Table 4.
Candidate genes for seed content that have altered expression in the wild-type and the mutant
| Gene ID | Wild-type gene expression (RPM) | Mutant gene expression (RPM) | Wild-type fold change | Mutant fold change | Gene enrichment | Annotation | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| E-L 15 | E-L 27 | E-L 38 | E-L 15 | E-L 27 | E-L 38 | E-L 27 vs E-L 15 | E-L 38 vs E-L 27 | E-L 38 vs E-L 15 | E-L 27 vs E-L 15 | E-L 38 vs E-L 27 | E-L 38 vs E-L 15 | |||
| Non-DE genes specific to the wild-type | ||||||||||||||
| VIT_09s0002g01980 | 0.5 | 0.7 | 0.2 | 0 | 0 | 0 | Myosin-like protein XIK | |||||||
| VIT_15s0048g01070 | 0.01 | 0.01 | 1.2 | 0 | 0 | 0 | Vacuolar iron transporter 1 | |||||||
| VIT_04s0044g01520 | 0 | 0.8 | 0 | 0 | 0 | 0 | GA 20-oxidase 2 | |||||||
| VIT_08s0058g01200 | 0 | 0.4 | 0 | 0 | 0 | 0 | sig | Alpha-expansin 2 | ||||||
| Non-DE genes specific to the mutant | ||||||||||||||
| VIT_13s0106g00290 | 0 | 0 | 0 | 0.01 | 0 | 0.1 | Histone deacetylase HDA14 | |||||||
| VIT_03s0088g00900 | 0 | 0 | 0 | 0 | 0.1 | 0.01 | Pathogenesis-related protein 1B | |||||||
| VIT_14s0006g00050 | 0 | 0 | 0 | 0.1 | 0 | 0 | Transposase, IS4 | |||||||
| Common genes differentially regulated in wild-type and mutant | ||||||||||||||
| VIT_01s0026g01680 | 0.02 | 24.6 | 0 | 0.01 | 1.9 | 0 | 1,133 | 0 | nd | 172.5 | nd | nd | sig | Pectate lyase |
| VIT_05s0020g04850 | 1.0 | 2.4 | 89.1 | 0.9 | 0.9 | 101.8 | nd | nd | 113.1 | nd | 153.3 | nd | sig | H1flk |
| VIT_15s0021g02700 | 0.3 | 7.4 | 1,103 | 0 | 2.0 | 1,396 | nd | nd | 4,154 | inf | nd | nd | sig | Beta-expansin (EXPB4) |
| VIT_15s0048g00510 | 9.1 | 170.5 | 4.4 | 8.8 | 74.9 | 2.4 | 18.8 | nd | nd | 8.7 | nd | nd | Pectinesterase family | |
| VIT_15s0021g02170 | 631.1 | 3.1 | 0.3 | 81.4 | 0.2 | 0.4 | 0.005 | nd | 0.0006 | 0.003 | nd | nd | Chalcone and stilbene synthase | |
| VIT_18s0089g00140 | 40.7 | 0.2 | 2.7 | 3.5 | 0 | 8.0 | 0.004 | nd | nd | 0 | nd | nd | 1,4-beta-mannan endohydrolase | |
| VIT_19s0015g00960 | 150.2 | 0.7 | 0 | 59.3 | 0.1 | 0.1 | 0.004 | nd | 0 | 0.002 | nd | nd | ABC transporter G member 4 | |
| VIT_18s0001g01760 | 969.1 | 8.1 | 0.04 | 854.3 | 3.2 | 1.0 | 0.008 | nd | 0.00005 | 0.004 | nd | nd | PISTILLATA (PI) floral homeotic protein | |
| VIT_18s0001g13460 | 107.1 | 13.8 | 0 | 84.4 | 7.9 | 0.1 | 0.1 | nd | 0 | 0.1 | nd | nd | MADS-box AP3 | |
| Differentially expressed genes specific to the wild-type | ||||||||||||||
| VIT_01s0011g06390 | 29.9 | 0.4 | 0.01 | 3.2 | 0.4 | 0.04 | 0.01 | nd | 0.0004 | nd | nd | nd | sig | MALE STERILITY 1 |
| VIT_08s0007g07100 | 20.5 | 0.8 | 0.02 | 3.7 | 0.06 | 0.04 | 0.04 | nd | nd | nd | nd | nd | sig | MALE STERILITY 2 |
| VIT_07s0005g05680 | 17.6 | 0.2 | 3.5 | 4.0 | 0.2 | 0.04 | 0.009 | nd | nd | nd | nd | nd | MALE STERILITY 5 | |
| VIT_07s0005g05720 | 29.3 | 1.6 | 2.3 | 14.5 | 2.6 | 1.2 | 0.06 | nd | nd | nd | nd | nd | MALE STERILITY 5 | |
| VIT_15s0107g00550 | 172.2 | 19.7 | 21.8 | 111.7 | 26.7 | 2.5 | 0.1 | nd | nd | nd | nd | nd | sig | MALE STERILITY 5 |
| VIT_19s0014g03940 | 7.7 | 0.2 | 0.06 | 4.5 | 0.3 | 0.06 | 0.02 | nd | nd | nd | nd | nd | SPOROCYTELESS | |
| VIT_12s0142g00040 | 49.6 | 2.6 | 0.07 | 12.5 | 0.7 | 0.08 | 0.05 | nd | 0.002 | nd | nd | nd | Glycerol-3-phosphate acyltransferase 1 | |
| VIT_00s1404g00010 | 17.5 | 22.6 | 0.04 | 18.1 | 14.6 | 0.04 | nd | 0.002 | nd | nd | nd | nd | sig | Calmodulin-binding |
| VIT_01s0026g01420 | 22.2 | 58.8 | 0.3 | 22.8 | 57.2 | 0.2 | nd | 0.007 | nd | nd | nd | nd | Wall-associated kinase 4 | |
| VIT_06s0061g00730 | 406.0 | 887.8 | 0.3 | 423.5 | 1,138 | 0.2 | nd | 0.0004 | 0.0009 | nd | nd | nd | Aquaporin GAMMA-TIP3/TIP1;3 | |
| VIT_18s0001g13200 | 31.7 | 143.9 | 0.3 | 38.7 | 110.9 | 0.5 | nd | 0.003 | nd | nd | nd | nd | Cytokinin dehydrogenase 5 precursor | |
| VIT_05s0094g00330 | 0.9 | 16.2 | 969.7 | 0.9 | 4.2 | 712.2 | 17.6 | nd | 1,332 | nd | nd | nd | Chitinase, class IV | |
| VIT_10s0003g03030 | 0.02 | 6.5 | 0.4 | 0.06 | 0.5 | 0.6 | 300.4 | nd | nd | nd | nd | nd | Cation/hydrogen exchanger (CHX15) | |
| VIT_01s0011g01560 | 0.2 | 14.2 | 0.07 | 0.4 | 2.4 | 0.07 | 72.6 | nd | nd | nd | nd | nd | TRANSPARENT TESTA16 | |
| VIT_18s0001g03010 | 0 | 1.5 | 0 | 0 | 0.2 | 0 | inf | nd | nd | nd | nd | nd | BZIP transcription factor | |
| VIT_18s0041g01880 | 9.5 | 67.4 | 33.2 | 9.8 | 10.7 | 26.7 | 7.1 | nd | nd | nd | nd | nd | sig | MADS-box protein SEEDSTICK |
| VIT_03s0038g04340 | 0.2 | 6.9 | 0.07 | 0.3 | 0.6 | 0.2 | 33.7 | nd | nd | nd | nd | nd | FERONIA receptor-like kinase | |
| VIT_17s0000g08110 | 1.1 | 23.1 | 0.01 | 0.2 | 1.4 | 0 | 20.1 | 0.0006 | nd | nd | nd | nd | Nodulin MtN3 | |
| VIT_17s0000g09000 | 0.8 | 0.4 | 36.3 | 0.5 | 0.009 | 0.04 | nd | 125.8 | nd | nd | nd | nd | Oleosin OLE-2 | |
| VIT_07s0151g00640 | 12.4 | 5.2 | 453.2 | 17.9 | 3.0 | 1.1 | nd | 109.3 | nd | nd | nd | nd | Globulin-1 S allele precursor | |
| VIT_14s0128g00200 | 0.04 | 0.1 | 42.5 | 0.09 | 0 | 0 | nd | 540.1 | 1,242 | nd | nd | nd | 7S globulin precursor | |
| VIT_13s0067g01250 | 0.06 | 0.1 | 26.0 | 0.02 | 0 | 0 | nd | 330.4 | 506.5 | nd | nd | nd | Em protein GEA6 (EM6) | |
| VIT_14s0108g00520 | 0 | 0.2 | 89.3 | 0.03 | 0.09 | 0.03 | nd | 637.6 | inf | nd | nd | nd | Protease inhibitor/seed storage/lipid transfer protein (LTP) | |
| VIT_16s0039g00220 | 0.4 | 0.2 | 25.2 | 0.3 | 0.1 | 0.7 | nd | 192.0 | nd | nd | nd | nd | Aquaporin BETA-TIP | |
| VIT_07s0005g05400 | 0 | 0.08 | 22.1 | 0.05 | 0 | 0 | nd | 360.2 | inf | nd | nd | nd | ABSCISIC ACID-INSENSITIVE protein 3 (ABI3) | |
| VIT_19s0014g04130 | 0.7 | 0.2 | 23.6 | 0.3 | 0.4 | 6.4 | nd | 179.8 | nd | nd | nd | nd | Serine/threonine-protein kinase receptor ARK3 | |
| VIT_18s0001g01570 | 0.2 | 0.5 | 265.1 | 0.3 | 0.07 | 0.3 | nd | 631.3 | 1,548 | nd | nd | nd | Seed maturation protein PM31 | |
| VIT_14s0128g00340 | 0.1 | 0.08 | 17.0 | 0.1 | 0 | 0 | nd | 277.3 | nd | nd | nd | nd | Seed maturation protein PM34 | |
| VIT_04s0008g01610 | 0 | 0.3 | 176.8 | 0 | 0 | 0 | nd | 776.9 | inf | nd | nd | nd | Heat shock protein 17.6 kDa class II | |
| Differentially expressed genes specific to the mutant | ||||||||||||||
| VIT_14s0219g00270 | 20.3 | 2.5 | 0.08 | 21.6 | 0.5 | 0.08 | nd | nd | nd | 0.03 | nd | nd | TEL1 (Terminal EAR1-like 1) | |
| VIT_12s0059g00560 | 14.6 | 1.1 | 1.1 | 17.8 | 0.6 | 0.4 | nd | nd | nd | 0.04 | nd | nd | Fimbrin 2 | |
| VIT_04s0008g04980 | 15.5 | 2.7 | 0.2 | 10.1 | 0.3 | 0.06 | nd | nd | nd | 0.03 | nd | nd | Boron transporter-like protein 4 | |
| VIT_09s0002g01670 | 9.0 | 1.1 | 0.03 | 11.8 | 0.09 | 0 | nd | nd | nd | 0.007 | nd | nd | Myb domain protein 26 | |
| VIT_09s0002g01370 | 13.2 | 1.3 | 0.2 | 14.0 | 0.3 | 0 | nd | nd | nd | 0.02 | nd | nd | AP2 AINTEGUMENTA | |
| VIT_14s0006g02950 | 25.4 | 12.6 | 37.4 | 53.1 | 5.4 | 123.3 | nd | nd | nd | 0.1 | nd | nd | LATERAL ORGAN BOUNDARIES protein 41 | |
| VIT_15s0046g03080 | 3.4 | 0.9 | 0.02 | 2.9 | 0 | 0 | nd | nd | nd | 0 | nd | nd | DTA2 (downstream target of AGL15 2) | |
| VIT_12s0134g00240 | 17.7 | 36.7 | 21.5 | 9.7 | 77.1 | 22.7 | nd | nd | nd | 8.1 | nd | nd | Avr9/Cf-9 rapidly elicited protein 20 | |
| VIT_12s0028g03270 | 14.2 | 30.5 | 48.0 | 7.3 | 62.5 | 55.7 | nd | nd | nd | 8.8 | nd | nd | Ethylene-responsive transcription factor 9 | |
| VIT_16s0013g00950 | 1.8 | 5.1 | 2.1 | 1.1 | 22.1 | 0.4 | nd | nd | nd | 20.5 | nd | nd | Ethylene-responsive transcription factor ERF105 | |
| VIT_16s0013g00990 | 2.4 | 5.0 | 0.7 | 1.2 | 18.6 | 0.4 | nd | nd | nd | 16.1 | nd | nd | Ethylene-responsive transcription factor ERF105 | |
| VIT_16s0013g01050 | 3.1 | 6.3 | 1.1 | 1.8 | 23.3 | 0.3 | nd | nd | nd | 13.2 | nd | nd | Ethylene-responsive transcription factor ERF105 | |
| VIT_16s0013g01120 | 3.2 | 13.2 | 63.7 | 3.1 | 29.5 | 49.1 | nd | nd | nd | 9.8 | nd | nd | Ethylene-responsive transcription factor ERF105 | |
Abbreviations : nd not detected in a pairwise comparison, inf infinity (when the mean of one stage in a pairwise comparison is the denominator with value 0), sig significant.