Table 1.
Functional annotation of putative candidate genes in 15 linkage groups of C. sinensis on reference tea genome.
| Nr | QTL | Parent | DArTseq Marker | LG | Position (cM) | LOD | PEV | E-value | Annotated protein | Function |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | qECGa | TRFK 303/577, GW Ejulu | 5128890 | 1 | 96.4 | 6.8 | 11.7 | 2.0E-25 | [‘Actin’] | Abiotic stress |
| 2 | qECa | TRFK 303/577, GW Ejulu | 5072338 | 2 | 2.2 | 4.1 | 5.6 | 2.0E-25 | [‘Peptidase family M3’] | Abiotic stress |
| 3 | qEGCa | GW Ejulu | 5124128 | 2 | 7.7 | 3.2 | 6.8 | 2.0E-18 | [‘Kinesin motor domain’] | Transport protein |
| 4 | qCaffeineb | TRFK 303/577, GW Ejulu | 5064585 | 2 | 50.9 | 3.4 | 5.8 | 6.0E-25 | [‘Peptidase C65 Otubain’] | Modification of cellular proteins |
| 5 | qECGa | TRFK 303/577, GW Ejulu | 5097659 | 4 | 17.1 | 4.6 | 7.8 | 1.0E-07 | [‘Rpp14/Pop5 family’] | — |
| 6 | qECGa | TRFK 303/577 | 5087113 | 4 | 17.7 | 4.7 | 22.9 | 6.0E-22 | [‘impB/mucB/samB family’] | UV protection through DNA repair |
| 7 | qECa | GW Ejulu | 5134490 | 4 | 26.4 | 12.6 | 43.7 | 3.0E-08 | [‘Aminotransferase class I and II’] | Phenylalanine, tyrosine and tryptophan biosynthesis |
| 8 | qEGCGa | GW Ejulu | 5134853 | 4 | 37.6 | 14.9 | 45.1 | 2.0E-06 | [‘Diacylglycerol kinase catalytic domain’] | Abiotic stress |
| 9 | qTF1a | TRFK 303/577, GW Ejulu | 5106352 | 4 | 26.0 | 14.7 | 45.6 | 2.0E-06 | [‘Thiolase, C-terminal domain’] | Benzoic acid biosynthesis |
| 10 | qECa | GW Ejulu | 5123475 | 4 | 27.2 | 14 | 51.5 | 1.0E-10 | CSA016461 | — |
| 11 | qEGCa | GW Ejulu | 5123475 | 4 | 27.2 | 3.7 | 51.5 | 1.0E-10 | CSA016461 | — |
| 12 | qECa | TRFK 303/577 | 5119221 | 4 | 32.7 | 3.1 | 53.8 | 1.0E-19 | [‘Histone acetyltransferase subunit NuA4’] | Drought response |
| 13 | qEGCGa | TRFK 303/577 | 5119221 | 4 | 20.6 | 3.3 | 53.8 | 1.0E-19 | [‘Histone acetyltransferase subunit NuA4’] | Drought response |
| 14 | qEGCa | TRFK 303/577, GW Ejulu | 5136058 | 4 | 27.6 | 46.1 | 54.1 | 1.0E-07 | [‘Autophagy-related protein 11’] | Abiotic stress |
| 15 | qTF4a | TRFK 303/577, GW Ejulu | 5136058 | 4 | 27.6 | 14.8 | 54.1 | 1.0E-07 | CSA024230 | — |
| 16 | qCaffeineb | TRFK 303/577, GW Ejulu | 5114692 | 4 | 68.6 | 3.8 | 6.1 | 4.0E-23 | [‘BT1 family’] | Transport protein |
| 17 | qCATb | TRFK 303/577 | 5119221 | 4 | 32.7 | 3.1 | 2.3 | 1.0E-19 | [‘Histone acetyltransferase subunit NuA4’] | Drought response |
| 18 | qECGa | TRFK 303/577 | 5136985 | 6 | 26.4 | 5.1 | 5.3 | 6.0E-28 | [‘KOW motif’] | — |
| 19 | qTF1a | TRFK 303/577 | 5136045 | 6 | 69.6 | 4.5 | 6.9 | 6.0E-19 | [‘Catalase’] | Abiotic stress |
| 20 | qECGb | TRFK 303/577, GW Ejulu | 5108503 | 6 | 56.5 | 4.8 | 8.2 | 2.0E-27 | [‘DnaJ domain’] | Drought response |
| 21 | qECGb | GW Ejulu | 5098382 | 6 | 56.9 | 4 | 8.7 | 6.0E-19 | [‘Asparagine synthase, Glutamine amidotransferase domain’] | Nitrogen mobilization |
| 22 | qRWCb | TRFK 303/577 | 5082606 | 6 | 66.2 | 3.3 | 5.7 | 9.0E-21 | [‘Alpha adaptin AP2’] | Abiotic stress |
| 23 | qCaffeineb | GW Ejulu | 5064391 | 7 | 48.1 | 3.7 | 6 | 2.0E-27 | [‘Lipase (class 3)’] | Lipid degradation, esterification and transesterification processes |
| 24 | qCaffeineb | TRFK 303/577, GW Ejulu | 5134558 | 8 | 18.8 | 3.9 | 7.5 | 9.0E-24 | [‘Nitronate monooxygenase’] | Catabolic or anabolic pathways |
| 25 | qRWCb | TRFK 303/577, GW Ejulu | 5130531 | 9 | 6.7 | 4 | 7 | 7.0E-06 | [‘MatE’] | Drought response, Sequestration of proanthocyanidins |
| 26 | qTF2a | TRFK 303/577, GW Ejulu | 5128967 | 10 | 28.7 | 3.5 | 7 | 2.0E-25 | [‘Acyl-CoA oxidase’] | Lipid catabolism and plant hormone biosynthesis |
| 27 | qECGa | GW Ejulu | 5072021 | 10 | 25.5 | 4.3 | 7.5 | 8.0E-09 | [‘ATPase family associated with various cellular activities (AAA)’] | Heat stress response |
| 28 | qECGb | GW Ejulu | 5136108 | 10 | 20.6 | 4.8 | 5.7 | 1.0E-10 | [‘Protein kinase domain’] | Abiotic stress |
| 29 | qECGb | TRFK 303/577, GW Ejulu | 5124207 | 10 | 20.4 | 3.1 | 5.3 | 8.0E-12 | [‘Acyltransferase’] | Phenylpropanoid and Shikimate pathway |
| 30 | qEGCGa | TRFK 303/577 | 5088456 | 12 | 47.9 | 3.9 | 9.8 | 4.0E-23 | [‘Protein kinase domain’] | Abiotic stress |
| 31 | qCATa | GW Ejulu | 5136077 | 12 | 42.8 | 6.6 | 11.2 | 5.0E-13 | CSA026168 | — |
| 32 | qEGCa | GW Ejulu | 5136077 | 12 | 42.8 | 5.6 | 11.2 | 5.0E-13 | CSA026168 | — |
| 33 | qCATa | TRFK 303/577, GW Ejulu | 5123751 | 12 | 43.0 | 6.1 | 11.5 | 2.0E-18 | [‘Bromodomain’] | Scaffolding proteins |
| 34 | qEGCa | TRFK 303/577, GW Ejulu | 5123751 | 12 | 43.0 | 14.9 | 11.5 | 2.0E-18 | [‘Bromodomain’] | Scaffolding proteins |
| 35 | qCaffeineb | TRFK 303/577, GW Ejulu | 5088162 | 13 | 29.7 | 4.7 | 5.4 | 6.0E-28 | [‘PA domain’] | — |
| 36 | qCATb | TRFK 303/577 | 5103784 | 13 | 50.6 | 3.8 | 6.1 | 8.0E-12 | CSA003424 | — |
| 37 | qCATb | TRFK 303/577 | 5122899 | 13 | 50.5 | 3.8 | 6 | 6.0E-19 | CSA033214 | — |
| 38 | qCATb | TRFK 303/577, GW Ejulu | 5133009 | 13 | 48.6 | 3.6 | 5.8 | 1.0E-16 | [‘Adaptor complexes medium subunit family’] | — |
| 39 | qCATb | TRFK 303/577 | 5122899 | 13 | 50.5 | 3.8 | 6 | 6.0E-22 | [‘Protein kinase domain’] | Abiotic stress |
| 40 | qCATb | TRFK 303/577 | 5122899 | 13 | 50.5 | 3.8 | 6 | 2.0E-21 | [‘14-3-3 protein’] | Abiotic stress |
| 41 | qCATb | TRFK 303/577 | 5122899 | 13 | 50.5 | 3.8 | 6 | 2.0E-21 | [‘NB-ARC domain’] | Disease resistance |
| 42 | qCATb | TRFK 303/577 | 5122899 | 13 | 50.5 | 3.8 | 6 | 2.0E-21 | [‘Pectinesterase’] | Drought response |
| 43 | qCATb | TRFK 303/577 | 5122899 | 13 | 50.5 | 3.8 | 6 | 1.0E-16 | [‘2OG-Fe(II) oxygenase superfamily’] | Abiotic stress |
| 44 | qCATb | TRFK 303/577, GW Ejulu | 5111268 | 13 | 50.6 | 4.1 | 7.2 | 6.0E-28 | [‘WD domain’] | Transport protein |
| 45 | qCATb | TRFK 303/577, GW Ejulu | 5123751 | 13 | 58.1 | 4.1 | 6.5 | 4.0E-23 | [‘Transmembrane amino acid transporter protein’] | Abiotic stress |
| 46 | qECGb | TRFK 303/577, GW Ejulu | 5088162 | 13 | 50.6 | 3.7 | 5.4 | 6.0E-28 | [‘PA domain’] | — |
| 47 | qEGCb | TRFK 303/577, GW Ejulu | 5123751 | 13 | 50.6 | 3.7 | 6.5 | 4.0E-23 | [‘Transmembrane amino acid transporter protein’] | Abiotic stress |
| 48 | qEGCa | GW Ejulu | 5116677 | 14 | 63.1 | 4.1 | 5.2 | 6.0E-28 | CSA002263 | — |
| 49 | qEGCa | GW Ejulu | 5116677 | 14 | 63.1 | 4.1 | 5.2 | 3.0E-11 | [‘Armadillo/beta-catenin-like repeat’] | Heat stress response |
| 50 | qBRTa | TRFK 303/577 | 5122986 | 14 | 65.4 | 3.7 | 7.5 | 7.0E-06 | [‘Glycosyl hydrolase family 9’] | Phenylpropanoid pathway |
| 51 | qCATb | — | 5132370 | 14 | 60.7 | 4.1 | 2.5 | 1.0E-10 | [‘Glutaminyl-tRNA synthetase’] | Chlorophyll biosynthesis |
| 52 | qECGb | GW Ejulu | 5111164 | 15 | 75.1 | 4.2 | 7.2 | 1.0E-07 | [‘Isocitrate/isopropylmalate dehydrogenase’] | Abiotic stress |
| 53 | qEGCGb | TRFK 303/577, GW Ejulu | 5114089 | 15 | 32.1 | 3.8 | 6.8 | 8.0E-12 | [‘Cytochrome P450’] | Biotic and abiotic stresses |
aPutative QTL identified based on Interval Mapping with LOD >3.0.
bPutative QTL identified based on Multiple QTL Model Mapping with LOD >3.0.
QTL- Quantitative trait loci; LG- Linkage group; LOD- Logarithm of odd ration; cM- Centimorgan, CAFF Caffeine, CAT Catechin, EC epicatechin, ECG epicatechin gallate, EGC epigallocatechin, EGCG epigallocatechin gallate, TF1 theaflavin, TF4- Theaflavin-3,3′-digallate, BRT brightness, %RWC percent relative water content.