Table 1.
A list of genes strongly correlated with the sugar/acid ratio in orange fruits
| CsGID | Pcc | FDR | Module | AtGID | Arabidopsis gene description |
|---|---|---|---|---|---|
| Transport (9) | |||||
| Cs1g13320 | 0.87 | 1.3E-05 | turquoise | At1g15460 | BOR4, Requires High Boron 4 |
| Cs1g25820 | 0.87 | 1.4E-05 | blue | At5g66110 | HIPP27, heavy metal associated isoprenylated plant protein 27 |
| Cs2g06990 | 0.89 | 8.7E-06 | blue | At4g05120 | FUR1, FUDR Resistant 1 |
| Cs4g20090 | 0.89 | 6.7E-06 | brown | At4g32650 | KAT3, potassium channel in Arabidopsis thaliana 3 |
| Cs5g17210 | 0.81 | 2.1E-04 | blue | At1g17810 | Beta-TIP, beta-tonoplast intrinsic protein |
| Cs5g24670 | −0.87 | 1.4E-05 | blue | At5g48490 | Putative lipid transfer/seed storage protein |
| Cs5g31010 | 0.83 | 1.5E-04 | blue | At3g22600 | Non-specific lipid-transfer/seed storage protein |
| Cs9g18100 | 0.80 | 3.2E-04 | turquoise | At5g53130 | CNGC1, cyclic nucleotide gated channel 1 |
| orange1.1 t01769 | 0.82 | 1.7E-04 | blue | At3g62150 | ABCB21, ATP-binding cassette B21 |
| Signaling (6) | |||||
| Cs1g01170 | 0.86 | 3.0E-05 | blue | At4g23160 | CRK8, cysteine-rich RLK (RECEPTOR-like protein kinase) 8 |
| Cs1g14800 | 0.90 | 5.0E-06 | blue | At3g47570 | probable LRR receptor-like serine/threonine protein kinase |
| Cs2g02680 | 0.88 | 8.7E-06 | brown | At3g21630 | CERK1, chitin elicitor receptor kinase 1 |
| Cs3g07510 | 0.80 | 3.2E-04 | blue | At1g03430 | AHP5, histidine-containing phosphotransfer factor 5 |
| Cs6g02710 | 0.81 | 2.3E-04 | turquoise | At1g16120 | WAKL1, wall associated kinase-like 1 |
| Cs6g05010 | 0.80 | 3.5E-04 | blue | At3g47570 | probable LRR receptorlike serine/threonineprotein kinase |
| Transcription (7) | |||||
| Cs3g01830 | 0.86 | 3.0E-05 | brown | At3g54460 | F-box family protein |
| Cs5g03630 | 0.83 | 1.4E-04 | brown | At5g23750 | remorin like |
| Cs6g03950 | −0.80 | 3.2E-04 | turquoise | At2g37260 | TTG2, Transparent testa Glabra 2, WRKY |
| Cs7g27620 | 0.85 | 4.1E-05 | brown | At1g07900 | LBD1, LOB domain-containing protein 1 |
| Cs9g08500 | 0.80 | 3.2E-04 | turquoise | At5g43630 | TZP, tandem zinc knuckle protein |
| orange1.1 t00185 | 0.83 | 1.2E-04 | blue | At4g00050 | UNE10, unfertilized embryo sac 10, bHLH |
| orange1.1 t00294 | 0.80 | 3.2E-04 | brown | At4g16110 | RR2/ARR2, response regulator 2 |
| Protein degradation (3) | |||||
| Cs8g05200 | 0.80 | 3.2E-04 | blue | At1g47128 | RD21A, responsive to dehydration 21A |
| orange1.1 t00281 | 0.88 | 8.7E-06 | brown | At4g00230 | XSP1, xylem serine peptidase 1 |
| orange1.1 t02370 | 0.83 | 1.2E-04 | blue | At2g31980 | CYS2, Phytocystatin 2 |
| Development (2) | |||||
| Cs4g15700 | 0.80 | 3.0E-04 | turquoise | At4g29860 | EMB2757, Embryo Deffective 2757 |
| orange1.1 t02243 | 0.83 | 1.4E-04 | blue | At5g06760 | LEA4–5, Late Embryogenesis Abundant 4–5 |
| Stress response (4) | |||||
| Cs5g18450 | 0.82 | 1.7E-04 | turquoise | At5g17680 | Leucine rich repeat-containing protein |
| Cs5g19950 | 0.85 | 4.3E-05 | turquoise | At5g17680 | TMV resistance protein N-like |
| Cs7g32260 | 0.80 | 3.5E-04 | turquoise | At5g59720 | HSP18.2, heat shock protein 18.2 |
| orange1.1 t01829 | 0.84 | 7.8E-05 | turquoise | At5g17680 | TMV resistance protein N-like |
| Metabolism (20) | |||||
| Cs1g03610 | 0.91 | 4.9E-06 | blue | At5g43330 | c-NAD-MDH2, cytosolic-NAD-dependent malate dehydrogenase 2 |
| Cs1g10530 | 0.81 | 2.3E-04 | turquoise | At2g18950 | HPT1, homogentisate phytyltransferase 1 |
| Cs1g25210 | −0.84 | 9.1E-05 | brown | At2g18020 | EMB2296, embryo defective 2296, ribosomal protein |
| Cs2g27550 | 0.80 | 3.2E-04 | blue | At3g01570 | Oleosin family protein |
| Cs3g12560 | 0.81 | 2.7E-04 | blue | At1g54740 | ribosomal protein |
| Cs3g24700 | 0.81 | 2.3E-04 | brown | At5g42740 | PGI, glucose-6-phosphate isomerase, cytosolic 1 |
| Cs4g14130 | 0.81 | 2.3E-04 | blue | At2g45550 | CYP76C4, cytochrome P450, family 76, subfamily C, polypeptide 4 |
| Cs5g18850 | 0.82 | 1.5E-04 | blue | At1g71250 | GDSL-motif esterase/acyltransferase/lipase |
| Cs5g20010 | 0.83 | 1.2E-04 | turquoise | At1g35190 | Hyoscyamine 6-dioxygenase |
| Cs7g13310 | −0.83 | 1.2E-04 | turquoise | At1g68530 | KCS6, 3-ketoacyl-CoA synthase 6 |
| Cs7g30920 | 0.81 | 2.2E-04 | blue | At2g40170 | GEA6/Em6, Late embryogenesis abundant 6 |
| Cs7g31620 | 0.80 | 3.0E-04 | blue | At2g38080 | IRX12, Irregular Xylem 12 |
| Cs8g06880 | −0.84 | 1.1E-04 | grey | At4g36750 | Minor allergen Alt a, lipid metabolism |
| Cs9g06700 | 0.86 | 3.0E-05 | brown | At1g31690 | Copper amine oxidase family protein |
| Cs9g07750 | −0.89 | 7.0E-06 | brown | At3g22890 | APS1, ATP sulfurylase 1 |
| Cs9g13750 | 0.81 | 2.3E-04 | blue | At5g07475 | Cupredoxin superfamily protein; copper ion binding |
| Cs9g17670 | 0.81 | 2.3E-04 | grey | At4g23420 | short chain dehydrogenase/reductase (SDR) |
| orange1.1 t00612 | 0.82 | 2.0E-04 | turquoise | At5g66460 | MAN7, endo-beta-mannase 7 |
| orange1.1 t02858 | 0.81 | 2.7E-04 | blue | At1g79640 | serine/threonine protein kinase, putative |
| orange1.1 t03587 | 0.83 | 1.2E-04 | turquoise | At1g17020 | SRG1, senescence-related gene 1 |
| Unknown function (11) | |||||
| Cs1g20290 | 0.80 | 3.0E-04 | blue | ||
| Cs1g20300 | 0.80 | 3.2E-04 | blue | ||
| Cs1g23800 | 0.80 | 3.2E-04 | blue | At2g18540 | vicilin GC72A like, cupin |
| Cs1g24590 | 0.81 | 2.3E-04 | blue | ||
| Cs2g06500 | −0.82 | 2.0E-04 | turquoise | At1g11090 | MGL, Monoglyceride lipase |
| Cs2g07220 | −0.88 | 1.2E-05 | blue | At3g13160 | pentatricopeptide repeat-containing protein |
| Cs2g20110 | 0.88 | 8.7E-06 | blue | ||
| Cs3g17860 | 0.81 | 2.1E-04 | brown | queuine tRNA ribosyltransferase like | |
| Cs5g05940 | 0.80 | 3.2E-04 | blue | ||
| Cs5g06080 | 0.88 | 9.3E-06 | turquoise | At5g50170 | C2 and GRAM domain-containing protein |
| Cs5g20400 | 0.81 | 2.2E-04 | turquoise | ||
| Cs5g23250 | 0.81 | 2.1E-04 | turquoise | At5g67550 | |
| Cs6g16160 | −0.89 | 7.0E-06 | blue | At4g24380 | hypothetical protein SORBIDRAFT_02g043510 |
| Cs7g06285 | 0.90 | 4.9E-06 | brown | ||
| Cs7g23240 | 0.86 | 2.9E-05 | blue | At5g04830 | hypothetical protein ARALYDRAFT_487267 |
| Cs7g25170 | −0.82 | 1.5E-04 | turquoise | ||
| Cs7g30380 | 0.83 | 1.5E-04 | blue | At2g40390 | |
| Cs8g10300 | 0.84 | 1.1E-04 | blue | ||
| Cs8g18390 | −0.80 | 3.0E-04 | turquoise | ||
| Cs8g19210 | 0.82 | 2.0E-04 | blue | ||
| orange1.1 t01135 | 0.84 | 7.8E-05 | blue | hypothetical protein ARALYDRAFT_487267 | |
A total of 72 citrus genes are highly correlated with the sugar/acid ratios in orange fruits of four varieties, with a Pearson correlation coefficient (Pcc) of above 0.80 or below −0.80 and an adjusted p-value (FDR, false discovery rate) of larger than 1.0E-04. CsGID, Cs gene ID. The number of genes for individual biological process is indicated in parenthesis and the module to which the genes belong is inidcated. The most closely related homologs of Arabidopsis gene for each citrus gene is presented as AtGID (At gene ID), with Arabidopsis gene description shown. Absence of AtGID indicates no Arabidopsis homolog for CsGID identified