Table 2.
Single-nucleotide polymorphisms associated with southern anthracnose and clover rot resistance
| SNP ID | Chr | Position (bp) | Coefficient(β) | Variance explained (%) | Red clover gene containing SNP | Annotation in Medicago truncatula |
|---|---|---|---|---|---|---|
| Southern anthracnose resistance, single-spore inoculation | ||||||
| LG1_6601280 | 1 | 6,601,280 | − 89.4a | 16.8 | Tp57577_TGAC_v2_gene4880 | MTR_1g103020 3-oxoacyl- (acyl carrier) synthase II |
| LG7_6328288 | 7 | 63,282,88 | − 56.3a | 9.0 | Tp57577_TGAC_v2_gene32177 | MTR_3g117330 kinesin motor catalytic domain protein |
| LG6_16830298 | 6 | 16,830,298 | 25.1a | 6.7 | Tp57577_TGAC_v2_gene23646 |
MTR_2g049640 RNA recognition motif 2 in plant MEI2-like protein |
| Scaf595_126629 | Scaf595 | 126,629 | − 20.9a | 6.3 | No gene | NA |
| LG1_2684496 | 1 | 2,684,496 | − 30.0a | 4.4 | Tp57577_TGAC_v2_gene14494 |
MTR_1g054675 RNA recognition motif |
| Scaf323_195382 | Scaf 323 | 195,382 | 19.4a | 4.0 | Tp57577_TGAC_v2_gene19649 |
MTR_1g041890 peptide chain release factor, putative |
| Scaf215_144740 | Scaf 215 | 144,740 | − 20.0a | 3.6 | Tp57577_TGAC_v2_gene10592 |
MTR_2g026595 Hypothetical protein |
| Scaf8613_1314 | Scaf 8613 | 1,314 | − 36.8a | 3.5 | Tp57577_TGAC_v2_gene22635 |
MTR_3g010210 nucleic acid-binding, OB-fold-like protein |
| Southern anthracnose resistance, mixed-spore inoculation | ||||||
| LG1_6601280 | 1 | 6,601,280 | − 85.bd | 14.3 | Tp57577_TGAC_v2_gene4880 |
MTR_1g103020 3-oxoacyl-(acyl carrier) synthase II |
| LG1_25782873 | 1 | 25,782,873 | 19.7bd | 6.3 | No gene | NA |
| Scaf753_87981 | Scaf 753 | 87,981 | 19.9bd | 3.9 | Tp57577_TGAC_v2_gene29929 | Nothing found |
| Scaf10964_710 | Scaf 10,964 | 710 | 18.7bd | 2.8 | Tp57577_TGAC_v2_gene39892 |
MTR_5g042410 acylamino-acid-releasing enzyme-like protein, putative |
| LG3_11481441 | 3 | 11,481,441 | 44.0bd | 2.6 | Tp57577_TGAC_v2_gene11903 |
MTR_3g037570 peptidylprolyl cis/trans isomerase, NIMA-interacting protein |
| LG7_6328288 | 7 | 6,328,288 | − 34.7 bd | 2.1 | Tp57577_TGAC_v2_gene32177 |
MTR_3g117330 kinesin motor catalytic domain protein |
| Clover rot resistance, single-spore inoculation | ||||||
| Scaf658_16191 | Scaf 658 | 16,191 | 13.8c | 12.8 | Tp57577_TGAC_v2_gene35789 |
MTR_7g079030 proline iminopeptidase-like protein |
| LG1_19399829 | 1 | 19,399,829 | 13.1c | 12.4 | Tp57577_TGAC_v2_gene37747 |
MTR_1g090690 putative disease resistance RPP13-like protein 3 |
| Scaf509_74106 | Scaf 509 | 74,106 | 10.4c | 11.2 | Tp57577_TGAC_v2_gene10001 |
MTR_6g015285 nuclear matrix constituent-like protein |
| Scaf1864_1986 | Scaf1864 | 1986 | −7.8c | 10.5 | Tp57577_TGAC_v2_gene5179 |
MTR_4g058730 cyclic nucleotide-gated ion channel protein |
| LG1_16117955 | 1 | 16,117,955 | −18.0c | 9.5 | Tp57577_TGAC_v2_gene33326 |
MTR_1g029410 small RNA degrading nuclease |
| Scaf430_104086 | Scaf 430 | 104,086 | 7.8c | 9.4 | No gene | Na |
| Scaf512_143846 | Scaf 512 | 143,846 | 14.8c | 8.5 | No gene | Na |
| Scaf3654_3161 | Scaf 3654 | 3161 | −6.4c | 5.9 | Tp57577_TGAC_v2_gene968 |
MTR_3g027470 putative disease resistance RPP13-like protein 1 |
SNP ID, chromosome (Chr), SNP position on the chromosome, effect size as regression coefficient (β), phenotypic variance explained by that SNP, red clover gene containing the SNP, and the gene name and gene function of the closest ortholog in M. truncatula are listed
aIntercept = 82.4
bIntercept = 48.5
cIntercept = 41.0
dBack-transformed BLUEs corrected means