TABLE 2.
Summary of significant SNPs observed for quality traits of the diversity panel in GWAS and meta-analysis.
| Trait | Candidate gene (distance from peak SNP in kb) | SNP IDs | NCBI ID | Chr. | Position |
GWAS |
Meta-analysis |
||||
| −log10(P) | PVE% | A.E. | MAF | Meta P value | N-level | ||||||
| Oil | CER26 (2.08) | A04_6252658 | 15236357 | A04 | 6252658 | 3.09 | 14.82 | 1.04 | 0.18 | 0.00 × 10–35 | N100 |
| GDSL esterase/lipase gene (13.96) | A06_26456373, 97, 466 | 15228051 | A06 | 26456373-6466 | 3.17 | 16.29 | 0.47 | 0.17 | 4.33 × 10–6 | N0, NP | |
| GDSL esterase/lipase gene (0.38) | A09_14737522 | 15228051 | A09 | 14737522 | 3.19 | 17.1 | -1.12 | 0.3 | 2.44 × 10–6 | N0, NP | |
| LACS5 (within gene, in intronic region) | A09_24082148, 2198, 3336 | 1032284411 | A09 | 24082148-3336 | 3.39 | 15.88 | 0.45 | 0.3 | 1.44 × 10–6 | N0, NP | |
| FAD6 (1.64) | B05_5272794, 95 | 15235766 | B05 | 5272794-2795 | 4.1 | 20.37 | 0.82 | 0.09 | 3.63 × 10–6 | N0, NP | |
| At1g06090 (within gene, in intronic region) ADS1 (2.31) | B06_19315729 | 1032298998 15221393 | B06 | 19315729 | 3.03 | 11.92 | -0.93 | 0.12 | 1.67 × 10–7 | N0, N100, NP | |
| DIR1 (3.83) | B08_34645905, 5977, 5991, 6006 | 18413820 | B08 | 34645905-6006 | 3.34 | 8.82 | -0.34 | 0.4 | 4.92 × 10–5 | N0, NP | |
| PTN | PASTICCINO 1 (1.46) | A04_12420732, 5239 | 3080740 | A04 | 12420732-5239 | 3.08 | 16.73 | 0 | 0.26 | 1.13 × 10–6 | N0, N100, NP |
| AtP4H3 (within gene, in exonic region) | A06_9257535, 68 | 18394842 | A06 | 9257535-7568 | 3.74 | 16.11 | 0 | 0.12 | 9.18 × 10–5 | N100, NP | |
| ASN1 (1.08) | A06_15534622, 4718, 4750 | 15232775 | A06 | 15534622-4750 | 3.02 | 14.09 | -0.23 | 0.12 | 0.00 × 10–96 | N100, NP | |
| GTR2 (6.84) | A06_17974981, 5007, 5009,5010 | 15241927 | A06 | 17974981-5010 | 3.3 | 15.04 | 0.35 | 0.12 | 0.00 × 10–79 | N100, NP | |
| At2g41640 (9.24) | A06_27490668, 71, 93 | 186499036 | A06 | 27490668-0693 | 4.03 | 23.21 | 0.83 | 0.25 | 8.72 × 10–6 | N0, NP | |
| PSP1 (3.71) | A09_30208138 | 30692244 | A09 | 30208138 | 3.08 | 15.94 | -1.05 | 0.11 | 6.28 × 10–6 | N0, NP | |
| PSP1 (1.91) | B03_3166770, 6905, 6907, 6926, 6935, 6980, 7018, 7058 | 42571535 | B03 | 3166770-7058 | 3.3 | 17.84 | 0.28 | 0.23 | 2.74 × 10–6 | N0, NP | |
| GSL | HB16 (2.29) SK1 (3.35) | A04_11732900, 2912, 2989, 3020, 3023, 3024, 3028, 3029 | 189303601 189303601 | A04 | 11732900-3029 | 3.99 | 15.48 | 2.37 | 0.19 | 7.99 × 10–7 | NP^ |
| AT2G35450 (1.20) | A05_5070339 | 79594244 | A05 | 5070339 | 3.08 | 13.17 | 7.37 | 0.05 | 1.34 × 10–5 | NP^ | |
| CM1 (1.70) | A06_24763290 | 9293913 | A06 | 24763290 | 3.05 | 13.75 | 2.73 | 0.5 | 6.59 × 10–7 | NP^ | |
| CM1 (1.70) | A06_24773388 | A06 | 24773388 | 3.34 | 13.86 | -3.05 | 0.4 | 2.47 × 10–7 | NP^ | ||
| JMT (1.92) | B03_19283625, 26 | 13676829 | B03 | 19283625-3626 | 3.05 | 15.28 | 0 | 0.08 | 0.00 × 10–7 | – | |
| CM1 (6.51) | B04_2285588, 589, 789 | 18406100 | B04 | 2285588-5789 | 3.11 | 15.53 | 3.38 | 0.04 | 0.00 × 10–73 | N0^ | |
| LINC4 (within gene, in exonic region) | B06_8990634, 55, 70 | 240256486 | B06 | 8990634-0670 | 3.55 | 17.46 | -1.51 | 0.49 | 6.61 × 10–5 | N0^ | |
| CYP81G1 (12.97) MYB44 (15.71) | B06_9279577, 727, 731 | 30698292 1263095 | B06 | 9279577-9731 | 3.19 | 15.88 | -4.8 | 0.28 | 1.35 × 10–5 | N0^ | |
^These had highest m-values and were non-significant for meta-analysis over N-levels. PTN, proteins; GSL, glucosinolates; Chr., chromosome; PVE, phenotypic variation explained; A.E., allelic effect; MAF, minor allele frequency.