Table 4.
List of 33 known chlorophyll-related genes within a ± 3 MB region of the 52 putative candidate SNPs identified from Soybase (www.soybase.org) for three total chlorophyll determination methods namely extractable chlorophyll (eChl_T), wavelet transformed spectral reflectance chlorophyll (tChl_T) and spectral reflectance index total chlorophyll (iChl_T)
| Loci | Gene a | Chromosome | Start | Stop | Soybase b/Pathway | Distance to SNP (Mb) | Functional annotation | Trait |
|---|---|---|---|---|---|---|---|---|
| 1 | Glyma02g40490 | Gm02 | 45747413 | 457,63,801 | Glyma 1.1 | 2.03 | Mitochondrial Fe/S cluster exporter, ABC superfamily | iChl_T |
| Glyma02g39990 | Gm02 | 451,89,739 | 451,97,024 | Glyma 1.1 | 2.61 | Translocon at the inner envelope membrane of chloroplasts | iChl_T | |
| Glyma02g44150 | Gm02 | 487,89,243 | 487,90,727 | Glyma 1.1 | 0.99 | Chlorophyll a biosynthetic process (geranylgeranyl reductase) | iChl_T | |
| Glyma02g47120 | Gm02 | 508,18,647 | 508,20,935 | Glyma 1.1 | 2.92 | Red chlorophyll catabolite reductase (RCC reductase) | iChl_T | |
| 2 | Glyma03g08280 | Gm03 | 91,32,182 | 91,34,276 | Glyma 1.1 | 1.28 | Chlorophyll A-B binding protein | tChl_T |
| 3 | Glyma03g27380 | Gm03 | 350,95,413 | 350,98,484 | Glyma 1.1 | 2.96 | Oxidation-reduction process (Rubrerythrin) | tChl_T |
| Glyma03g29330 | Gm03 | 373,17,236 | 373,23,794 | Glyma 1.1 | 1.04 | Magnesium chelatase activity | tChl_T | |
| 5 | Glyma04g37740 | Gm04 | 441,63,842 | 441,70,887 | Glyma 1.1 | 0.98 | Regulation of Transcription (ATP-dependent CLP protease) | eChl_T |
| 6 | Glyma05g01000 | Gm05 | 6,06,608 | 6,08,812 | Glyma 1.1 | 1.11 | Electron transfer flavoprotein-ubiquinone oxidoreductase | eChl_T |
| 7 | Glyma05g05450 | Gm05 | 47,64,696 | 47,66,688 | Glyma 1.1 | 2.95 | Chlorophyll A-B binding family protein | eChl_T |
| 8 | Glyma05g38510 | Gm05 | 418,44,917 | 418,50,362 | Glyma 1.1 | 0.40 | Regulation of transcription, DNA-templated (ATP-dependent CLP protease) | tChl_T |
| Glyma05g38570 | Gm05 | 384,15,657 | 384,18,787 | KEGG Pathway | 2.98 | Magnesium protoporphyrin IX methyltransferase activity (chlorophyll biosynthetic process) | tChl_T | |
| 10 | Glyma07g18470 | Gm07 | 184,08,168 | 184,13,639 | Glyma 1.1 | 1.05 | UbiA prenyltransferase family (prenyltransferase activity) | eChl_T |
| 11 | Glyma08g07880 | Gm08 | 56,44,333 | 56,45,834 | Glyma 1.1 | 1.49 | Chlorophyll A-B binding protein | iChl_T |
| Glyma08g08770 | Gm08 | 62,68,835 | 62,70,396 | Glyma 1.1 | 0.87 | Chlorophyll A-B binding protein | iChl_T | |
| Glyma08g08920 | Gm08 | 63,57,088 | 63,63,013 | Glyma 1.1 | 0.78 | Magnesium chelatase activity (chlorophyll biosynthetic process) | iChl_T | |
| 12 | Glyma08g12070 | Gm08 | 87,20,805 | 87,26,588 | Glyma 1.1 | 1.59 | Chlorophyllide a oxygenase [overall] activity | iChl_T |
| 13 | Glyma09g05240 | Gm09 | 40,35,167 | 40,41,182 | Glyma 1.1 | 0.80 | Magnesium chelatase activity (chlorophyll biosynthetic process) | tChl_T |
| Glyma09g07310 | Gm09 | 61,57,184 | 61,57,688 | Glyma 1.1 | 1.32 | Chlorophyll A-B binding protein | tChl_T | |
| 14 | Glyma09g08260 | Gm09 | 73,39,820 | 73,42,548 | Glyma 1.1 | 2.51 | Chlorophyll A-B binding protein | tChl_T |
| 15 | Glyma10g25710 | Gm10 | 341,46,057 | 341,58,388 | KEGG Pathway | 0.84 | Coenzyme F420 hydrogenase | tChl_T and iChl_T |
| 16 | Glyma10g27890 | Gm10 | 366,89,550 | 366,94,993 | Glyma 1.1 | 0.84 | Oxidation-reduction process (Protoporphyrinogen oxidase) | tChl_T and iChl_T |
| 17 | Glyma10g32080 | Gm10 | 405,24,508 | 405,27,468 | Glyma 1.1 | 0.27 | Chlorophyll A-B binding protein | eChl_T |
| 18 | Glyma11g12110 | Gm11 | 86,45,442 | 86,50,623 | Glyma 1.1 | 0.75 | Magnesium chelatase activity (chlorophyll biosynthetic process) | iChl_T |
| 20 | Glyma15g16570 | Gm15 | 128,69,848 | 128,76,153 | Glyma 1.1 | 1.49 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_T and tChl_T |
| 21 | Glyma16g24570 | Gm16 | 285,47,662 | 285,50,487 | Glyma 1.1 | 0.65 | Chlorophyll catabolic process (Chlorophyllase.) | eChl_T |
| Glyma16g26130 | Gm16 | 303,09,204 | 303,11,593 | Glyma 1.1 | 2.41 | Chlorophyll A-B binding protein | eChl_T | |
| 24 | Glyma19g30350 | Gm19 | 379,57,536 | 379,60,664 | Glyma 1.1 | 1.17 | Oxidation-reduction process (Rubrerythrin) | eChl_T, tChl_T and iChl_T |
| Glyma19g32070 | Gm19 | 398,43,036 | 398,49,603 | Glyma 1.1 | 2.96 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_T, tChl_T and iChl_T | |
| 25 | Glyma19g40370 | Gm19 | 467,94,372 | 467,99,578 | Glyma 1.1 | 0.27 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_T and iChl_T |
| 26 | Glyma20g28890 | Gm20 | 378,38,174 | 378,39,638 | Glyma 1.1 | 2.90 | Chlorophyll A-B binding protein | tChl_T |
| 27 | Glyma20g35530 | Gm20 | 438,24,060 | 438,26,992 | Glyma 1.1 | 1.36 | Chlorophyll A-B binding protein | eChl_T, tChl_T and iChl_T |
| Glyma20g38941 | Gm20 | 464,38,179 | 464,39,540 | Glyma 1.1 | 0.73 | Homogentisate phytyltransferase 1 | eChl_T, tChl_T and iChl_T |
a As reported in Soybase
b Annotation version information based on Soybase