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Table 5 qRT-PCR validations with metabolic resistance candidate genes in flixweed

From: Target-site and non-target-site based resistance to the herbicide tribenuron-methyl in flixweed (Descurainia sophia L.)

Gene ID

Function annotation

Padja

FPKM b (R/S)

Fold change: qRT-PCR validation (2-â–³Ct)

RNA-Seq samples

Addtional samples

c29425_g1

Cyt P450, CYP77B1/77A3

1.31 × 10−15

69.5

33.88*

0.57

c1867_g1

CytP450, CYP96A13

2.55 × 10−10

24.94

16.55**

11.94**

c21381_g1

Cyt P450, CYP71A3

4. 25 × 10−3

22.63

4.06

1.28

c22393_g1

Cyt P450, CYP86B1

9.35 × 10−11

20.82

4.24*

2.75*

c17043_g1

CytP450, CYP96A15

2.28 × 10−6

16.58

448.6***

24.76*

c18590_g1

CytP450, CYP71B14

3.9 × 10−2

12.87

1.82

1.3

c17358_g1

CytP450, CYP734A1

8.39 × 10−3

2.91

1.95

0.85

c25953_g1

Cyt P450, CYP81F1/81 F3

4.33 × 10−2

2.64

2.69

0.27

c11932_g1

ABC transporter, ABCC1

3.42 × 10−12

Inf c

153.43*

9.26***

c31018_g1

ABC transporter, ABCF5

1.82 × 10−2

2.46

1.21

0.6

c25791_g1

GST, F11

2.46 × 10−3

3.11

1.24

1.56

c21822_g2

GST, U17

7.10 × 10−3

2.87

1.46

0.86

c19559_g2

UDP-glycosyltransferase 78D4

1.06 × 10−3

14.87

2.42

0.94

c33777_g2

UDP-glycosyltransferase 91A1

4.03 × 10−3

6.52

2.36

0.74

c24861_g1

UDP-glycosyltransferase 84A1

1.33 × 10−3

5.76

5.33*

0.98

c12944_g1

UDP-glycosyltransferase 71B1

3.02 × 10−6

5.01

2.60

0.5

c31999_g1

UDP-glycosyltransferase 71C2

8.92 × 10−5

4.49

1.98

0.67

c5029_g1

UDP-glycosyltransferase 79B6

9.54 × 10−5

4.15

3.62

0.54

c15368_g1

UDP-glycosyltransferase 91A1

4.68 × 10−3

3.71

2.91

0.7

c19559_g1

UDP-glycosyltransferase 78D4

2.38 × 10−2

3.58

4.82*

0.89

c33777_g1

UDP-glycosyltransferase 91A1

1.53 × 10−3

3.08

3.16*

0.53

c29603_g1

Glycosyl transferases group 1

1.64 × 10−2

2.67

1.86

0.92

c30538_g1

Glycosyl transferase family 21

3.56 × 10−2

2.56

2.03

0.9

c31908_g1

Glycosyl transferase family 21

2.28 × 10−2

2.51

1.46

0.78

c29566_g1

UDP-glycosyltransferase 74D1

4.07 × 10−2

2.51

1.65

1.18

c28527_g1

peroxidase activity

2.89 × 10−2

4.01

2.15

1.14

  1. Identification of differentially expressed contigs between tribenuron-methyl susceptible (SD8) and resistant (N11) flixweed populations by RNA-Seq, and the expression levels of the contigs were validated using qRT-PCR with RNA-Seq samples (n = 2) and additional samples from resistant N11 (n = 12) relative to susceptible SD8 (n = 11). Fold-change in gene expression (2-△Ct) was calculated relative to the susceptible samples, where △CT = [CT target gene-CT mean of two internal control genes]. P-value of <0.05, 0.01, 0.001 is indicated by *, **, and ***, respectively (from SPSS analysis)
  2. a Padj, adjusted P-value, the differentially expressed contigs were fliterred by Padj < 0.05 from DESeq analysis
  3. b FPKM, fragments per kilobase of transcript sequence per millions base pairs sequenced
  4. c Inf indicates readcount of SD8 samples = 0 in RNA-Seq
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BMC Genomics

ISSN: 1471-2164

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