Table 2. Cis eQTL pertaining to fruit-expressed genes in F. ×ananassa.
| R-gene Name | eQTL phase | IStraw35 AX- | MAF | p-value (FDR) | h2 estimate | Mara | Elya-na | Radi-ance | Festi-val | Winter dawn | Description |
|---|---|---|---|---|---|---|---|---|---|---|---|
| augustus_masked-fvb1-2-processed-gene-27.2 | cis | 89817565 | 0.43 | 0.0418 | 30.4% | 36.6 | 113.3 | 32.2 | 21.3 | 34.3 | uncharacterized protein LOC101293711 |
| augustus_masked-fvb1-4-processed-gene-7.11 | cis | 166502627 | 0.16 | 0.0150 | 43.4% | 2.3 | 0.6 | 4.0 | 3.8 | 1.6 | PLT5_ARATH Sugar-proton symporter PLT5 |
| augustus_masked-fvb2-4-processed-gene-105.5 | cis | 166503861 | 0.29 | 0.0114 | 80.9% | 0.0 | 0.0 | 2.8 | 1.8 | 1.3 | TMVRN_NICGU TMV resistance N |
| augustus_masked-fvb3-1-processed-gene-107.3 | cis | 166511589 | 0.50 | 0.0294 | 41.8% | 0.0 | 0.5 | 0.7 | 0.8 | 0.3 | DRL30_ARATH Probable disease resistance At5g04720 |
| augustus_masked-fvb3-3-processed-gene-283.7 | cis | 89786873 | 0.38 | 0.0009 | 30.4% | 0.8 | 0.4 | 0.0 | 2.6 | 0.4 | DRL1_ARATH Probable disease resistance At1g12280 |
| augustus_masked-fvb3-3-processed-gene-38.8 | cis | 166513199 | 0.23 | 0.0032 | 81.7% | 6.0 | 3.0 | 5.5 | 0.8 | 4.9 | Y4294_ARATH LRR receptor-like serine threonine- kinase |
| augustus_masked-fvb3-4-processed-gene-19.4 | cis | 166504873 | 0.28 | 0.0014 | 100% | 0.1 | 4.8 | 5.6 | 8.0 | 0.1 | DR100_ARATH DNA damage-repair toleration DRT100 |
| augustus_masked-fvb4-1-processed-gene-166.2 | cis | 166505902 | 0.43 | 0.0083 | 91.5% | 0.6 | 0.4 | 2.5 | 1.4 | 1.8 | MKKA_DICDI Mitogen-activated kinase kinase |
| augustus_masked-fvb4-2-processed-gene-107.10 | cis | 166527457 | 0.18 | 0.0202 | 100% | 0.0 | 0.0 | 1.2 | 1.0 | 0.1 | RGA1_SOLBU disease resistance RGA1 RGA3-blb |
| augustus_masked-fvb4-2-processed-gene-258.8 | cis | 166505336 | 0.35 | 0.0015 | 25.1% | 4.6 | 0.0 | 1.4 | 1.3 | 0.1 | LRX2_ARATH Leucine-rich repeat extensin 2 |
| augustus_masked-fvb5-1-processed-gene-238.7 | cis | 123365994 | 0.09 | 0.0012 | 74.1% | 0.8 | 0.8 | 1.4 | 2.8 | 0.5 | HSL1_ARATH Receptor kinase HSL1 HAESA-LIKE1 |
| augustus_masked-fvb5-1-processed-gene-71.8 | cis | 166524323 | 0.48 | 0.0080 | 35.5% | 1.7 | 0.0 | 10.3 | 4.4 | 3.0 | TIR_ARATH Toll interleukin-1 receptor |
| augustus_masked-fvb5-3-processed-gene-135.4 | cis | 166523635 | 0.26 | 0.0124 | 63.7% | 0.5 | 0.2 | 0.1 | 0.0 | 0.0 | MKKA_DICDI Mitogen-activated kinase kinase |
| augustus_masked-fvb5-4-processed-gene-18.1 | cis | 166518037 | 0.35 | 0.0110 | 26.6% | 0.8 | 1.4 | 0.7 | 2.5 | 0.8 | RGA1_SOLBU disease resistance RGA1 RGA3-blb |
| augustus_masked-fvb5-4-processed-gene-241.6 | cis | 123525092 | 0.44 | 0.0007 | 64.9% | 1.4 | 0.1 | 2.5 | 2.1 | 1.8 | LRX2_ARATH Leucine-rich repeat extensin 2 2 LRR |
| augustus_masked-fvb6-1-processed-gene-345.10 | cis | 166524541 | 0.21 | 0.0050 | 31.7% | 1.8 | 0.7 | 4.1 | 4.1 | 2.2 | HSL1_ARATH Receptor kinase HSL1 HAESA-LIKE1 |
| augustus_masked-fvb7-1-processed-gene-57.2 | cis | 166509572 | 0.12 | 0.0003 | 73.3% | 0.5 | 0.2 | 0.6 | 0.2 | 13.2 | TIR_ARATH Toll interleukin-1 receptor |
| augustus_masked-fvb7-2-processed-gene-302.13 | cis | 166517211 | 0.29 | 0.0083 | 69.2% | 2.3 | 0.0 | 2.1 | 0.1 | 0.0 | MKKA_DICDI Mitogen-activated kinase kinase |
| augustus_masked-fvb7-2-processed-gene-53.6 | cis | 166509530 | 0.49 | 0.0118 | 35.7% | 1.2 | 0.2 | 0.5 | 0.4 | 2.2 | RGA1_SOLBU disease resistance RGA1 RGA3-blb |
| augustus_masked-fvb7-2-processed-gene-54.1 | cis | 166509530 | 0.49 | 0.0121 | 100% | 9.9 | 0.1 | 0.4 | 0.3 | 11.5 | LRX2_ARATH Leucine-rich repeat extensin 2 2 LRR |
| maker-fvb1-4-augustus-gene-30.48 | cis | 123365069 | 0.33 | 0.0175 | 63.8% | 2.5 | 0.4 | 3.1 | 4.2 | 2.5 | HSL1_ARATH Receptor kinase HSL1 HAESA-LIKE1 |
| maker-fvb2-1-augustus-gene-182.42 | cis | 89877559 | 0.46 | 0.0225 | 80.9% | 2.1 | 3.8 | 2.2 | 3.2 | 0.8 | MKKA_DICDI Mitogen-activated kinase |
| maker-fvb2-1-snap-gene-111.27 | cis | 166503168 | 0.29 | 0.0002 | 100% | 0.5 | 0.0 | 0.0 | 2.0 | 1.2 | RGA1_SOLBU disease resistance RGA1 RGA3-blb |
| maker-fvb7-1-snap-gene-223.45 | cis | 123540423 | 0.45 | 0.0077 | 70.3% | 2.4 | 0.1 | 0.1 | 0.0 | 1.7 | LRX2_ARATH Leucine-rich repeat extensin 2 2 LRR |
| maker-fvb7-4-snap-gene-48.49 | cis | 166508582 | 0.34 | 0.0357 | 75.1% | 0.3 | 0.4 | 0.1 | 0.0 | 0.2 | HSL1_ARATH Receptor kinase HSL1 HAESA-LIKE1 |
| maker-fvb7-4-snap-gene-59.59 | cis | 166518351 | 0.50 | 0.0064 | 4.7% | 0.9 | 0.4 | 1.8 | 0.1 | 1.6 | TIR_ARATH Toll interleukin-1 receptor |
| maker-fvb7-4-snap-gene-59.63 | cis | 166518351 | 0.50 | 0.0092 | 44.8% | 0.1 | 0.0 | 0.6 | 0.0 | 0.4 | MKKA_DICDI Mitogen-activated kinase |
| maker-fvb7-4-snap-gene-69.51 | cis | 123359450 | 0.17 | 0.0002 | 82.6% | 2.3 | 1.8 | 2.1 | 3.6 | 2.2 | RGA1_SOLBU disease resistance RGA1 RGA3-blb |
| snap_masked-fvb1-2-processed-gene-79.33 | cis | 123359751 | 0.08 | 0.0068 | 98.3% | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | LRX2_ARATH Leucine-rich repeat extensin 2 2 LRR |
| snap_masked-fvb2-1-processed-gene-107.14 | cis | 89780995 | 0.22 | 0.0011 | 75.1% | 2.1 | 2.6 | 8.5 | 4.0 | 3.4 | HSL1_ARATH Receptor kinase HSL1 HAESA-LIKE1 |
| snap_masked-fvb3-2-processed-gene-11.25 | cis | 166509770 | 0.37 | 0.0084 | 11.4% | 0.2 | 0.2 | 1.1 | 1.5 | 0.7 | TIR_ARATH Toll interleukin-1 receptor |
| snap_masked-fvb3-3-processed-gene-288.15 | cis | 123361033 | 0.45 | 0.0095 | 98.9% | 0.9 | 0.5 | 2.0 | 1.4 | 1.3 | MKKA_DICDI Mitogen-activated kinase kinase kinase A |
| snap_masked-fvb6-1-processed-gene-37.31 | cis | 166519417 | 0.34 | 0.0411 | 24.2% | 13.3 | 19.2 | 0.9 | 0.5 | 0.0 | RGA1_SOLBU disease resistance RGA1 |
| snap_masked-fvb7-2-processed-gene-254.35 | cis | 123357141 | 0.33 | 0.0011 | 36.5% | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | LRX2_ARATH Leucine-rich repeat extensin 2 2 |
| maker-fvb7-1-snap-gene-273.51 | cis | 166508667 | 0.43 | 0.0319 | 35.7% | 0.0 | 0.0 | 0.0 | 0.4 | 0.0 | Y3475_ARATH LRR receptor-like serine threonine- kinase |
| maker-fvb3-4-augustus-gene-265.40 | cis | 166513103 | 0.13 | 0.0007 | 54.7% | 4.4 | 5.3 | 2.6 | 18.8 | 5.2 | GLO5_ARATH Peroxisomal(S)-2-hydroxy-acid oxidase GLO5 |
| maker-fvb5-1-snap-gene-191.37 | cis | 166523649 | 0.13 | 0.0000 | 36.5% | 0.0 | 0.0 | 0.0 | 0.0 | 0.1 | RPM1_ARATH Disease resistance RPM1 |
| maker-fvb5-2-augustus-gene-59.20 | cis | 123364094 | 0.46 | 0.0036 | 46.0% | 0.0 | 0.3 | 4.0 | 12.0 | 0.8 | probable LRR receptor-like serine threonine- kinase At5g48740 |
| maker-fvb5-2-augustus-gene-61.13 | cis | 123364094 | 0.46 | 0.0014 | 71.7% | 0.0 | 0.3 | 2.2 | 1.6 | 0.8 | P2B10_ARATH F-box PP2-B10 PHLOEM PROTEIN 2-LIKE |
| maker-fvb5-2-augustus-gene-63.17 | cis | 123364094 | 0.46 | 0.0072 | 16.5% | 0.0 | 0.0 | 3.5 | 3.7 | 1.1 | P2B11_ARATH F-box PP2-B11 PHLOEM PROTEIN 2-LIKE |
| maker-fvb5-2-snap-gene-4.75 | cis | 166506813 | 0.32 | 0.0000 | 29.9% | 2.1 | 9.3 | 37.2 | 43.0 | 1.4 | DRL28_ARATH Probable disease resistance At4g27220 |
| maker-fvb5-2-snap-gene-61.17 | cis | 123364094 | 0.46 | 0.0291 | 78.4% | 0.0 | 0.2 | 1.3 | 1.4 | 0.3 | P2B11_ARATH F-box PP2-B11 PHLOEM PROTEIN 2-LIKE |
| maker-fvb5-3-augustus-gene-135.25 | cis | 89832439 | 0.37 | 0.0040 | 11.5% | 0.0 | 0.0 | 1.6 | 0.3 | 1.3 | RPM1_ARATH Disease resistance RPM1 |
| maker-fvb4-3-snap-gene-155.68 | cis | 123524810 | 0.21 | 0.0016 | 100% | 0.1 | 0.2 | 0.6 | 0.1 | 0.5 | TMVRN_NICGU TMV resistance N |
| maker-fvb5-3-snap-gene-221.67 | cis | 89893608 | 0.11 | 0.0045 | 94.4% | 0.5 | 0.2 | 0.1 | 1.6 | 0.1 | TMVRN_NICGU TMV resistance N |
| maker-fvb5-3-snap-gene-254.50 | cis | 166523796 | 0.21 | 0.0155 | 51.8% | 0.1 | 0.1 | 0.4 | 0.5 | 0.1 | TMVRN_NICGU TMV resistance N |
| maker-fvb5-4-snap-gene-125.42 | cis | 166506186 | 0.18 | 0.0078 | 93.2% | 0.6 | 0.0 | 2.0 | 2.3 | 1.4 | RGA3_SOLBU RGA3 Blight resistance B149 |
| maker-fvb6-1-augustus-gene-153.32 | cis | 166507404 | 0.17 | 0.0000 | 76.3% | 0.0 | 0.0 | 23.5 | 6.8 | 17.5 | RGA3_SOLBU RGA3 Blight resistance B149 |
| maker-fvb5-2-augustus-gene-61.14 | cis | 123358673 | 0.47 | 0.0167 | 44.9% | 0.0 | 0.1 | 0.7 | 1.2 | 0.3 | P2B10_ARATH F-box PP2-B10 PHLOEM PROTEIN 2-LIKE |
| augustus_masked-fvb7-1-processed-gene-284.2 | cis | 123359573 | 0.4 | 0.0139 | 95.1% | 0.3 | 0 | 0.1 | 0.3 | 0.2 | EMS1_ARATH Leucine-rich repeat receptor kinase EMS1 |
| snap_masked-fvb6-2-processed-gene-263.31 | cis | 89781514 | 0.24 | 0.0084 | 54.9% | 0 | 0 | 4.3 | 4.3 | 2.2 | TMVRN_NICGU TMV resistance N |
| maker-fvb6-1-augustus-gene-160.45 | cis | 166515747 | 0.21 | 0.0340 | 38.4% | 12.6 | 8.8 | 11.9 | 4.2 | 10.3 | DGK5_ARATH Diacylglycerol kinase 5 |
Genetic association results for 61 transcriptomes are shown, detailing cis genetic factors controlling differentially expressed R-genes. The most significant marker name, minor allele frequency, FDR-adjusted p-value, narrow sense heritability, transcript accumulation in cultivars, and BLAST2GO description are shown.