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Table 1 Candidate genes used for real-time quantitative RT-PCR validation.

From: Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

  

t-test1

Ratio2

 

Annotation

Probe Set ID

No mask

Double- mask

No mask

Double- mask

ΔΔCT3

Cell Wall-related Genes

      

Chitinase

Msa.3005.1.S1_at

+

+

-2.8

-3.4

-2.2**

Peroxidase

Mtr.40028.1.S1_at

-

+

-4.5

-5.2

-2.2**

Chitinase

Mtr.40130.1.S1_at

+

+

-1.8

-2.1

-1.2**

Reversibly glycosylated polypeptide

Mtr.4595.1.S1_at

-

+

0.8

2.4

1.9**

Cellulose synthase-like

Mtr.45005.1.S1_at

-

+

0.8

1.1

0.3**

Endo-1,4-beta glucanase

Mtr.31102.1.S1_at

-

+

0.9

1.1

1.1**

Xyloglucan endotransglusoxylase

Mtr.6499.1.S1_at

-

+

-0.7

-1.6

-1.3**

UDP-glucose dehydrogenase

Msa.2895.1.S1_at

+

+

1.3

1.6

0.4*

Acetyl-CoA C-acetyltransferase

Mtr.10429.1.S1_at

-

+

-0.5

-2.7

-2.3**

Cinnamyl-alcohol dehydrogenase

Mtr.8985.1.S1_at

-

+

-0.3

-1.3

-0.9**

Caffeoyl-CoA O-methyltransferase

Mtr.4850.1.S1_at

-

+

-1.3

-2

-1.5**

Glycosyl hydrolase

Mtr.2288.1.S1_at

-

+

0.4

2

0.6

UDP-glucosyl transferase

Mtr.37847.1.S1_at

+

+

2.2

4.1

3.0**

Transcription Factors

      

LOB gene family

Mtr.28784.1.S1_at

-

+

1.8

2.4

1.2*

bZIP transcription factor

Mtr.17513.1.S1_s_at

+

+

2.3

2.8

2.7**

C2H2 zinc finger family

Mtr.972.1.S1_at

-

+

2

3.2

2.6**

C2H2 zinc finger family

Mtr.50483.1.S1_at

+

+

1.6

1.5

1.0**

C2H2 zinc finger family

Mtr.39849.1.S1_at

-

+

-1.5

-2.8

-1.4**

Homeobox transcription factor

Mtr.24122.1.S1_at

+

+

-1

-1.3

-0.4

Homeobox transcription factor

Mtr.46916.1.S1_at

-

+

-0.9

-1.9

-1.1**

Homeobox transcription factor

Mtr.38132.1.S1_a_at

-

+

-0.6

-1

-0.7**

JUMONJI family

Mtr.17177.1.S1_at

-

+

2

2.1

3.0**

MYB transcription factor

Mtr.42648.1.S1_at

-

+

0.6

2.4

1.0**

NAC transcription factor

Mtr.14808.1.S1_at

-

+

-0.9

-1.2

-0.7*

PHD finger family

Mtr.39174.1.S1_at

-

+

-1.1

-1.9

-0.2

Zinc finger family

Mtr.33527.1.S1_at

+

+

3.2

3.6

2.7**

WRKY family

Mtr.23120.1.S1_s_at

+

+

3.8

3.4

3.8**

WRKY family

Mtr.12866.1.S1_at

-

+

2.1

2.2

2.2**

Signal Transduction Genes

      

Transducin family

Mtr.11654.1.S1_at

-

+

0.8

2.1

1.8

FAR1-related

Mtr.47127.1.S1_at

+

+

3

3

2.1**

MAP kinase

Mtr.5102.1.S1_at

+

+

-1.3

-1.7

-0.8**

Receptor-like kinase

Mtr.1545.1.S1_at

-

+

0.7

2.5

4.2**

Receptor-like kinase

Mtr.9480.1.S1_at

+

+

1.3

1.5

0.4

Receptor-like kinase

Mtr.3024.1.S1_at

-

+

0.6

2.1

2.2**

  1. 1+ indicates genes that were detected as differentially-expressed between PES internodes of genotypes 252 and 1283 after a t-test (p < 0.001, FDR < 0.05, ≥2-fold difference) using the GeneChip data with no masking or after double-masking.
  2. 2Log2 (252PES/1283PES) value obtained from the GeneChip data with no masking or after double-masking.
  3. 3ΔΔCT = [CT(1283PES) - CT(18s)] — [CT(252PES) - CT(18s)] from real-time quantitative RT-PCR data. CT18s rRNA values were stable in the tissues examined and were used to normalize data. *,** indicates probe sets that were detected as differentially expressed after a t-test (P < 0.01 or P < 0.001) respectively, The t-test of the real-time quantitative RT-PCR data for PES internodes of genotypes 252 and 1283 was performed with ΔCT values (12 data points = 2 plates × 3 wells × 2 genotypes).