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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-Ct)
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