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Table 2 Assessment of average DNA yields, purity and Sequenom iPLEX ® Gold assay assay performance

From: Extraction of high purity genomic DNA from pine for use in a high-throughput Genotyping Platform

Extraction method Total number of extractions Average conc. (ng/μL)1 Average yield (ng DNA/mg tissue) Absorption at 260 nm /230 nm2 % Samples with conc. < 20 ng/μL % Missing genotypes3 % Loci departing from HWE % Inaccurate genotypes4
Standard CTAB DNA extractions
S 1927 234 ± 211 39 ND 2 21.4 63.8 1.0
Stage 1: Testing eight methods
C 47 413 ± 34 138 1.6 ± 0.1 0 11.0 10.3 0.1
CE 47 454 ± 22 151 2.0 ± 0.1 0 6.5 13.8 0.3
CQ 47 180 ± 39 60 2.0 ± 0.1 0 5.9 12.1 0.2
CZ 47 232 ± 33 77 2.5 ± 0.1 0 11.0 15.5 0.3
CG 47 80 ± 8 60 2.5 ± 0.5 9 4.2 15.5 0.8
N 44 30 ± 22 60 2.1 ± 0.2 38 7.4 17.2 0.7
F 47 52 ± 49 34 0.9 ± 0.3 30 34.7 13.8 1.8
D 43 35 ± 26 141 1.6 ± 0.4 37 4.6 19.0 1.1
Stage 2: Scaled up test of four methods
SQ 70 165 ± 110 33 2.6 ± 0.5 12 9.0 12.9 0.1
CQ 79 397 ± 32 159 2.3 ± 0.2 0 7.6 12.9 0.1
N96 79 158 ± 63 198 2.2 ± 0.2 0 8.3 6.5 0.0
D+ 77 65 ± 12 191 2.9 ± 1.5 0 13.5 6.5 0.2
  1. 1 ± Standard Deviation.
  2. 2 ± Standard Deviation. Note: ideal range for A260/A230 ratios is 1.8 – 2.2.
  3. 3 Fail rates calculated for all samples across all assays.
  4. 4 Inconsistent genotypes across replicate samples.