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 |