Table 2.
Most significant MTAs identified in the study.
| Marker ID1/ | SNP2/ | SNP position (bp)3/ | P value4/ | R25/ | MTA | Corresponding gene; protein | Amino acid change |
|---|---|---|---|---|---|---|---|
| Xuos526258 | T/G | Chr7:112,789,055 | 1.10E−05 | 20.7 | Xuos526258_WFS | SECCE7Rv1G0469720.1;Benzothiadiazole-induced protein phosphatase 2C1 (BIPP2C1) | V/G |
| 1.50 E−05 | 18.5 | Xuos526258_FLN | |||||
| 3.84 E−05 | 16.4 | Xuos526258_PGH | |||||
| 4.17 E−05 | 17.9 | Xuos526258_LTT | |||||
| Xuos530120 | G/C | Chr7:23,476,102 | 5.66 E−05 | 14.5 | Xuos530120_WFS | SECCE7Rv1G0458910.1;Ice recrystallization inhibition protein 1 (IRIP1) | G/R |
| 6.62 E−05 | 16.3 | Xuos530120_PGH | |||||
| 6.80 E−05 | 16.2 | Xuos530120_LTT | |||||
| Xuos615052 | T/A | Chr3:937,715,414 | 7.94 E−05 | 14.7 | Xuos615052_WFS | SECCE3Rv1G0209310.1;Inducer of CBF expression 1 (ICE1) | L/H |
| 8.06 E−05 | 15.8 | Xuos615052_FLN | |||||
| 8.12 E−05 | 14.7 | Xuos615052_PGH | |||||
| 1.04 E−04 | 15.6 | Xuos615052_LTT | |||||
| Xuos519455 | T/A | Chr6:434,208,045 | 1.10 E−04 | 13.1 | Xuos519455_WFS | SECCE6Rv1G0399250.1;Phenylalanine ammonia lyase 8 (PAL8) | F/I |
| Xuos613978 | A/G | Chr5:727,383,264 | 1.11 E−04 | 15.5 | Xuos613978_WFS | SECCE5Rv1G0354870.1, SECCE5Rv1G0354880.1;Cold-regulated plasma membrane 413 protein (COR413-PM) | T/A |
| Chr5:727,387,758 | 1.18 E−04 | 15.3 | Xuos613978_FLN | ||||
| Xuos75199 | A/C | Chr1:716,318,047 | 1.20 E−04 | 15.3 | Xuos75199_WFS | SECCE1Rv1G0061510.1;Jasmonat E−resistant 1 (JAR1) | N/T |
| 1.33 E−04 | 14.6 | Xuos75199_FLN | |||||
| Xuos76228a | C/G | Chr2:933,364,125 | 1.39 E−04 | 14.5 | Xuos76228a_WFS | SECCE2Rv1G0140890.1;Chalcone synthase 2 (CHS2) | Q/E |
| Xuos76228b | C/T | Chr2:933,364,201 | 1.44 E−04 | 13.4 | Xuos76228b_WFS | A/V | |
| Xuos2264 | T/G | Chr1:109,131,359 | 1.45 E−04 | 12.5 | Xuos2264_WFS | SECCE1Rv1G0013960.1;Chloroplast unusual positioning protein 1 (CHUP1) | None (G/G) |
| 1.45 E−04 | 14.4 | Xuos2264_PGH | |||||
| 1.46 E−04 | 14.8 | Xuos2264_FLN | |||||
| Xuos372616 | C/A | Chr5:755,939,404 | 1.47 E−04 | 14.8 | Xuos372616_WFS | FRIGIDA-like 4 (FRL4-like) | None (A/A) |
1/Number refers to matching rye Lo7_v2_scaffold number3; 2/Reference/alternative allele; 3/Position on rye Lo7 pseudomolecules version 1 assembly4; 4/Calculated upon Bonferroni correction. 5/Explained variation.