Table 3.
Validation of SNPs with conventional sequencing.
| Amplicon | Sequence | Description | Number of predicted SNPs | Validated | Non-validated | New SNPs | Abiotic or biotic stress |
|---|---|---|---|---|---|---|---|
| Amplicon1 | contig02491 | Flavonoid 3 -monooxygenase-like | 11 | 11 | 0 | 4 | Abiotic |
| Amplicon2 | contig25532 | Protein chloroplastic-like | 10 | 10 | 0 | 0 | |
| Amplicon3 | isotig02731 | Chlorophyll a–b binding protein chloroplastic-like | 14 | 13 | 1 | 0 | Abiotic |
| Amplicon4 | isotig11158 | Snf7 family protein | 10 | 7 | 3 | 2 | |
| Amplicon5 | isotig11256 | Mannose-1-phosphate guanylyltransferase alpha-like | 9 | 9 | 0 | 3 | Abiotic and biotic |
| Amplicon6 | isotig11583 | Eukaryotic initiation factor 4a-11 | 9 | 3 | 6 | 1 | Abiotic |
| Amplicon7 | isotig13076 | Lipid-transfer protein dir1 | 10 | 10 | 0 | 1 | Abiotic |
| Amplicon8 | isotig13078 | Cationic amino acid transporter vacuolar-like | 10 | 9 | 1 | 1 | Biotic |
| Amplicon9 | isotig13259 | Transcription factor myb44-like | 14 | 13 | 1 | 0 | Abiotic and biotic |
| Amplicon10 | isotig13272 | Anthocyanidin reductase | 13 | 12 | 1 | 0 | |
| Amplicon11 | isotig18769 | Atp synthase subunit | 10 | 10 | 0 | 2 | Abiotic |
| Amplicon12 | isotig19674 | Probable aldo-keto reductase 1 | 10 | 10 | 0 | 0 | |
| Amplicon13 | isotig20847 | —NA— | 12 | 6 | 6 | 0 | |
| Total | 142 | 123 (87%) | 19 (13%) | 14 |
Number and percentage of validated, non-validated and new SNPs for each of the amplicons from the tree genotypes (J-CA2, M-DV4/5, and TO-AL1) sequenced with dideoxy-based methods. Sequences associated with response to abiotic or biotic stimulus are shown.