Table 2.
Pathway | Comparisons between in planta and in vitro at equivalent developmental stages | Comparisons between in vitro developmental stages | ||||||
---|---|---|---|---|---|---|---|---|
3 dpi IP > 4 dpi IV | 3 dpi IP < 4 dpi IV | 5 dpi IP > 4 dpi IV | 5 dpi IP < 4 dpi IV | Late IP > 16 dpi IV | Late IP < 16 dpi IV | 4 dpi IV > 16 dpi IV | 4 dpi IV < 16 dpi IV | |
4‐Aminobutyrate degradation III (4 genes) | 2 | 1 | 3 | |||||
Arginine biosynthesis II (acetyl cycle) (9 genes) | 4 | 4 | ||||||
Chorismate biosynthesis (7 genes) | 1 | 2 | 1 | |||||
Cyclopropane fatty acid (CFA) biosynthesis (2 genes) | 2 | |||||||
Ergosterol biosynthesis (6 genes) | 2 | 1 | 1 | 1 | ||||
Fatty acid biosynthesis—initial steps I (10 genes) | 2 | |||||||
Fatty acid elongation—saturated (25 genes) | 5 | 7 | 6 | 1 | 9 | 1 | 4 | |
Fatty acid β‐oxidation II (core pathway) (16 genes) | 2 | 2 | 1 | 1 | 3 | 2 | ||
Fatty acid β‐oxidation IV (unsaturated, even number) (7 genes) | 2 | 1 | ||||||
Folate polyglutamylation I (5 genes) | 2 | |||||||
Folate transformations (8 genes) | 1 | 1 | 4 | |||||
Gluconeogenesis (13 genes) | 2 | 2 | 1 | 1 | 1 | |||
Glutamate biosynthesis III (2 genes) | 2 | 2 | 2 | |||||
Homogalacturonan degradation (5 genes) | 2 | 1 | 2 | 1 | ||||
Glycogen biosynthesis II (from UDP‐d‐glucose) (4 genes) | 1 | 1 | 2 | |||||
Glycogen degradation II (5 genes) | 2 | 1 | 3 | 3 | 1 | |||
Isoleucine biosynthesis from threonine (13 genes) | 4 | 3 | 1 | 2 | 3 | |||
Isoleucine degradation I (14 genes) | 3 | 3 | 2 | 2 | 2 | |||
l‐Arabinose degradation II (1 gene) | 1 | |||||||
l‐Cysteine degradation I (6 genes) | 1 | 1 | 1 | |||||
Leucine biosynthesis (10 genes) | 3 | 3 | 2 | 1 | ||||
Leucine degradation I (13 genes) | 3 | 1 | 3 | 1 | 2 | 1 | ||
l‐Serine degradation (2 genes) | 2 | 2 | ||||||
Lysine biosynthesis IV (6 genes) | 2 | 1 | 2 | 3 | 1 | |||
Melibiose degradation (4 genes) | 2 | 2 | 2 | |||||
Methionine degradation I (to homocysteine) (4 genes) | 2 | 2 | 2 | |||||
Nitrate reduction V (assimilatory) (7 genes) | 4 | 2 | 4 | |||||
Ornithine biosynthesis (6 genes) | 2 | 3 | 3 | |||||
Oxidative ethanol degradation I (22 genes) | 6 | 4 | 5 | 2 | 8 | 1 | 1 | 1 |
Pantothenate biosynthesis I (10 genes) | 4 | 4 | 4 | 1 | 1 | |||
Phenylalanine biosynthesis I (4 genes) | 1 | 2 | 2 | |||||
Phospholipases (8 genes) | 3 | 1 | ||||||
Proline biosynthesis I (7 genes) | 2 | 2 | 2 | |||||
Purine nucleotides de novo biosynthesis II (11 genes) | 3 | 1 | 2 | 3 | ||||
Pyruvate fermentation to ethanol II (17 genes) | 5 | 4 | 3 | 3 | 6 | 2 | 1 | 1 |
Removal of superoxide radicals (9 genes) | 1 | 1 | 1 | 2 | 1 | |||
S‐Adenosyl‐l‐methionine cycle (4 genes) | 2 | 2 | 3 | |||||
Salvage pathways of adenine, hypoxanthine and their nucleosides (5 genes) | 2 | 2 | 1 | |||||
Sorbitol utilization (5 genes) | 4 | 4 | 4 | 1 | ||||
Spermidine biosynthesis (2 genes) | 2 | 1 | 1 | |||||
β‐Alanine biosynthesis V (8 genes) | 1 | 1 | 2 | 2 | 1 | |||
β‐Alanine degradation I (3 genes) | 2 | 1 | 2 | |||||
Sucrose degradation to ethanol and lactate (anaerobic) (25 genes) | 5 | 6 | 3 | 4 | 6 | 3 | 3 | 1 |
Sulphite oxidation IV (3 genes) | 1 | 1 | 2 | |||||
Tetrapyrrole biosynthesis II (5 genes) | 1 | 2 | 1 | 1 | ||||
Trehalose degradation II (trehalase) (5 genes) | 1 | 3 | 1 | 1 | 1 | |||
Triacylglycerol biosynthesis (8 genes) | 1 | 3 | ||||||
tRNA charging pathway (25 genes) | 2 | 1 | 1 | |||||
Tryptophan degradation to 2‐amino‐3‐carboxymuconate semialdehyde (4 genes) | 2 | 1 | 1 | 2 | 1 | 2 | ||
Tryptophan degradation VI (via tryptamine) (8 genes) | 5 | 1 | 3 | 1 | 3 | 1 | ||
Tyrosine degradation I (7 genes) | 1 | 2 | 5 | 1 | ||||
UDP‐N‐Acetyl‐d‐galactosamine biosynthesis II (4 genes) | 2 | 1 | ||||||
Urate biosynthesis (5 genes) | 2 | 2 | 1 | |||||
Valine biosynthesis (12 genes) | 4 | 3 | 1 | 2 | 3 | |||
Valine degradation II (24 genes) | 5 | 7 | 3 | 6 | 6 | 4 | 2 | 1 |
Xylitol degradation (4 genes) | 1 | 2 | 1 | 1 |
UDP, uridine diphosphate.