Table 4.
Details of KASP assays designed from marker associations identified from exome capture sequencing.
| Marker | Type (QTL) | Chromosome | Position (Mb) | Gene | Functional desctription | Est AFD | True AFD | χ2 | −log10p |
|---|---|---|---|---|---|---|---|---|---|
| SNP Assay 1 | Winter (Wnt-1) | chr1H | 4,190,695 | HORVU1Hr1G001960 | 12-oxophytodienoate reductase 2 | 0.92 | 0.71 | 14.29 | 3.80 |
| SNP Assay 2 | Winter (Wnt-2) | chr2H | 677,198,003 | HORVU2Hr1G096960 | glutathione peroxidase 6 | 0.80 | 0.40 | 3.2 | 1.13 |
| SNP Assay 3 | Winter (Wnt-3) | chr4H | 636,354,086 | HORVU4Hr1G087230 | Ectonucleoside triphosphate diphosphohydrolase 5 | 0.79 | 0.60 | 10.8 | 2.99 |
| SNP Assay 4 | Winter (Wnt-4) | chr7H | 4,498,971 | HORVU7Hr1G002370 | Glutathione S-transferase family protein | 0.89 | 0.57 | 9.14 | 2.60 |
| SNP Assay 5 | Winter (Wnt-4) | chr7H | 15,062,551 | HORVU7Hr1G010690 | Acid phosphatase 1 | 0.80 | 0.82 | 14.73 | 3.91 |
| SNP Assay 6 | Winter (Wnt-5) | chr7H | 74,643,257 | HORVU7Hr1G034860 | Unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein. | 0.78 | 0.85 | 18.62 | 4.80 |
| SNP Assay 7 | Winter (Wnt-5) | chr7H | 75,226,930 | HORVU7Hr1G035020 | Alpha-amylase/trypsin inhibitor | 0.78 | 0.80 | 12.8 | 3.46 |
| SNP Assay 8 | Winter (Wnt-6) | chr7H | 647,757,050 | – | - | 0.92 | 0.50 | 8 | 2.33 |
| SNP Assay 9 | Spring (Spr-1) | chr4H | 642,563,684 | HORVU4Hr1G089510 (Bmy1) | beta-amylase 5 | 0.55 | 0.06 | 0.12 | 0.144 |
| SNP Assay 10 | Spring (Spr-1) | chr4H | 644,846,286 | HORVU4Hr1G090300 | Transcriptional coactivator/pterin dehydratase | 0.98 | 0.85 | 18.62 | 4.80 |
| SNP Assay 11 | Spring (Spr-2) | chr5H | 589,149,449 | HORVU5Hr1G092740 | unknown function | 0.76 | 0.80 | 12.8 | 3.46 |
| SNP Assay 12 | Spring (Spr-3) | chr7H | 625,333,886 | – | – | 0.75 | 0.33 | 4 | 1.34 |
| SNP Assay 13 | Spring (Spr-3) | chr7H | 635,239,502 | HORVU7Hr1G112360 | Alpha-amylase | 0.61 | 0.14 | 0.29 | 0.23 |
The population from which the association was identified (along with the QTL) is indicated along with its chromosome and physical location, and the name and functional description of the gene containing the SNP. Estimated absolute allele frequencies (High DP set–Low DP set) from the exome capture and sequencing are shown along with the true allele frequency (from individual genotyping). Results from a chi-squared test of homogeneity are also shown.