Identification of Differentially Expressed Genes between “Honeycrisp” and “Golden Delicious” Apple Fruit Tissues Reveal Candidates for Crop Improvement
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling Strategy
2.2. Differential Display
2.3. Cloning and Sequencing
2.4. Annotation of Differential Display Fragments
2.5. Quantitative Real Time PCR Validation of Differential Expression
2.6. Comparison of Expression with Previous Studies
3. Results and Discussion
3.1. Differential Display
3.2. Quantitative Reverse Transcription PCR Validation of Differential Expression
3.3. Comparison of Expression with Previous Studies
3.4. Differentially Expressed Homologs in Heterologous Systems
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Gene Identifier | Blast2GO Annotation | 129 DAA-2007 Season | 160 DAA-2007 Season | Cellular Localization | ||||||
---|---|---|---|---|---|---|---|---|---|---|
GDE | GDP | HCE | HCP | GDE | GDP | HCE | HCP | |||
MDP0000037251 | cinnamyl alcohol dehydrogenase-like protein | ++ | ++ | + | ++ | ++ | ++ | + | ++ | _ |
MDP0000128468 | abscisic acid stress ripening protein homolog | ++ | ++ | ++ | + | ++ | ++ | ++ | + | M |
MDP0000129664 | 3-ketoacyl-thiolase | - | - | + | + | - | - | + | + | _ |
MDP0000138340 | NAC domain ipr003441 | ++ | ++ | + | + | ++ | ++ | + | + | _ |
MDP0000152947 | wound-induced protein | + | ++ | + | + | + | + | + | + | _ |
MDP0000161275 | mitochondrial substrate carrier family protein | + | + | + | ++ | + | + | + | ++ | _ |
MDP0000166116 | acyl:CoA ligase acetate-coa synthetase-like protein | + | + | + | + | ++ | ++ | +++ | +++ | _ |
MDP0000172863 | protein | - | - | - | - | - | + | - | - | S |
MDP0000176723 | acyl:CoA ligase acetate-coa synthetase-like protein | ++ | ++ | + | + | ++ | ++ | + | + | _ |
MDP0000180389 | disease resistance protein at3g14460-like | ++ | ++ | + | + | ++ | ++ | + | + | S |
MDP0000200646 | NAC domain ipr003441 | + | + | + | + | + | + | ++ | ++ | _ |
MDP0000213808 | probable ubiquitin conjugation factor e4-like | ++ | ++ | + | + | ++ | ++ | + | + | _ |
MDP0000220601 | zinc finger CCCH domain-containing protein 53-like | + | + | + | + | + | + | + | ++ | _ |
MDP0000232309 | transmembrane BAX inhibitor motif-containing protein 4 | + | + | + | + | ++ | ++ | + | + | _ |
MDP0000233229 | Unknown protein | + | + | + | + | + | + | + | ++ | _ |
MDP0000234325 | WWE protein-protein interaction domain family protein | - | - | + | - | - | - | + | - | _ |
MDP0000237908 | metallothionein-like protein | ++ | ++ | + | + | ++ | ++ | + | + | _ |
MDP0000253074 | abscisic acid stress ripening protein homolog | - | - | + | + | - | - | + | + | _ |
MDP0000255887 | TIR-NBS-LRR resistance protein | - | + | - | - | - | + | - | - | _ |
MDP0000273484 | SKP1-like protein | - | + | - | - | - | + | - | - | _ |
MDP0000281279 | Unknown protein | ++ | + | + | + | ++ | + | + | + | _ |
MDP0000286959 | dentin sialophosphoprotein | + | + | - | - | + | + | - | - | _ |
MDP0000292888 | GYF domain-containing protein | - | - | - | + | - | - | - | + | C |
MDP0000296716 | ethylene-responsive transcription factor RAP2-7-like | ++ | + | ++ | ++ | ++ | + | ++ | ++ | _ |
MDP0000304285 | xanthine uracil permease family expressed | - | - | - | + | - | - | - | + | _ |
MDP0000310811 | cysteine protease inhibitor | - | - | - | - | - | - | - | + | M |
MDP0000316244 | probable ADP-ribosylation factor GTPase-activating protein AGD15-like | + | + | ++ | ++ | ++ | ++ | + | + | _ |
MDP0000320533 | proteasome assembly chaperone | - | - | - | + | - | - | - | + | _ |
MDP0000378585 | at4g03420 f9h3_4 | + | + | ++ | + | + | + | ++ | + | _ |
MDP0000443265 | Unknown protein | - | - | - | - | - | - | + | - | C |
MDP0000523205 | Unknown protein | - | - | - | - | - | + | - | - | _ |
MDP0000547450 | UNC93-like protein | + | ++ | + | + | + | ++ | + | + | _ |
MDP0000572242 | probable xyloglucan glycosyltransferase 12-like | + | ++ | + | + | + | ++ | + | + | _ |
MDP0000580900 | porin voltage-dependent anion-selective channel protein | + | - | - | - | + | - | - | - | _ |
MDP0000584042 | protein | + | + | - | - | + | + | - | - | S |
MDP0000606453 | probable nitrite transporter at1g68570-like | - | - | - | - | - | - | + | - | _ |
MDP0000618650 | NAC domain ipr003441 | - | - | - | + | - | - | - | + | _ |
MDP0000689999 | protein disulfide isomerase | ++ | + | + | + | ++ | + | + | + | S |
MDP0000697474 | reverse transcriptase | - | + | - | - | - | + | - | - | _ |
MDP0000712586 | protein SCAI-like | + | + | ++ | ++ | ++ | ++ | + | + | S |
MDP0000875654 | hydroquinone glucosyltransferase | ++ | ++ | + | + | + | + | + | + | _ |
MDP0000876817 | Unknown protein | - | - | - | - | - | - | + | - | _ |
MDP0000883284 | PREDICTED: uncharacterized protein LOC100248602 [Vitis vinifera] | + | + | - | - | + | + | - | - | S |
MDP0000901731 | Unknown protein | - | - | - | + | - | - | - | + | S |
MDP0000920333 | putative protein phosphatase 2C 10 | - | - | - | + | - | - | - | + | _ |
Gene ID | Location | Gene | At Homolog | Sl Homolog | Potential Trait/Fruit Characteristic Influenced | Reference(s) |
---|---|---|---|---|---|---|
Transcriptional Regulation | ||||||
MDP0000138340 | chr1:12,793,865..12,795,081 | NAC transcription factor-like 9 | AT4G35580 | XP_004239709.1 | Stress response | [15] |
MDP0000200646 | chr1:12,796,087..12,797,315 | NAC transcription factor-like 9 | AT4G35580 | XP_004239709.1 | Stress response | [15] |
MDP0000618650 | chr15:14,098,214..14,102,470 | NAC domain containing protein 75 | AT4G29230 | XP_004239596.1 | Stress response/general ripening regulation | [15] |
MDP0000296716 | chr3:9,357,237..9,360,502 | AP2 transcription factor SlAP2d | AT2G28550 | NP_001234647.1 | Ethylene-regulated response | [16,17] |
Secondary Biosynthetic Processes | ||||||
MDP0000037251 | chr1:6,887,281..6,890,898 | Putative cinnamyl alcohol dehydrogenase 9 | AT4G39330 | XP_004250169.1 | Fruit firmness | [18] |
MDP0000572242 | chr15:1,231,253..1,235,097 | Probable xyloglucan glycosyltransferase 12-like | AT4G07960 | XP_004238064.1 | Fruit firmness | [19] |
MDP0000875654 | chr7:16,340,110..16,341,528 | Hydroquinone glucosyltransferase | AT4G01070 | XP_004231207.1 | Volatile/polyphenol glycosylation | [20,21] |
MDP0000523205 | chr7:5,077,703..5,080,814 | Flavonoid biosynthesis oxidoreductase protein | AT4G10490 | NP_001233840.1 | Flavanoid synthesis | [22] |
Signaling | ||||||
MDP0000128468 | chr16:4,935,225..4,935,891 | Abscisic acid stress ripening (ASR1) protein | No hit | NM_001247208.2 | Abiotic stress response, developmental response to sugar levels | [23,24] |
MDP0000176723 | chr17:23,896,643..23,897,062 | Acyl:CoA ligase acetate-CoA synthase-like protein | AT5G16370 | XP_004231630.1 | Abiotic stress response/ripening | [25,26,27] |
MDP0000920333 | chr10:29,789,438..29,789,994 | Putative protein phosphatase 2C-10 | AT1G34750 | XP_004237914.1 | Ripening/abiotic stress response | [28,29] |
MDP0000213808 | chr17:4,103,927..4,109,528 | putative ubiquitin conjugation factor E4 | AT5G15400 | XP_004232186.1 | Ethylene production, development, ripening | [30] |
Cell/Organ Development | ||||||
MDP0000232309 | chr16:13,766,655..13,768,223 | BAX inhibitor-1 like protein | No hit | No hit | Cell elongation/fruit size | [31,32] |
MDP0000547450 | chr7:26,032,235..26,033,783 | UNC93-like protein 1-like | AT1G18000 | XP_004235041.1 | Apogamy | [33] |
Stress Response | ||||||
MDP0000712586 | chr14:27,117,925..27,120,988 | SCAI-like protein | No Hit | No Hit | Redox homeostasis/respiration | [34] |
MDP0000161275 | chr12:24,524,346..24,526,137 | Mitochondrial succinate-fumarate transporter 1-like | AT5G01340 | XP_004249636.1 | Hypoxia-induced fermentation/respiration | [35,36] |
MDP0000310811 | chr7:3,004,269..3,005,959 | Cysteine proteinase inhibitor 6 | AT3G12490 | XP_004228480.1 | Abiotic stress tolerance | [37,38] |
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Schaeffer, S.; Hendrickson, C.; Fox, R.; Dhingra, A. Identification of Differentially Expressed Genes between “Honeycrisp” and “Golden Delicious” Apple Fruit Tissues Reveal Candidates for Crop Improvement. Horticulturae 2016, 2, 11. https://doi.org/10.3390/horticulturae2030011
Schaeffer S, Hendrickson C, Fox R, Dhingra A. Identification of Differentially Expressed Genes between “Honeycrisp” and “Golden Delicious” Apple Fruit Tissues Reveal Candidates for Crop Improvement. Horticulturae. 2016; 2(3):11. https://doi.org/10.3390/horticulturae2030011
Chicago/Turabian StyleSchaeffer, Scott, Christopher Hendrickson, Rachel Fox, and Amit Dhingra. 2016. "Identification of Differentially Expressed Genes between “Honeycrisp” and “Golden Delicious” Apple Fruit Tissues Reveal Candidates for Crop Improvement" Horticulturae 2, no. 3: 11. https://doi.org/10.3390/horticulturae2030011
APA StyleSchaeffer, S., Hendrickson, C., Fox, R., & Dhingra, A. (2016). Identification of Differentially Expressed Genes between “Honeycrisp” and “Golden Delicious” Apple Fruit Tissues Reveal Candidates for Crop Improvement. Horticulturae, 2(3), 11. https://doi.org/10.3390/horticulturae2030011