Table 3 SNP and indel variants between resistant and susceptible NILs within the targeted 3AL QTL interval
No. | Variant type | Variant (R/S) | Variant in RefV1.0 | Variant physical position | Associated gene | Gene function | Note |
|---|---|---|---|---|---|---|---|
1 | SNP | C/G | C | 697,456,690 | TraesCS3A01G461800 | F-box domain containing protein | Within gene exon |
2 | SNP | G/A | A | 702,901,184 | TraesCS3A01G471100 | Salicylate O-methyltransferase | 2629 bp away from the gene |
3 | SNP | C/A | C | 698,019,550 | TraesCS3A01G463700 | Transmembrane protein 45B | Within gene exon |
4 | SNP | T/C | T | 697,250,101 | TraesCS3A01G461100 | Succinate dehydrogenase subunit 4 | 49 bp away from the gene |
5 | SNP | C/G | C | 697,561,360 | TraesCS3A01G462400 | 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily protein | Within gene exon |
6 | Indel | GT/− | G | 695,515,689 | TraesCS3A01G458300 | F-box-like protein | Within gene exon |
7 | Indel | GATATTC/− | G | 695,516,298 | “ | “ | Within gene exon |
8 | Indel | C/CT | C | 695,585,583 | TraesCS3A01G458400 | Nucleotide-diphospho-sugar transferases superfamily protein | 52,358 bp away from the gene |
9 | Indel | A/− | AG | 703,016,114 | TraesCS3A01G471400 | Basic 7S globulin 2 | 194 bp away from the gene |
10 | Indel | G/− | GA | 703,016,906 | “ | “ | 986 bp away from the gene |
11 | Indel | C/− | CCG | 688,767,420 | TraesCS3A01G449300 | Auxin response factor | 73,788 bp away from the gene |
12 | Indel | CAA/− | C | 688,767,424 | “ | “ | 73,784 bp away from the gene |
13 | Indel | AT/− | A | 688,768,940 | “ | “ | 43,715 bp away from the gene |
14 | Indel | C/− | CGAG | 700,588,842 | TraesCS3A01G467100 | UV-stimulated scaffold protein A-like protein | 2576 bp away from the gene |
15 | Indel | G/− | GATGCGGTC | 695,658,402 | TraesCS3A01G609800LC | Glucose-1-phosphate adenylyltransferase | Within gene UTR |
16 | Indel | −/G | GC | 686,681,832 | TraesCS3A01G592100LC | Retrovirus-related Pol polyprotein from transposon opus | 3374 bp away from the gene |