Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry
Abstract
:1. Introduction
2. Results
2.1. Characterization of MYB10 in Diploid and Octoploid Species of Fragaria
2.2. Structure and Phylogeny of MYB10 in Diploid and Octoploid Species of Fragaria
2.3. RNA-Seq Based Expression Profiling of MYB10 and Anthocyanin Biosynthesis Genes
2.4. Relative Expression Analysis of MYB10 and Anthocyanin Biosynthesis Genes
2.5. Identification of QTLs Associated with Fruit Color
2.6. Identification of Predicted Candidate Genes Associated with Fruit Color Using QTL and RNA-Seq Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Identification of MYB10 Transcription Factors in Fragaria
4.3. Analysis of Conserved Motifs, Gene Structures, and Cis-Elements
4.4. RNA-Seq Analysis of Skin and Flesh
4.5. RT-PCR Analysis
4.6. QTL Analysis and Identification of Candidate Genes
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Species | Chr. | Gene ID | Location | Ploidy Level |
---|---|---|---|---|
F. iinumae | 1 | evm.model.scaf_28.444 | 14,574,366–14,576,255 | Diploid |
F. nilgerensis | 1 | evm.model.ctg92.252_scbg_v1.0 | 17,100,850–17,104,063 | Diploid |
F. nubicola | 1 | evm.model.ctg173.372 | 15,072,390–15,075,138 | Diploid |
F. viridis | 1 | evm.model.ctg108.134 | 13,877,866–13,880,523 | Diploid |
F. vesca | 1 | FvH4_1g22020 | 13,950,290–13,952,507 | Diploid |
F. × ananassa ‘Wongyo 3115’ | 1-1 | g00101712 | 13,223,169–13,223,636 | Octoploid |
1-2 | g00119641 | 12,622,806–12,626,007 | ||
1-3 | g00115370 | 13,537,353–13,539,011 | ||
1-4 | g00128511 | 13,235,156–13,238,279 | ||
F. × ananassa ‘Camarosa’ | 1-1 | maker-Fvb1-1-snap-gene-139.18 | 13,899,904–13,911,034 | Octoploid |
1-2 | maker-Fvb1-2-snap-gene-157.15 | 15,722,359–15,726,641 | ||
1-3 | maker-Fvb1-3-augustus-gene-144.30 | 14,468,714–14,470,589 | ||
1-3 | maker-Fvb1-3-augustus-gene-143.29 | 14,315,382–14,315,713 |
QTL | Chr. | Physical Position (Mbp) | Trait | Position (cM) | LOD | Additive Effect 1 | Dominant Effect 2 | R2 (%) |
---|---|---|---|---|---|---|---|---|
Col_1-2 | 1-2 | 12.1–24.5 | Flesh_color (2020) | 79.1–124.5 | 28.77 | 0.68 | −0.35 | 75.94 |
Achene_color (2020) | 81.2–88.2 | 4.51 | 0.12 | −0.45 | 29.78 | |||
Core_color (2020) | 82.2–142.9 | 32.02 | 0.41 | 0.30 | 38.48 | |||
Achene_color (2020) | 89.2–111.5 | 4.40 | −0.17 | −0.43 | 10.00 | |||
Skin_color (2019) | 97.5–142.9 | 7.19 | 0.23 | 0.18 | 12.91 | |||
Skin_color (2020) | 97.5–142.9 | 11.49 | 0.45 | 0.23 | 20.19 | |||
Col_1-4 | 1-4 | 11.8–15.9 | Achene_color (2020) | 53.4–66.6 | 5.67 | −0.22 | −0.10 | 10.04 |
Col_2-1_1 | 2-1 | 18.8–20.8 | Flesh_color (2020) | 74.5–100.4 | 4.45 | 0.91 | −0.89 | 55.68 |
Col_2-1_2 | 2-1 | 21.2–26.9 | Flesh_color (2020) | 30.7–47.3 | 5.52 | −0.28 | −0.07 | 6.06 |
Col_6-4_1 | 6-4 | 3.0–6.9 | Achene_color (2019) | 7.0–17.9 | 3.97 | −0.03 | −0.25 | 5.67 |
Col_6-4_2 | 6-4 | 15.5–29.7 | Skin_color (2019) | 127.7–143.7 | 5.00 | 0.30 | −0.25 | 0.62 |
Achene_color (2020) | 138.7–144.2 | 4.17 | −0.26 | 0.11 | 15.09 | |||
Col_7-4 | 7-4 | 17.8–21.8 | Achene_color (2020) | 58.5–68.1 | 4.49 | −0.18 | −0.05 | 6.50 |
QTL | Gene ID | Chr. | Description | Function |
---|---|---|---|---|
Col_6-4_1 | g00015421 | 6-4 | DFR: Bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase | Anthocyanin biosynthesis/Secondary metabolism |
Col_6-4_2 | g00017208 | 6-4 | ANS1: Leucoanthocyanidin dioxygenase 1 | Anthocyanin biosynthesis/Secondary metabolism |
Col_6-4_2 | g00018684 | 6-4 | C1: Anthocyanin regulatory C1 protein | Anthocyanin biosynthesis |
Col_7-4 | g00137772 | 7-4 | CHI3: Probable chalcone--flavonone isomerase 3 | Anthocyanin biosynthesis/Secondary metabolism |
Col_7-4 | g00138590 | 7-4 | GT1: Anthocyanidin 3-O-glucosyltransferase 1 | Anthocyanin biosynthesis/Secondary metabolism |
Col_1-2 | g00119641 | 1-2 | MYB113: Transcription factor MYB113/MYB10 | DNA binding/Secondary metabolism |
Col_1-4 | g00128511 | 1-4 | Similar to PNS1: Protein PNS1/MYB10 | DNA binding/Secondary metabolism |
Col_7-4 | g00138251 | 7-4 | UGT88B1: UDP-glycosyltransferase 88B1 | |
Col_6-4_2 | g00018719 | 6-4 | CYP750A1: Cytochrome P450 750A1 | ABA biosynthesis |
Col_6-4_2 | g00019239 | 6-4 | GT6: UDP-glucose flavonoid 3-O-glucosyltransferase 6 | Anthocyanin biosynthesis/Secondary metabolism |
Col_6-4_2 | g00018681 | 6-4 | GPI: Glucose-6-phosphate isomerase | Sugar metabolism |
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Manivannan, A.; Han, K.; Lee, S.Y.; Lee, H.-E.; Hong, J.P.; Kim, J.; Lee, Y.-R.; Lee, E.S.; Kim, D.-S. Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry. Int. J. Mol. Sci. 2021, 22, 12587. https://doi.org/10.3390/ijms222212587
Manivannan A, Han K, Lee SY, Lee H-E, Hong JP, Kim J, Lee Y-R, Lee ES, Kim D-S. Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry. International Journal of Molecular Sciences. 2021; 22(22):12587. https://doi.org/10.3390/ijms222212587
Chicago/Turabian StyleManivannan, Abinaya, Koeun Han, Sun Yi Lee, Hye-Eun Lee, Jong Pil Hong, Jinhee Kim, Ye-Rin Lee, Eun Su Lee, and Do-Sun Kim. 2021. "Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry" International Journal of Molecular Sciences 22, no. 22: 12587. https://doi.org/10.3390/ijms222212587