Table 5 Annotated function of differentially expressed genes identified within or near the QTLs affecting chalkiness trait
No. | Gene ID | H-Pool vs. L-Pool | PYZX vs. P02428 | Symbol | Description | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fold change | log2(FC) | FDR | Sig. | Fold change (qRT-PCR) | Fold change | log2(FC) | FDR | Sig. | ||||
qPGWC5 (qDEC5) | ||||||||||||
 1 | Os05g0214300 | (−)11.74 | −3.554 | 0.003 | yes | (−)15.33 | (+)430.00 | 8.748 | 0.029 | yes | OsSWEET3a | Similar to Bidirectional sugar transporter SWEET3a. |
 2 | Os05g0215300 | (−)2.07 | −1.046 | 0.000 | yes | (−)4.55 | (+)22.53 | 4.494 | 0.000 | yes |  | UDP-glucuronosyl/UDP-glucosyltransferase family protein. |
 3 | Os05g0231900 | (+)2.85 | 1.511 | 0.013 | yes |  | (−)1263.33 | −10.303 | 0.009 | yes | prx73 | Hypothetical conserved gene. |
qPGWC7 (qDEC7) | ||||||||||||
 1 | Os07g0597000 | (−)2.24 | −1.163 | 0.000 | yes |  | (+)1.84 | 0.878 | 0.000 | no |  | Similar to Eukaryotic translation initiation factor 5A (eIF-5A). |
 2 | Os07g0597050 | (−)2.78 | −1.473 | 0.000 | yes |  | (+)6.30 | 2.654 | 0.000 | yes |  | Hypothetical gene. |
 3 | Os07g0597100 | (−)2.62 | −1.392 | 0.000 | yes |  | (+)5.74 | 2.522 | 0.000 | yes |  | Similar to Saccharopine dehydrogenase. |
 4 | Os07g0597400 | (−)7.63 | −2.931 | 0.000 | yes |  | (+)168.27 | 7.395 | 0.000 | yes |  | Conserved hypothetical protein. |
 5 | Os07g0599300 | (−)4.27 | −2.094 | 0.033 | yes |  | (+)15.84 | 3.986 | 0.002 | yes |  | Hypothetical protein. |
 6 | Os07g0599500 | (−)3.73 | −1.900 | 0.004 | yes |  | (+)2483.33 | 11.278 | 0.000 | yes |  | Hypothetical protein. |
 7 | Os07g0599600 | (−)4.39 | −2.135 | 0.000 | yes |  | (+)6.29 | 2.652 | 0.000 | yes |  | Hypothetical protein. |
 8 | Os07g0599700 | (−)3.69 | −1.885 | 0.000 | yes |  | (+)3.88 | 1.955 | 0.000 | yes |  | Similar to Surface protein PspC. |
 9 | Os07g0599900 | (−)6.15 | −2.620 | 0.000 | yes |  | (+)14.53 | 3.861 | 0.000 | yes |  | Conserved hypothetical protein. |
 10 | Os07g0600300 | (−)2.67 | −1.415 | 0.005 | yes |  | (+)2.22 | 1.153 | 0.052 | no |  | Protein of unknown function DUF794, plant family protein. |
 11 | Os07g0601100 | (−)6.04 | −2.594 | 0.000 | yes |  | (+)4.60 | 2.201 | 0.000 | yes | DHFR | Similar to NADPH HC toxin reductase (Fragment). |
 12 | Os07g0602000 | (−)2.21 | −1.142 | 0.001 | yes |  | (+)26.60 | 4.733 | 0.000 | yes | DHFR | Similar to NADPH HC toxin reductase (Fragment). |
 13 | Os07g0602900 | (−)4.42 | −2.144 | 0.001 | yes |  | (+)1.75 | 0.805 | 0.029 | no |  | Protein of unknown function DUF1675 domain containing protein;Similar to UPF0737 protein 1. |
 14 | Os07g0604800 | (−)3.52 | −1.815 | 0.000 | yes | (−)2.63 | (+)2.09 | 1.062 | 0.000 | yes | OsUAM3 | Similar to Alpha-1,4-glucan-protein synthase [UDP-forming] 1 (EC 2.4.1.112) (UDP- glucose:protein transglucosylase 1) (UPTG 1). |
 15 | Os07g0607500 | (−)2.09 | −1.067 | 0.049 | yes |  | (+)2.59 | 1.371 | 0.035 | yes |  | Protein of unknown function DUF1195 family protein. |
 16 | Os07g0616750 | (+)2.13 | 1.090 | 0.034 | yes |  | (−)2.34 | −1.229 | 0.012 | yes |  | Hypothetical gene. |
 17 | Os07g0617100 | (−)2.17 | −1.120 | 0.000 | yes |  | (+)1.01 | 0.017 | 1.000 | no |  | Plant disease resistance response protein family protein. |
qPGWC8 (qDEC8) | ||||||||||||
 1 | Os08g0101500 | (−)2.64 | −1.403 | 0.000 | yes |  | (+)1.22 | 0.281 | 0.538 | no | OsSultr5;2 | Similar to sulfate transporter. |
 2 | Os08g0101800 | (−)2.80 | −1.485 | 0.020 | yes |  | (+)2.68 | 1.420 | 0.000 | yes |  | Protein of unknown function DUF821, CAP10-like family protein. |
 3 | Os08g0104400 | 9.27 | −3.212 | 0.000 | yes |  | (+)2.94 | 1.554 | 0.000 | yes |  | Conserved hypothetical protein. |
 4 | Os08g0106100 | (−)5.57 | −2.477 | 0.000 | yes |  | (+)5793.33 | 12.500 | 0.000 | yes |  | Conserved hypothetical protein. |
 5 | Os08g0111200 | (−)3.14 | −1.652 | 0.007 | yes | (−)2.87 | (+)1.69 | 0.760 | 0.362 | no |  | Beta-glucosidase, GBA2 type domain containing protein. |
 6 | Os08g0112300 | (−)3.54 | −1.824 | 0.006 | yes |  | (+)2.10 | 1.071 | 0.002 | yes |  | Transferase domain containing protein. |
 7 | Os08g0113000 | (−)3.67 | −1.877 | 0.006 | yes |  | (+)2.43 | 1.279 | 0.000 | yes | prx117 | Similar to Peroxidase 47 precursor (EC 1.11.1.7) (Atperox P47) (ATP32). |
 8 | Os08g0114300 | (−)3.16 | −1.660 | 0.000 | yes |  | (+)1.62 | 0.699 | 0.008 | no |  | D-arabinono-1,4-lactone oxidase domain containing protein. |
 9 | Os08g0114400 | (−)4.85 | −2.277 | 0.000 | yes |  | (+)1.88 | 0.912 | 0.003 | no |  | Hypothetical protein. |
 10 | Os08g0116800 | (−)3.77 | −1.913 | 0.016 | yes |  | (+)4.95 | 2.309 | 0.155 | no |  | Exoribonuclease domain containing protein. |
 11 | Os08g0120600 | (−)2.33 | −1.219 | 0.005 | yes | (−)5.67 | (+)1.42 | 0.501 | 0.343 | no |  | Similar to Fructose-bisphosphate aldolase, cytoplasmic isozyme (EC 4.1.2.13). |
 12 | Os08g0122800 | (−)6.45 | −2.689 | 0.003 | yes |  | (+)240.50 | 7.910 | 0.000 | yes |  | Conserved hypothetical protein. (Os08t0122800-01); Kringle, conserved site domain containing protein. |
 13 | Os08g0124500 | (−)306.67 | −8.261 | 0.018 | yes |  | (+)96.67 | 6.595 | 0.114 | no |  | Similar to Resistance protein candidate (Fragment); Similar to Resistance protein candidate (Fragment). |