Table 2.
SNP Markers associated to morphological and biochemical traits in Italian tomato landraces.
| Phenotypic class | Traita | SolCap IDb | Chrc | Position | Solyc ID | p-value |
|---|---|---|---|---|---|---|
| Morphological traits | ED | 5624 | 02 | 47148187 | Solyc02g083900.2.1 | 2.82E-05 |
| 5625 | 02 | 47218361 | Solyc02g083990.2.1 | 5.07E-05 | ||
| 4597 | 02 | 52417091 | Solyc02g090960.1.1 | 4.47E-06 | ||
| 7584 | 03 | 64512996 | Solyc03g114560.2.1 | 5.31E-06 | ||
| 2501(2) | 04 | 1170841 | Solyc04g007500.1.1 | 2.82E-05 | ||
| 2020 | 06 | 41163560 | Solyc06g065720.1.1 | 2.82E-05 | ||
| 6943 | 07 | 62062707 | –d | 3.77E-05 | ||
| 112 | 12 | 66795414 | Solyc12g099800.1.1 | 2.82E-05 | ||
| GS | 1722 | 07 | 64287991 | Solyc07g056430.2.1 | 4.36E-05 | |
| PI | 7583 | 03 | 64588871 | Solyc03g114690.2.1 | 2.12E-05 | |
| LN | 518 | 01 | 730154 | Solyc01g006050.2.1 | 1.40E-06 | |
| 2557 | 02 | 40887642 | Solyc02g071440.2.1 | 9.13E-07 | ||
| 5731 | 02 | 45515428 | Solyc02g081640.2.1 | 3.71E-07 | ||
| 2994 | 02 | 45761358 | Solyc02g082030.2.1 | 3.71E-07 | ||
| 7465 | 03 | 62386150 | Solyc03g111740.2.1 | 1.45E-06 | ||
| 6980 | 04 | 1163761 | Solyc04g007490.2.1 | 3.71E-07 | ||
| 5963 | 07 | 57927159 | Solyc07g044870.2.1 | 2.51E-07 | ||
| 1981 | 10 | 58672684 | Solyc10g074950.1.1 | 8.30E-08 | ||
| 3617 | 11 | 54854070 | Solyc11g071340.1.1 | 1.45E-06 | ||
| 2076 (2) | 11 | 54970033 | Solyc11g071530.1.1 | 1.45E-06 | ||
| 3534 | 11 | 55072385 | Solyc11g071660.1.1 | 9.13E-07 | ||
| 504 | 11 | 55074586 | Solyc11g071670.1.1 | 1.45E-06 | ||
| Glycoalkaloids | Total | 377 | 08 | 230545 | Solyc08g005300.1.1 | 3.80E-05 |
| 1745 | 10 | 51335068 | – | 3.80E-05 | ||
| 7469 | 10 | 51524389 | Solyc10g051110.1.1 | 3.80E-05 | ||
| 5993 (3) | 10 | 54449604 | Solyc10g054010.1.1 | 3.80E-05 | ||
| 5984 (2) | 10 | 54518281 | Solyc10g054030.1.1 | 3.80E-05 | ||
| 1982 | 10 | 58189616 | – | 3.80E-05 | ||
| Phenolics | Coumaric acid hexoside | 1678 | 03 | 52079075 | Solyc03g080190.2.1 | 4.68E-06 |
| 7575 | 03 | 65365147 | – | 5.20E-07 | ||
| 2374 | 03 | 66796966 | Solyc03g117760.2.1 | 5.68E-06 | ||
| 2373 | 03 | 66806264 | Solyc03g117770.2.1 | 5.18E-05 | ||
| 2372 (2) | 03 | 66807096 | Solyc03g117780.2.1 | 5.18E-05 | ||
| 4652 | 03 | 70262451 | Solyc03g123390.2.1 | 6.96E-06 | ||
| 4651 | 03 | 70365262 | Solyc03g123530.2.1 | 7.32E-06 | ||
| 2193 | 10 | 57397425 | Solyc10g055760.1.1 | 5.68E-06 | ||
| 7535 | 10 | 64340240 | Solyc10g084990.1.1 | 5.68E-06 | ||
| 7534 | 10 | 64340314 | – | 5.68E-06 | ||
| Naringin | 2099 | 04 | 7569869 | Solyc04g017610.2.1 | 6.35E-06 | |
| 6122 | 04 | 36996123 | Solyc04g047750.2.1 | 6.35E-06 | ||
| 1875 | 08 | 63328385 | Solyc08g079900.1.1 | 6.35E-06 | ||
| Amino acids | Ala | 7498 | 02 | 39605044 | Solyc02g069780.2.1 | 3.51E-05 |
| 7499 (2) | 02 | 39617885 | Solyc02g069780.2.1 | 3.51E-05 | ||
| 6407 | 03 | 54696154 | Solyc03g093400.2.1 | 1.45E-05 | ||
| 1572 | 05 | 3898119 | Solyc05g009700.2.1 | 2.71E-05 | ||
| 2915 | 05 | 3947680 | Solyc05g009740.1.1 | 2.71E-05 | ||
| 1327 | 06 | 37080820 | Solyc06g054270.2.1 | 4.73E-05 | ||
| 7664 | 10 | 4260136 | Solyc10g011960.1.1 | 8.55E-06 | ||
| 7122 | 11 | 12993630 | – | 3.41E-05 | ||
| Asn | 1106 | 11 | 55733112 | – | 1.60E-05 | |
| Glu | 3340 | 10 | 6769606 | Solyc10g018140.1.1 | 5.20E-05 | |
| 531 | 10 | 7464111 | Solyc10g018340.1.1 | 5.20E-05 | ||
| 1983 | 10 | 58003053 | Solyc10g074470.1.1 | 5.20E-05 | ||
| 3455 | 10 | 58307818 | Solyc10g074700.1.1 | 5.20E-05 | ||
| Pro | 1918 (4) | 07 | 2870461 | Solyc07g008160.2.1 | 3.30E-05 | |
| 1914 | 07 | 2883786 | Solyc07g008170.2.1 | 3.30E-05 |
For each marker the position in bp on the related chromosome is reported, together with the corresponding gene (Solyc ID) according to SL2.50 and the p-value.
a
Abbreviation as detailed in Materials and Methods.
b
Numbers in brackets indicate multiple significant markers within the same gene.
c
Chromosome.
d
-Not in gene region.