighteen candidate genes related to plant morphology, chemical composition, or transcription regulation were evaluated by in silico analysis. Primers were designed from T. repens genomic sequence, and length polymorphisms were assayed in 92 members of population MP2 using intron-spanning PCR for all loci except TrANR and TrSTP, which were assayed by SNP and exon size variation, respectively. Tr LG=white clover linkage group; Mt PM=Medicago truncatula genome assembly 3.0 pseudomolecule; Ref=cited reference; no hit=not found in M. truncatula databases and n/i=no intron in this gene. Note that BAC AC235671 is not incorporated into the M. truncatula assembly.
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BMC Genomics

ISSN: 1471-2164

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