Table 2.
Summary of epigenetic quantitative trait loci (QTLepi) detected in the Arabidopsis epigenetic recombinant inbred lines (epiRIL) population by multiple QTL mapping (MQM)
| Trait | Condition | Test location | QTL | Chr | Pos | Lod | Closest peak marker | Confidence interval (cM) | R 2 (%) | R 2 for all QTL by trait | Favourable allele | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| G‐Rbi | Infected | Growth room‐2 | Rbiepi‐At1 | 1 | 56.00 | 3.04 | MM147 | 8.00 | 62.33 | 6.67 | 44.59 | WT |
| Growth room‐2 | Rbiepi‐At2a | 2 | 32.00 | 7.48 | MM383 | 28.00 | 35.62 | 17.91 | WT | |||
| Growth room‐2 | Rbiepi‐At2b | 2 | 40.00 | 6.18 | MM385 | 36.00 | 46.00 | 14.42 | ddm1‐2 | |||
| Growth room‐2 | Rbiepi‐At4 | 4 | 28.00 | 4.79 | MM686 | 22.02 | 36.00 | 10.88 | WT | |||
| G‐Lfi | Infected | Growth room‐1 | Lfi1epi‐At1 | 1 | 33.60 | 6.51 | MM 52 | 20.00 | 44.00 | 15.50 | 43.82 | WT |
| Growth room‐1 | Lfi1epi‐At3 | 3 | 46.10 | 6.32 | MM427 | 44.36 | 50.59 | 15.01 | WT | |||
| Growth room‐1 | Lfi1epi‐At5 | 5 | 37.80 | 3.60 | MM728 | 16.00 | 52.00 | 8.11 | WT | |||
| Growth room‐2 | Lfi2epi‐At1 | 1 | 37.05 | 5.14 | MM91 | 18.00 | 56.00 | 15.65 | 26.16 | WT | ||
| Growth room‐2 | Lfi2epi‐At3 | 3 | 49.45 | 4.04 | MM515 | 44.37 | 52.00 | 12.06 | WT | |||
| G‐Pb | Infected | Growth room‐1 | Pb1epi‐At1 | 1 | 42.00 | 4.36 | MM123 | 20.00 | 45.93 | 14.64 | 19.59 | WT |
| Growth room‐1 | Pb1epi‐At4 | 4 | 0.00 | 2.95 | MM550 | 0.00 | 8.00 | 9.65 | ddm1‐2 | |||
| Growth room‐2 | Pb2epi‐At4 | 4 | 42.99 | 3.05 | MM693 | 32.00 | 50.00 | 10.86 | 10.86 | ddm1‐2 | ||
| GT‐Lfi | Infected | Growth room‐2 | LfiepiGT‐At1 | 1 | 52.00 | 3.32 | MM128 | 33.07 | 61.20 | 10.67 | 19.34 | WT |
| Growth room‐2 | LfiepiGT‐At3 | 3 | 49.45 | 2.47 | MM547 | 6.00 | 82.00 | 7.81 | WT | |||
| GT‐Rbi | Infected | Growth room‐2 | RbiepiGT‐At3 | 3 | 46.65 | 2.52 | MM432 | 40.00 | 50.59 | 9.06 | 9.06 | WT |
| GT‐Pb | Infected | Growth room‐2 | PbepiGT‐At4a | 4 | 22.00 | 2.38 | MM679 | 1.73 | 30.00 | 8.04 | 15.89 | ddm1‐2 |
| Growth room‐2 | PbepiGT‐At4b | 4 | 36.00 | 4.50 | MM689 | 22.02 | 42.00 | 15.88 | ddm1‐2 | |||
| G‐Lfni | Noninfected | Growth room‐2 | Lfniepi‐At1 | 1 | 44.80 | 8.32 | MM126 | 41.15 | 61.20 | 19.66 | 46.20 | WT |
| Growth room‐2 | Lfniepi‐At3 | 3 | 49.46 | 5.75 | MM515 | 48.32 | 52.00 | 12.93 | WT | |||
| Growth room‐2 | Lfniepi‐At5 | 5 | 20.00 | 4.76 | MM713 | 12.73 | 31.00 | 10.49 | WT | |||
| G‐Rbni | Noninfected | Growth room‐2 | Rbniepi‐At1 | 1 | 44.80 | 3.39 | MM126 | 18.00 | 56.00 | 10.44 | 22.93 | WT |
| Growth room‐2 | Rbniepi‐At4 | 4 | 42.43 | 3.72 | MM691 | 34.00 | 50.00 | 11.51 | WT | |||
| G‐ΔLf | Noninfected – Infected | Growth room‐2 | ΔLfepi‐At1 | 1 | 20.00 | 3.79 | MM10 | 16.45 | 52.00 | 10.44 | 31.55 | ddm1‐2 |
| Growth room‐2 | ΔLfepi‐At3 | 3 | 49.46 | 3.68 | MM515 | 30.00 | 62.00 | 10.11 | ddm1‐2 | |||
| Growth room‐2 | ΔLfepi‐At5 | 5 | 47.36 | 3.08 | MM854 | 37.80 | 54.00 | 8.38 | ddm1‐2 | |||
Confidence intervals are in cM. Peak positions are indicated in cM and with the marker nearest to the logarithm of odds (LOD) score peak. R², phenotypic variation explained by the QTLepi. Chr, chromosome. For Lfi and Rbi, favourable alleles are associated with an increase in the value. For Pb, favourable alleles are associated with a decrease in the value. G‐Rbi, G‐Lfi and G‐Pb represent epigenetic QTL for each trait in infected condition. G‐Lfni and G‐Rbni represent epigenetic QTL for each trait in control condition. G‐ΔLf represents epigenetic QTL obtained by difference between leaf length in infected condition and leaf length in control condition. GT‐Rbi, GT‐Lfi and GT‐Pb represent epigenetic × temperature QTL for each trait.WT, wild‐type; ddm1‐2, mutant allele.DI, disease index; Pb, pathogen DNA quantity; Lfi, leaf length in infected condition; Rbi, root biomass in infected condition; Lfni and Rbni, respectively, leaf length and root biomass in control (noninfected) condition; ΔLf, change in leaf length.